Add example flow

Reviewed-on: #6

README.md

@@ -1,17 +1,20 @@
-# reactor
+# Reactor: Advanced Hydraulic Tank & Biological Process Simulator
 
-Reactor: Advanced Hydraulic Tank & Biological Process Simulator
+A comprehensive reactor class for wastewater treatment simulation featuring non-ideal plug flow hydraulics and ASM3 biological modeling.
 
-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.
+## How to use this Node
+### Set Node Properties
+- Set reactor type: Continuously Stirred Tank Reactor (CSTR) or Plug Flow Reactor (PFR)
+- Configure reactor sizing: Set reactor volume [ $m^3$ ] and (for PFRs) set the reactor length [ $m$ ]
+- (For PFRs) set reactor spatial resolution: A value of 10 or 20 is good. A higher resolution means more accurate simulation, at higher computational expense. Note that connected reactors must have similar Δx values.
+- Set initial state of reactor: set the intial concentrations of all relevant reaction species.
+- (Optional) set $k_L a$ to calculate OTR internally, rather than providing it explicitly, using simple mass transfer model.
 
-Key Features:
+### Accepted Node inputs
-
+- \{ topic: clock, payload: \<timestamp [ $ms$ ]\> \} - **required** clock signal to make reactor update state.
-Plug Flow Hydraulics: Multi-section reactor with configurable sectioning factor and dispersion modeling
+- \{ topic: Fluent, payload: \{ F: \<flow rate [ $m^3 d^{-1}$ ]\>, C: \<array with concentrations\> \} \} - sets inflow composition and flow rate.
-ASM1 Integration: Complete biological nutrient removal modeling with 13 state variables (COD, nitrogen, phosphorus)
+- \{ topic: Dispersion, payload: \<dispersion coefficient in [ $m d^{-2}$ ]\> \} - sets PFR dispersion coefficient.
-Dynamic Volume Control: Automatic section management with overflow handling and retention time calculations
+- \{ topic: OTR, payload: \<oxygen transfer rate [ $ g d^{-1} m^{-3}$ ]\> \} - sets current oxygen transfer rate.
-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.
 
+## Troubleshooting
+Check for possible numerical warnings. These tell you which simulation parameters to change. If solutions appear to be oscillate, try reducing the time step. If solutions appear to be too dispersive, try increasing the reactor resolution.

example_flow/reactor_flows.json

@@ -0,0 +1,838 @@
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+        "model": "VegaSolidsProbe",
+        "unit": "g/m³",
+        "enableLog": true,
+        "logLevel": "error",
+        "positionVsParent": "atEquipment",
+        "positionIcon": "⊥",
+        "hasDistance": false,
+        "distance": "",
+        "x": 930,
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+        "wires": [
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+        "type": "function",
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+        "name": "Data_converter",
+        "func": "if (msg.topic != \"Fluent\" || msg.payload.inlet == 1 || msg.payload.inlet == 2) {\n    return;\n}\n\nconst [S_O, S_I, S_S, S_NH, S_N2, S_NO, S_HCO, X_I, X_S, X_H, X_STO, X_A, X_TS] = msg.payload.C;\n\nmsg = {payload: [\n    { \"Series\": \"S_O\",      \"Y\": S_O},\n    { \"Series\": \"S_I\",      \"Y\": S_I},\n    { \"Series\": \"S_S\",      \"Y\": S_S},\n    { \"Series\": \"S_NH\",     \"Y\": S_NH},\n    { \"Series\": \"S_N2\",     \"Y\": S_N2},\n    { \"Series\": \"S_NO\",     \"Y\": S_NO},\n    { \"Series\": \"S_HCO\",    \"Y\": S_HCO}\n    ]};\n\nreturn msg;",
+        "outputs": 1,
+        "timeout": 0,
+        "noerr": 0,
+        "initialize": "",
+        "finalize": "",
+        "libs": [],
+        "x": 1320,
+        "y": 420,
+        "wires": [
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+        "pointShape": "circle",
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+        "removeOlderUnit": "3600",
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+        "interpolation": "linear",
+        "x": 1520,
+        "y": 420,
+        "wires": [
+            []
+        ]
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+        "name": "Group 3",
+        "page": "ca564642bfc5606c",
+        "width": 6,
+        "height": 1,
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+        "showTitle": true,
+        "className": "",
+        "visible": "true",
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+        "groupType": "default"
+    },
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+        "type": "ui-group",
+        "name": "Group 4",
+        "page": "ca564642bfc5606c",
+        "width": 6,
+        "height": 1,
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+        "showTitle": true,
+        "className": "",
+        "visible": "true",
+        "disabled": "false",
+        "groupType": "default"
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+        "id": "ca564642bfc5606c",
+        "type": "ui-page",
+        "name": "PFR",
+        "ui": "90eb5f47d95b4087",
+        "path": "/page2",
+        "icon": "home",
+        "layout": "grid",
+        "theme": "2c8bcaa0046b4323",
+        "breakpoints": [
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+                "px": "0",
+                "cols": "3"
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+                "px": "576",
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+                "px": "768",
+                "cols": "9"
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+                "px": "1024",
+                "cols": "12"
+            }
+        ],
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+        "className": "",
+        "visible": "true",
+        "disabled": "false"
+    },
+    {
+        "id": "90eb5f47d95b4087",
+        "type": "ui-base",
+        "name": "Dashboard",
+        "path": "/dashboard",
+        "appIcon": "",
+        "includeClientData": true,
+        "acceptsClientConfig": [
+            "ui-notification",
+            "ui-control"
+        ],
+        "showPathInSidebar": false,
+        "headerContent": "page",
+        "navigationStyle": "default",
+        "titleBarStyle": "default",
+        "showReconnectNotification": true,
+        "notificationDisplayTime": 1,
+        "showDisconnectNotification": true,
+        "allowInstall": true
+    },
+    {
+        "id": "2c8bcaa0046b4323",
+        "type": "ui-theme",
+        "name": "Default",
+        "colors": {
+            "surface": "#ffffff",
+            "primary": "#0094ce",
+            "bgPage": "#eeeeee",
+            "groupBg": "#ffffff",
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+            "pagePadding": "12px",
+            "groupGap": "12px",
+            "groupBorderRadius": "4px",
+            "widgetGap": "12px"
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+]

