diff-grok 1.1.0 → 1.2.0

package/docs/media/cyclic-model.js

@@ -0,0 +1,102 @@
+/* eslint-disable max-len */
+/** This example shows how to apply pipelines and cyclic models.
+    This approach can be used for in-webworkers analysis of models.
+
+    Here, we consider pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model.
+*/
+import * as DGL from '../../index';
+/** 1. Model specification */
+const model = `#name: PK-PD
+#tags: model
+#description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
+#equations:
+  d(depot)/dt = -KA * depot
+  d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
+  d(peri)/dt  = Q * C2 - Q * C3
+  d(eff)/dt  = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
+
+#expressions:
+  C2 = centr / V2
+  C3 = peri / V3
+
+#loop:
+  _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
+  depot += dose
+
+#argument: t
+  _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
+  _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
+  _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]  
+
+#inits:  
+  depot = 0 {category: Initial values}
+  centr = 0 {category: Initial values} [Central]
+  peri = 0 {category: Initial values} [Peripheral]
+  eff = 0.2 {category: Initial values} [Effective compartment rate]
+
+#parameters:  
+  dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
+  KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
+  CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
+  V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
+  Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
+  V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
+  EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
+  Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
+  Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
+  
+#tolerance: 1e-9
+
+#meta.solver: {method: 'rkdp'; maxTimeMs: 5000}`;
+/** 2. Generate IVP-objects: for the main thread & for computations in webworkers */
+const ivp = DGL.getIVP(model);
+const ivpWW = DGL.getIvp2WebWorker(ivp);
+/** 3. Perform computations */
+try {
+    // 3.1) Extract names of outputs
+    const outputNames = DGL.getOutputNames(ivp);
+    const outSize = outputNames.length;
+    // 3.2) Set model inputs
+    const inputs = {
+        _count: 10,
+        _t0: 0,
+        _t1: 16,
+        _h: 1,
+        depot: 0,
+        centr: 0,
+        peri: 0,
+        eff: 0.2,
+        dose: 10000,
+        KA: 0.63,
+        CL: 3.2,
+        V2: 6.58,
+        Q: 0.622,
+        V3: 35.6,
+        EC50: 5.41,
+        Kin: 0.272,
+        Kout: 0.276,
+    };
+    const inputVector = DGL.getInputVector(inputs, ivp);
+    // 3.3) Create a pipeline
+    const creator = DGL.getPipelineCreator(ivp);
+    const pipeline = creator.getPipeline(inputVector);
+    // 3.4) Apply pipeline to perform computations
+    const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+    // 3.5) Print results
+    // 3.5.1) Table header
+    let line = '         ';
+    outputNames.forEach((name) => line += name + '           ');
+    console.log(line);
+    // 3.5.2) Table with solution
+    const length = solution[0].length;
+    for (let i = 0; i < length; ++i) {
+        line = '';
+        for (let j = 0; j < outSize; ++j)
+            line += solution[j][i].toFixed(8) + '     ';
+        console.log(line);
+    }
+}
+catch (err) {
+    console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+}
+//# sourceMappingURL=cyclic-model.js.map

package/docs/media/cyclic-model.js.map

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package/docs/media/cyclic-model.ts

@@ -0,0 +1,112 @@
+/* eslint-disable max-len */
+/** This example shows how to apply pipelines and cyclic models.
+    This approach can be used for in-webworkers analysis of models.
+
+    Here, we consider pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model.
+*/
+
+import * as DGL from '../../index';
+
+/** 1. Model specification */
+const model = `#name: PK-PD
+#tags: model
+#description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
+#equations:
+  d(depot)/dt = -KA * depot
+  d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
+  d(peri)/dt  = Q * C2 - Q * C3
+  d(eff)/dt  = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
+
+#expressions:
+  C2 = centr / V2
+  C3 = peri / V3
+
+#loop:
+  _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
+  depot += dose
+
+#argument: t
+  _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
+  _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
+  _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]  
+
+#inits:  
+  depot = 0 {category: Initial values}
+  centr = 0 {category: Initial values} [Central]
+  peri = 0 {category: Initial values} [Peripheral]
+  eff = 0.2 {category: Initial values} [Effective compartment rate]
+
+#parameters:  
+  dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
+  KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
+  CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
+  V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
+  Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
+  V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
+  EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
+  Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
+  Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
+  
+#tolerance: 1e-9
+
+#meta.solver: {method: 'rkdp'; maxTimeMs: 5000}`;
+
+/** 2. Generate IVP-objects: for the main thread & for computations in webworkers */
+const ivp = DGL.getIVP(model);
+const ivpWW = DGL.getIvp2WebWorker(ivp);
+
+/** 3. Perform computations */
+try {
+  // 3.1) Extract names of outputs
+  const outputNames = DGL.getOutputNames(ivp);
+  const outSize = outputNames.length;
+
+  // 3.2) Set model inputs
+  const inputs = {
+    _count: 10,
+    _t0: 0,
+    _t1: 16,
+    _h: 1,
+    depot: 0,
+    centr: 0,
+    peri: 0,
+    eff: 0.2,
+    dose: 10000,
+    KA: 0.63,
+    CL: 3.2,
+    V2: 6.58,
+    Q: 0.622,
+    V3: 35.6,
+    EC50: 5.41,
+    Kin: 0.272,
+    Kout: 0.276,
+  };
+  const inputVector = DGL.getInputVector(inputs, ivp);
+
+  // 3.3) Create a pipeline
+  const creator = DGL.getPipelineCreator(ivp);
+  const pipeline = creator.getPipeline(inputVector);
+
+  // 3.4) Apply pipeline to perform computations
+  const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+
+  // 3.5) Print results
+
+  // 3.5.1) Table header
+  let line = '         ';
+  outputNames.forEach((name) => line += name + '           ');
+  console.log(line);
+
+  // 3.5.2) Table with solution
+  const length = solution[0].length;
+  for (let i = 0; i < length; ++i) {
+    line = '';
+
+    for (let j = 0; j < outSize; ++j)
+      line += solution[j][i].toFixed(8) + '     ';
+
+    console.log(line);
+  }
+} catch (err) {
+  console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+}