reactor.html

@@ -31,7 +31,7 @@
             enableLog: { value: false },
             logLevel: { value: "error" },
 
-            positionVsParent: { value: "" },
+            positionVsParent: { value: "" }
         },
         inputs: 1,
         outputs: 3,
@@ -102,6 +102,19 @@
             } else {
                 $(".PFR").show();
             }
+
+            const updateDx = () => {
+                const length = parseFloat($("#node-input-length").val()) || 0;
+                const resolution = parseFloat($("#node-input-resolution_L").val()) || 1;
+                const dx = resolution > 0 ? (length / resolution).toFixed(6) : "N/A";
+                $("#dx-output").text(dx + " m");
+            };
+
+            // Set up event listeners for real-time updates
+            $("#node-input-length, #node-input-resolution_L").on("change keyup", updateDx);
+            
+            // Initial calculation
+            updateDx();
         },
         oneditsave: function() {
             // save logger fields
@@ -140,10 +153,19 @@
         <label for="node-input-length"><i class="fa fa-tag"></i> Reactor length [m]</label>
         <input type="text" id="node-input-length" placeholder="m">
     </div>
+    <h2> Simulation parameters </h2>
+    <div class="form-row">
+        <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 PFR">
-        <label for="node-input-resolution_L"><i class="fa fa-tag"></i> Resolution</label>
+        <label for="node-input-resolution_L"><i class="fa fa-tag"></i> Spatial resolution</label>
         <input type="text" id="node-input-resolution_L" placeholder="#">
     </div>
+    <div class="form-row PFR">
+        <label for="node-input-dx"><i class="fa fa-tag"></i> Δx (length / resolution) [m]</label>
+        <span id="dx-output" style="display: inline-block; padding: 8px; font-weight: bold;">--</span>
+    </div>
     <h3> Internal mass transfer calculation (optional) </h3>
     <div class="form-row">
         <label for="node-input-kla"><i class="fa fa-tag"></i> kLa [d-1]</label>
@@ -203,11 +225,6 @@
         <label for="node-input-X_TS_init"><i class="fa fa-tag"></i> Initial total suspended solids [g TSS m-3]</label>
         <input type="text" id="node-input-X_TS_init" class="concentrations">
     </div>
-    <h2> Simulation parameters </h2>
-    <div class="form-row">
-        <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>
 
     <!-- Logger fields injected here -->
 	<div id="logger-fields-placeholder"></div>

src/nodeClass.js

@@ -34,7 +34,6 @@ class nodeClass {
             switch (msg.topic) {
                 case "clock":
                     this.source.updateState(msg.timestamp);
-                    send([msg, null, null]);
                     break;
                 case "Fluent":
                     this.source.setInfluent = msg;
@@ -42,9 +41,6 @@ class nodeClass {
                 case "OTR":
                     this.source.setOTR = msg;
                     break;
-                case "Temperature":
-                    this.source.setTemperature = msg;
-                    break;
                 case "Dispersion":
                     this.source.setDispersion = msg;
                     break;

src/reaction_modules/asm3_class Koch.js

@@ -2,9 +2,67 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 
+const KINETIC_CONSTANTS = {
+  // 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] 
+  // Heterotrophs
+  k_STO:    12.,  // storage rate constant          [g S_S g-1 X_H d-1]
+  nu_NO:    0.5,  // anoxic reduction factor        [-]
+  K_O:      0.2,  // saturation constant S_0        [g O2 m-3]
+  K_NO:     0.5,  // saturation constant S_NO       [g NO3-N m-3]
+  K_S:      10.,  // saturation constant S_s        [g COD m-3]
+  K_STO:    0.1,  // saturation constant X_STO      [g X_STO g-1 X_H]
+  mu_H_max: 3.,   // maximum specific growth rate   [d-1]
+  K_NH:     0.01, // saturation constant S_NH3      [g NH3-N m-3]
+  K_HCO:    0.1,  // saturation constant S_HCO      [mole HCO3 m-3]
+  b_H_O:    0.3,  // aerobic respiration rate       [d-1]
+  b_H_NO:   0.15, // anoxic respiration rate        [d-1]
+  b_STO_O:  0.3,  // aerobic respitation rate X_STO [d-1]
+  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_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]
+  b_A_NO:   0.10  // anoxic respiration rate        [d-1]
+};
+
+const STOICHIOMETRIC_CONSTANTS = {
+  // Fractions
+  f_SI:     0.,   // fraction S_I from hydrolysis   [g S_I g-1 X_S]
+  f_XI:     0.2,  // fraction X_I from decomp X_H   [g X_I g-1 X_H]
+  // Yields
+  Y_STO_O:  0.80, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
+  Y_STO_NO: 0.70, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
+  Y_H_O:    0.80, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
+  Y_H_NO:   0.65, // anoxic yield X_H per X_STO     [g X_H g-1 X_STO]
+  Y_A:      0.24, // anoxic yield X_A per S_NO      [g X_A g-1 NO3-N]
+  // Composition (COD via DoR)
+  i_CODN:  -1.71, // COD content (DoR)              [g COD g-1 N2-N]
+  i_CODNO: -4.57, // COD content (DoR)              [g COD g-1 NO3-N]
+  // Composition (nitrogen)
+  i_NSI:    0.01, // nitrogen content S_I           [g N g-1 S_I]
+  i_NSS:    0.03, // nitrogen content S_S           [g N g-1 S_S]
+  i_NXI:    0.04, // nitrogen content X_I           [g N g-1 X_I]
+  i_NXS:    0.03, // nitrogen content X_S           [g N g-1 X_S]
+  i_NBM:    0.07, // nitrogen content X_H / X_A     [g N g-1 X_H / X_A]
+  // Composition (TSS)
+  i_TSXI:   0.75, // TSS content X_I                [g TS g-1 X_I]
+  i_TSXS:   0.75, // TSS content X_S                [g TS g-1 X_S]
+  i_TSBM:   0.90, // TSS content X_H / X_A          [g TS g-1 X_H / X_A]
+  i_TSSTO:  0.60, // TSS content X_STO (PHB based)  [g TS g-1 X_STO]
+  // Composition (charge)
+  i_cNH:    1/14, // charge per S_NH                [mole H+ g-1 NH3-N]
+  i_cNO:   -1/14  // charge per S_NO                [mole H+ g-1 NO3-N]
+};
+
 /**
  * ASM3 class for the Activated Sludge Model No. 3 (ASM3). Using Koch et al. 2000 parameters.
  */
@@ -15,65 +73,13 @@ class ASM3 {
      * Kinetic parameters for ASM3 at 20 C. Using Koch et al. 2000 parameters.
      * @property {Object} kin_params - Kinetic parameters
      */
-    this.kin_params = {
+    this.kin_params = KINETIC_CONSTANTS;
-      // 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] 
-      // Heterotrophs
-      k_STO:    12.,  // storage rate constant          [g S_S g-1 X_H d-1]
-      nu_NO:    0.5,  // anoxic reduction factor        [-]
-      K_O:      0.2,  // saturation constant S_0        [g O2 m-3]
-      K_NO:     0.5,  // saturation constant S_NO       [g NO3-N m-3]
-      K_S:      10.,  // saturation constant S_s        [g COD m-3]
-      K_STO:    0.1,  // saturation constant X_STO      [g X_STO g-1 X_H]
-      mu_H_max: 3.,   // maximum specific growth rate   [d-1]
-      K_NH:     0.01, // saturation constant S_NH3      [g NH3-N m-3]
-      K_HCO:    0.1,  // saturation constant S_HCO      [mole HCO3 m-3]
-      b_H_O:    0.3,  // aerobic respiration rate       [d-1]
-      b_H_NO:   0.15, // anoxic respiration rate        [d-1]
-      b_STO_O:  0.3,  // aerobic respitation rate X_STO [d-1]
-      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_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]
-      b_A_NO:   0.10  // anoxic respiration rate        [d-1]
-    };
 