package/docs/media/e5.js

@@ -0,0 +1,36 @@
+/** Kintetic constants for the E5 model */
+var E5;
+(function (E5) {
+    E5[E5["K1"] = 7.89e-10] = "K1";
+    E5[E5["K2"] = 1130000000] = "K2";
+    E5[E5["K3"] = 11000000] = "K3";
+    E5[E5["K4"] = 1130] = "K4";
+})(E5 || (E5 = {}));
+;
+/** The E5 model (chemical pyrolysis: https://archimede.uniba.it/~testset/report/e5.pdf) */
+export const e5 = {
+    name: 'E5',
+    arg: { name: 't', start: 0, finish: 1e13, step: 2.5e8 },
+    initial: [0.00176, 0, 0, 0],
+    func: (t, y, output) => {
+        // extract function values
+        const y1 = y[0];
+        const y2 = y[1];
+        const y3 = y[2];
+        const y4 = y[3];
+        // compute output
+        output[0] = -E5.K1 * y1 - E5.K3 * y1 * y3;
+        output[1] = E5.K1 * y1 - E5.K2 * y2 * y3;
+        output[2] = E5.K1 * y1 - E5.K2 * y2 * y3 - E5.K3 * y1 * y3 + E5.K4 * y4;
+        output[3] = E5.K3 * y1 * y3 - E5.K4 * y4;
+    },
+    tolerance: 1e-6,
+    solutionColNames: ['y1', 'y2', 'y3', 'y4'],
+};
+export const e5ReferencePoint = new Float64Array([
+    0.1152903278711829E-290,
+    0.8867655517642120E-22,
+    0.8854814626268838E-22,
+    0,
+]);
+//# sourceMappingURL=e5.js.map

package/docs/media/e5.js.map

@@ -0,0 +1 @@
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package/docs/media/e5.ts

@@ -0,0 +1,36 @@
+ /** Kintetic constants for the E5 model */
+ enum E5 {
+    K1 = 7.89e-10,
+    K2 = 1.13e9,
+    K3 = 1.1e7,
+    K4 = 1.13e3,
+  };
+
+/** The E5 model (chemical pyrolysis: https://archimede.uniba.it/~testset/report/e5.pdf) */
+export const e5 = {
+  name: 'E5',
+  arg: {name: 't', start: 0, finish: 1e13, step: 2.5e8},
+  initial: [0.00176, 0, 0, 0],
+  func: (t: number, y: Float64Array, output: Float64Array) => {
+    // extract function values
+    const y1 = y[0];
+    const y2 = y[1];
+    const y3 = y[2];
+    const y4 = y[3];
+
+    // compute output
+    output[0] = -E5.K1 * y1 - E5.K3 * y1 * y3;
+    output[1] = E5.K1 * y1 - E5.K2 * y2 * y3;
+    output[2] = E5.K1 * y1 - E5.K2 * y2 * y3 - E5.K3 * y1 * y3 + E5.K4 * y4;
+    output[3] = E5.K3 * y1 * y3 - E5.K4 * y4;
+  },
+  tolerance: 1e-6,
+  solutionColNames: ['y1', 'y2', 'y3', 'y4'],
+};
+
+export const e5ReferencePoint = new Float64Array([
+  0.1152903278711829E-290,
+  0.8867655517642120E-22,
+  0.8854814626268838E-22,
+  0,
+]);