     /**
      * Stoichiometric and composition parameters for ASM3. Using Koch et al. 2000 parameters.
      * @property {Object} stoi_params - Stoichiometric parameters
      */
-    this.stoi_params = {
+    this.stoi_params = STOICHIOMETRIC_CONSTANTS;
-      // Fractions
-      f_SI:     0.,   // fraction S_I from hydrolysis   [g S_I g-1 X_S]
-      f_XI:     0.2,  // fraction X_I from decomp X_H   [g X_I g-1 X_H]
-      // Yields
-      Y_STO_O:  0.80, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
-      Y_STO_NO: 0.70, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
-      Y_H_O:    0.80, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
-      Y_H_NO:   0.65, // anoxic yield X_H per X_STO     [g X_H g-1 X_STO]
-      Y_A:      0.24, // anoxic yield X_A per S_NO      [g X_A g-1 NO3-N]
-      // Composition (COD via DoR)
-      i_CODN:  -1.71, // COD content (DoR)              [g COD g-1 N2-N]
-      i_CODNO: -4.57, // COD content (DoR)              [g COD g-1 NO3-N]
-      // Composition (nitrogen)
-      i_NSI:    0.01, // nitrogen content S_I           [g N g-1 S_I]
-      i_NSS:    0.03, // nitrogen content S_S           [g N g-1 S_S]
-      i_NXI:    0.04, // nitrogen content X_I           [g N g-1 X_I]
-      i_NXS:    0.03, // nitrogen content X_S           [g N g-1 X_S]
-      i_NBM:    0.07, // nitrogen content X_H / X_A     [g N g-1 X_H / X_A]
-      // Composition (TSS)
-      i_TSXI:   0.75, // TSS content X_I                [g TS g-1 X_I]
-      i_TSXS:   0.75, // TSS content X_S                [g TS g-1 X_S]
-      i_TSBM:   0.90, // TSS content X_H / X_A          [g TS g-1 X_H / X_A]
-      i_TSSTO:  0.60, // TSS content X_STO (PHB based)  [g TS g-1 X_STO]
-      // Composition (charge)
-      i_cNH:    1/14, // charge per S_NH                [mole H+ g-1 NH3-N]
-      i_cNO:   -1/14  // charge per S_NO                [mole H+ g-1 NO3-N]
-    };
 
     /**
      * Temperature theta parameters for ASM3. Using Koch et al. 2000 parameters.
@@ -213,4 +219,4 @@ class ASM3 {
   }
 }
 
-module.exports = { ASM3, ASM_CONSTANTS };
+module.exports = { ASM3, ASM_CONSTANTS, KINETIC_CONSTANTS, STOICHIOMETRIC_CONSTANTS };

src/reaction_modules/asm3_class.js

@@ -2,9 +2,67 @@ const math = require('mathjs');
 
 const ASM_CONSTANTS = {
   S_O_INDEX: 0,
+  S_NH_INDEX: 3,
+  S_NO_INDEX: 5,
   NUM_SPECIES: 13
 };
 
+const KINETIC_CONSTANTS = {
+  // 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] 
+  // Heterotrophs
+  k_STO:    5.,   // storage rate constant          [g S_S g-1 X_H d-1]
+  nu_NO:    0.6,  // anoxic reduction factor        [-]
+  K_O:      0.2,  // saturation constant S_0        [g O2 m-3]
+  K_NO:     0.5,  // saturation constant S_NO       [g NO3-N m-3]
+  K_S:      2.,   // saturation constant S_s        [g COD m-3]
+  K_STO:    1.,   // saturation constant X_STO      [g X_STO g-1 X_H]
+  mu_H_max: 2.,   // maximum specific growth rate   [d-1]
+  K_NH:     0.01, // saturation constant S_NH3      [g NH3-N m-3]
+  K_HCO:    0.1,  // saturation constant S_HCO      [mole HCO3 m-3]
+  b_H_O:    0.2,  // aerobic respiration rate       [d-1]
+  b_H_NO:   0.1,  // anoxic respiration rate        [d-1]
+  b_STO_O:  0.2,  // aerobic respitation rate X_STO [d-1]
+  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_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]
+  b_A_NO:   0.05  // anoxic respiration rate        [d-1]
+};
+
+const STOICHIOMETRIC_CONSTANTS = {
+  // Fractions
+  f_SI:     0.,   // fraction S_I from hydrolysis   [g S_I g-1 X_S]
+  f_XI:     0.2,  // fraction X_I from decomp X_H   [g X_I g-1 X_H]
+  // Yields
+  Y_STO_O:  0.85, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
+  Y_STO_NO: 0.80, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
+  Y_H_O:    0.63, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
+  Y_H_NO:   0.54, // anoxic yield X_H per X_STO     [g X_H g-1 X_STO]
+  Y_A:      0.24, // anoxic yield X_A per S_NO      [g X_A g-1 NO3-N]
+  // Composition (COD via DoR)
+  i_CODN:  -1.71, // COD content (DoR)              [g COD g-1 N2-N]
+  i_CODNO: -4.57, // COD content (DoR)              [g COD g-1 NO3-N]
+  // Composition (nitrogen)
+  i_NSI:    0.01, // nitrogen content S_I           [g N g-1 S_I]
+  i_NSS:    0.03, // nitrogen content S_S           [g N g-1 S_S]
+  i_NXI:    0.02, // nitrogen content X_I           [g N g-1 X_I]
+  i_NXS:    0.04, // nitrogen content X_S           [g N g-1 X_S]
+  i_NBM:    0.07, // nitrogen content X_H / X_A     [g N g-1 X_H / X_A]
+  // Composition (TSS)
+  i_TSXI:   0.75, // TSS content X_I                [g TS g-1 X_I]
+  i_TSXS:   0.75, // TSS content X_S                [g TS g-1 X_S]
+  i_TSBM:   0.90, // TSS content X_H / X_A          [g TS g-1 X_H / X_A]
+  i_TSSTO:  0.60, // TSS content X_STO (PHB based)  [g TS g-1 X_STO]
+  // Composition (charge)
+  i_cNH:    1/14, // charge per S_NH                [mole H+ g-1 NH3-N]
+  i_cNO:   -1/14  // charge per S_NO                [mole H+ g-1 NO3-N]
+};
+
 /**
  * ASM3 class for the Activated Sludge Model No. 3 (ASM3).
  */
@@ -15,65 +73,13 @@ class ASM3 {
      * Kinetic parameters for ASM3 at 20 C.
      * @property {Object} kin_params - Kinetic parameters
      */
-    this.kin_params = {
+    this.kin_params = KINETIC_CONSTANTS;
-      // 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] 
-      // Heterotrophs
-      k_STO:    5.,   // storage rate constant          [g S_S g-1 X_H d-1]
-      nu_NO:    0.6,  // anoxic reduction factor        [-]
-      K_O:      0.2,  // saturation constant S_0        [g O2 m-3]
-      K_NO:     0.5,  // saturation constant S_NO       [g NO3-N m-3]
-      K_S:      2.,   // saturation constant S_s        [g COD m-3]
-      K_STO:    1.,   // saturation constant X_STO      [g X_STO g-1 X_H]
-      mu_H_max: 2.,   // maximum specific growth rate   [d-1]
-      K_NH:     0.01, // saturation constant S_NH3      [g NH3-N m-3]
-      K_HCO:    0.1,  // saturation constant S_HCO      [mole HCO3 m-3]
-      b_H_O:    0.2,  // aerobic respiration rate       [d-1]
-      b_H_NO:   0.1,  // anoxic respiration rate        [d-1]
-      b_STO_O:  0.2,  // aerobic respitation rate X_STO [d-1]
-      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_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]
-      b_A_NO:   0.05  // anoxic respiration rate        [d-1]
-    };
 
     /**
      * Stoichiometric and composition parameters for ASM3.
      * @property {Object} stoi_params - Stoichiometric parameters
      */
-    this.stoi_params = {
+    this.stoi_params = STOICHIOMETRIC_CONSTANTS;
-      // Fractions
-      f_SI:     0.,   // fraction S_I from hydrolysis   [g S_I g-1 X_S]
-      f_XI:     0.2,  // fraction X_I from decomp X_H   [g X_I g-1 X_H]
-      // Yields
-      Y_STO_O:  0.85, // aerobic yield X_STO per S_S    [g X_STO g-1 S_S]
-      Y_STO_NO: 0.80, // anoxic yield X_STO per S_S     [g X_STO g-1 S_S]
-      Y_H_O:    0.63, // aerobic yield X_H per X_STO    [g X_H g-1 X_STO]
-      Y_H_NO:   0.54, // anoxic yield X_H per X_STO     [g X_H g-1 X_STO]
-      Y_A:      0.24, // anoxic yield X_A per S_NO      [g X_A g-1 NO3-N]
-      // Composition (COD via DoR)
-      i_CODN:  -1.71, // COD content (DoR)              [g COD g-1 N2-N]
-      i_CODNO: -4.57, // COD content (DoR)              [g COD g-1 NO3-N]
-      // Composition (nitrogen)
-      i_NSI:    0.01, // nitrogen content S_I           [g N g-1 S_I]
-      i_NSS:    0.03, // nitrogen content S_S           [g N g-1 S_S]
-      i_NXI:    0.02, // nitrogen content X_I           [g N g-1 X_I]
-      i_NXS:    0.04, // nitrogen content X_S           [g N g-1 X_S]
-      i_NBM:    0.07, // nitrogen content X_H / X_A     [g N g-1 X_H / X_A]
-      // Composition (TSS)
-      i_TSXI:   0.75, // TSS content X_I                [g TS g-1 X_I]
-      i_TSXS:   0.75, // TSS content X_S                [g TS g-1 X_S]
-      i_TSBM:   0.90, // TSS content X_H / X_A          [g TS g-1 X_H / X_A]
-      i_TSSTO:  0.60, // TSS content X_STO (PHB based)  [g TS g-1 X_STO]
-      // Composition (charge)
-      i_cNH:    1/14, // charge per S_NH                [mole H+ g-1 NH3-N]
-      i_cNO:   -1/14  // charge per S_NO                [mole H+ g-1 NO3-N]
-    };
 
     /**
      * Temperature theta parameters for ASM3.
@@ -213,4 +219,4 @@ class ASM3 {
   }
 }
 
-module.exports = { ASM3, ASM_CONSTANTS };
+module.exports = { ASM3, ASM_CONSTANTS, KINETIC_CONSTANTS, STOICHIOMETRIC_CONSTANTS };

src/specificClass.js

@@ -10,9 +10,9 @@ const mathConfig = {
 
 const math = create(all, mathConfig);
 
-const BC_PADDING = 2;
+const BC_PADDING = 2; // Boundary Condition padding for open boundaries in extendedState variable
 const DEBUG = false;
-const DAY2MS = 1000 * 60 * 60 * 24;
+const DAY2MS = 1000 * 60 * 60 * 24; // convert between days and milliseconds
 
 class Reactor {
   /**
@@ -25,13 +25,14 @@ class Reactor {
     this.logger = new logger(this.config.general.logging.enabled, this.config.general.logging.logLevel, config.general.name);
     this.emitter = new EventEmitter();
     this.measurements = new MeasurementContainer();
-    this.childRegistrationUtils = new childRegistrationUtils(this); // Child registration utility
+    this.childRegistrationUtils = new childRegistrationUtils(this); // child registration utility
 
+    // placeholder variables for children and parents
     this.upstreamReactor = null;
     this.downstreamReactor = null;
     this.returnPump = null;
 
-    this.asm = new ASM3();
+    this.asm = new ASM3(); // Reaction model
 
     this.volume = config.volume; // fluid volume reactor [m3]
 
@@ -42,9 +43,9 @@ class Reactor {
 
     this.kla = config.kla; // if NaN, use externaly provided OTR [d-1]
 
-    this.currentTime = Date.now(); // milliseconds since epoch [ms]
+    this.currentTime = null; // milliseconds since epoch [ms]
     this.timeStep = 1 / (24*60*60) * this.config.timeStep; // time step in seconds, converted to days.
-    this.speedUpFactor = 100; // speed up factor for simulation, 60 means 1 minute per simulated second
+    this.speedUpFactor = 1; // speed up factor for simulation, 60 means 1 minute per simulated second
   }
 
   /**
@@ -113,6 +114,11 @@ class Reactor {
     }
   }
 
+  /**
+   * Register child function required for child registration.
+   * @param {object} child 
+   * @param {string} softwareType 
+   */
   registerChild(child, softwareType) {
     if(!child) {
       this.logger.error(`Invalid ${softwareType} child provided.`);
@@ -161,18 +167,14 @@ class Reactor {
 
   _connectReactor(reactorChild) {
     if (reactorChild.config.functionality.positionVsParent != "upstream") {
-      this.logger.warn("Reactor children of reactors should always be upstream.");
+      this.logger.warn("Reactor children of other reactors should always be upstream!");
-    }
-
-    if (math.abs(reactorChild.d_x - this.d_x) / this.d_x < 0.025) {
-      this.logger.warn("Significant grid sizing discrepancies between adjacent reactors! Change resolutions to match reactors grid step, or implement boundary value interpolation.");
     }
 
     // set upstream and downstream reactor variable in current and child nodes respectively for easy access
     this.upstreamReactor = reactorChild;
     reactorChild.downstreamReactor = this;
 
-    reactorChild.emitter.on("stateChange", (eventData) => {
+    reactorChild.emitter.on("stateChange", (eventData) => { // Triggers state update in downstream reactor.
       this.logger.debug(`State change of upstream reactor detected.`);
       this.updateState(eventData);
     });
@@ -203,20 +205,32 @@ class Reactor {
    * Update the reactor state based on the new time.
    * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
    */
-  updateState(newTime = Date.now()) { // expect update with timestamp
+  updateState(newTime) {
-    if (this.upstreamReactor) {
+    if (!this.currentTime) { // initialise currentTime variable
-      this.setInfluent = this.upstreamReactor.getEffluent[0]; // grab main effluent upstream reactor
+      this.currentTime = newTime;
+      return;
+    }
+
+    if (this.upstreamReactor) { // grab main effluent upstream reactor
+      this.setInfluent = this.upstreamReactor.getEffluent[0];
     }
 
     const n_iter = Math.floor(this.speedUpFactor * (newTime-this.currentTime) / (this.timeStep*DAY2MS));
-    if (n_iter) {
+
-      let n = 0;
+    if (n_iter == 0) { // no update required, change in currentTime smaller than time step
-      while (n < n_iter) {
+      return;
-        this.tick(this.timeStep);
+    }
-        n += 1;
+
-      }
+    let n = 0;
-      this.currentTime += n_iter * this.timeStep * DAY2MS / this.speedUpFactor;
+    while (n < n_iter) {
-      this.emitter.emit("stateChange", this.currentTime);
+      this.tick(this.timeStep);
+      n += 1;
+    }
+    this.currentTime += n_iter * this.timeStep * DAY2MS / this.speedUpFactor;
+    this.emitter.emit("stateChange", this.currentTime); // update downstream reactors
+
+    if (this.returnPump) { // update recirculation pump state
+      this.returnPump.updateSourceSink();
     }
   }
 }
@@ -231,6 +245,23 @@ class Reactor_CSTR extends Reactor {
       this.state = config.initialState;
   }
 
+  _updateMeasurement(measurementType, value, position, context) {
+
+    switch(measurementType) {
+      case "quantity (oxygen)":
+        this.state[ASM_CONSTANTS.S_O_INDEX] = value;
+        break;
+      case "quantity (ammonium)":
+        this.state[ASM_CONSTANTS.S_NH_INDEX] = value;
+        break;
+      case "quantity (nox)":
+        this.state[ASM_CONSTANTS.S_NO_INDEX] = value;
+        break;
+      default:
+        super._updateMeasurement(measurementType, value, position, context);
+    }
+  }
+
   /**
    * Tick the reactor state using the forward Euler method.
    * @param {number} time_step - Time step for the simulation [d].
@@ -241,7 +272,7 @@ class Reactor_CSTR extends Reactor {
     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(ASM_CONSTANTS.NUM_SPECIES).fill(0.0);
-    transfer[ASM_CONSTANTS.S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[S_O_INDEX], this.temperature); // calculate OTR if kla is not NaN, otherwise use externaly calculated OTR
+    transfer[ASM_CONSTANTS.S_O_INDEX] = isNaN(this.kla) ? this.OTR : this._calcOTR(this.state[ASM_CONSTANTS.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
@@ -290,13 +321,23 @@ class Reactor_PFR extends Reactor {
     this.D = this._constrainDispersion(input.payload);
   }
 
+  _connectReactor(reactorChild) {
+    if (math.abs(reactorChild.d_x - this.d_x) / this.d_x < 0.025) {
+      this.logger.warn("Significant grid sizing discrepancies between adjacent reactors! Change resolutions to match reactors grid step, or implement boundary value interpolation.");
+    }
+    super._connectReactor(reactorChild);
+  }
+
+  /**
+   * Update the reactor state based on the new time. Performs checks specific to PFR.
+   * @param {number} newTime - New time to update reactor state to, in milliseconds since epoch.
+   */
   updateState(newTime) {
     super.updateState(newTime);
-    // let Pe_local = this.d_x*math.sum(this.Fs)/(this.D*this.A)
+    
-    this.D = this._constrainDispersion(this.D);
+    this.D = this._constrainDispersion(this.D); // constrains D to minimum dispersion, so that local Péclet number is always above 2
     const Co_D = this.D*this.timeStep/(this.d_x*this.d_x);
 
-    // (Pe_local >= 2) && this.logger.warn(`Local Péclet number (${Pe_local}) is too high! Increase reactor resolution.`);
     (Co_D >= 0.5) && this.logger.warn(`Courant number (${Co_D}) is too high! Reduce time step size.`);
 
     if(DEBUG) {
@@ -326,8 +367,8 @@ class Reactor_PFR extends Reactor {
         transfer[i][ASM_CONSTANTS.S_O_INDEX] = this.OTR * this.n_x/(this.n_x-2);
       }
     } else {
-    for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
+      for (let i = BC_PADDING+1; i < BC_PADDING+this.n_x - 1; i++) {
-        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature)  * this.n_x/(this.n_x-2);
+        transfer[i][ASM_CONSTANTS.S_O_INDEX] = this._calcOTR(this.extendedState[i][ASM_CONSTANTS.S_O_INDEX], this.temperature);
       }
     }
 
@@ -349,10 +390,19 @@ class Reactor_PFR extends Reactor {
   }
 
   _updateMeasurement(measurementType, value, position, context) {
+    const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+
+    // naive approach for reconciling measurements and simulation
+    // could benefit from Kalman filter?
     switch(measurementType) {
       case "quantity (oxygen)":
-        const grid_pos = Math.round(context.distance / this.config.length * this.n_x);
+        this.state[grid_pos][ASM_CONSTANTS.S_O_INDEX] = value;
-        this.state[grid_pos][0] = value; // naive approach for reconciling measurements and simulation
+        break;
+      case "quantity (ammonium)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NH_INDEX] = value;
+        break;
+      case "quantity (nox)":
+        this.state[grid_pos][ASM_CONSTANTS.S_NO_INDEX] = value;
         break;
       default:
         super._updateMeasurement(measurementType, value, position, context);
@@ -366,8 +416,8 @@ class Reactor_PFR extends Reactor {
    */
   _applyBoundaryConditions() {
     // Upstream BC
-    if (this.upstreamReactor) {
+    if (this.upstreamReactor && this.upstreamReactor.config.reactor_type == "PFR") {
-      // Open boundary
+      // Open boundary, if upstream reactor is PFR
       this.extendedState.splice(0, BC_PADDING, ...this.upstreamReactor.state.slice(-BC_PADDING)); 
     } else {
       if (math.sum(this.Fs) > 0) {
@@ -375,6 +425,7 @@ class Reactor_PFR extends Reactor {
         const BC_C_in = math.multiply(1 / math.sum(this.Fs), [this.Fs], this.Cs_in)[0];
         const BC_dispersion_term = this.D*this.A/(math.sum(this.Fs)*this.d_x);
         this.extendedState[BC_PADDING] = math.multiply(1/(1+BC_dispersion_term), math.add(BC_C_in, math.multiply(BC_dispersion_term, this.extendedState[BC_PADDING+1])));
+        // Numerical boundary condition (first-order accurate)
         this.extendedState[BC_PADDING-1] = math.add(math.multiply(2, this.extendedState[BC_PADDING]), math.multiply(-2, this.extendedState[BC_PADDING+2]), this.extendedState[BC_PADDING+3]);
       } else {
         // Neumann BC (no flux)
@@ -383,8 +434,8 @@ class Reactor_PFR extends Reactor {
     }
 
     // Downstream BC
-    if (this.downstreamReactor) {
+    if (this.downstreamReactor && this.downstreamReactor.config.reactor_type == "PFR") {
-      // Open boundary
+      // Open boundary, if downstream reactor is PFR
       this.extendedState.splice(this.n_x+BC_PADDING, BC_PADDING, ...this.downstreamReactor.state.slice(0, BC_PADDING));
     } else {
       // Neumann BC (no flux)
@@ -394,7 +445,6 @@ class Reactor_PFR extends Reactor {
 
   /**
    * 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;
@@ -410,7 +460,6 @@ class Reactor_PFR extends Reactor {
 
   /**
    * 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;
@@ -423,6 +472,9 @@ class Reactor_PFR extends Reactor {
     return D2;
   }
 
+  /**
+   * Constrains dispersion so that local Péclet number stays below 2. Needed for stable central differencing method.
+   */
   _constrainDispersion(D) {
     const Dmin = math.sum(this.Fs) * this.d_x / (1.999 * this.A);
     if (D < Dmin) {