package/docs/media/hires.js

@@ -0,0 +1,39 @@
+/** High Irradiance Responses of photomorphogenesis (see https://archimede.uniba.it/~testset/problems/hires.php) */
+export const hires = {
+    name: 'HIRES',
+    arg: { name: 't', start: 0, finish: 321.8122, step: 0.01 },
+    initial: [1, 0, 0, 0, 0, 0, 0, 0.0057],
+    func: (t, y, output) => {
+        // extract function values
+        const y1 = y[0];
+        const y2 = y[1];
+        const y3 = y[2];
+        const y4 = y[3];
+        const y5 = y[4];
+        const y6 = y[5];
+        const y7 = y[6];
+        const y8 = y[7];
+        // compute output
+        output[0] = -1.71 * y1 + 0.43 * y2 + 8.32 * y3 + 0.0007;
+        output[1] = 1.71 * y1 - 8.75 * y2;
+        output[2] = -10.03 * y3 + 0.43 * y4 + 0.035 * y5;
+        output[3] = 8.32 * y2 + 1.71 * y3 - 1.12 * y4;
+        output[4] = -1.745 * y5 + 0.43 * y6 + 0.43 * y7;
+        output[5] = -280 * y6 * y8 + 0.69 * y4 + 1.71 * y5 - 0.43 * y6 + 0.69 * y7;
+        output[6] = 280 * y6 * y8 - 1.81 * y7;
+        output[7] = -280 * y6 * y8 + 1.81 * y7;
+    },
+    tolerance: 1e-10,
+    solutionColNames: ['y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7', 'y8'],
+}; // hires
+export const hiresReferencePoint = new Float64Array([
+    0.7371312573325668E-3,
+    0.1442485726316185E-3,
+    0.5888729740967575E-4,
+    0.1175651343283149E-2,
+    0.2386356198831331E-2,
+    0.6238968252742796E-2,
+    0.2849998395185769E-2,
+    0.2850001604814231E-2,
+]);
+//# sourceMappingURL=hires.js.map

package/docs/media/hires.js.map

@@ -0,0 +1 @@
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package/docs/media/hires.ts

@@ -0,0 +1,40 @@
+/** High Irradiance Responses of photomorphogenesis (see https://archimede.uniba.it/~testset/problems/hires.php) */
+export const hires = {
+  name: 'HIRES',
+  arg: {name: 't', start: 0, finish: 321.8122, step: 0.01},
+  initial: [1, 0, 0, 0, 0, 0, 0, 0.0057],
+  func: (t: number, y: Float64Array, output: Float64Array) => {
+    // extract function values
+    const y1 = y[0];
+    const y2 = y[1];
+    const y3 = y[2];
+    const y4 = y[3];
+    const y5 = y[4];
+    const y6 = y[5];
+    const y7 = y[6];
+    const y8 = y[7];
+
+    // compute output
+    output[0] = -1.71 * y1 + 0.43 * y2 + 8.32 * y3 + 0.0007;
+    output[1] = 1.71 * y1 - 8.75 * y2;
+    output[2] = -10.03 * y3 + 0.43 * y4 + 0.035 * y5;
+    output[3] = 8.32 * y2 + 1.71 * y3 - 1.12 * y4;
+    output[4] = -1.745 * y5 + 0.43 * y6 + 0.43 * y7;
+    output[5] = -280 * y6 * y8 + 0.69 * y4 + 1.71 * y5 - 0.43 * y6 + 0.69 * y7;
+    output[6] = 280 * y6 * y8 - 1.81 * y7;
+    output[7] = -280 * y6 * y8 + 1.81 * y7;
+  },
+  tolerance: 1e-10,
+  solutionColNames: ['y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7', 'y8'],
+}; // hires
+
+export const hiresReferencePoint = new Float64Array([
+  0.7371312573325668E-3,
+  0.1442485726316185E-3,
+  0.5888729740967575E-4,
+  0.1175651343283149E-2,
+  0.2386356198831331E-2,
+  0.6238968252742796E-2,
+  0.2849998395185769E-2,
+  0.2850001604814231E-2,
+]);

package/docs/media/model-updates.js

@@ -0,0 +1,112 @@
+/* eslint-disable max-len */
+/** This example shows how to apply pipelines and models with updates.
+    This approach can be used for in-webworkers analysis of models.
+
+    Here, we consider gluconic acid (GA) production by Aspergillus niger modeling.
+*/
+import * as DGL from '../../index';
+/** 1. Model specification */
+const model = `#name: GA-production
+#tags: model
+#description: Gluconic acid (GA) production by Aspergillus niger modeling
+#equations:
+  dX/dt = rX
+  dS/dt = -gamma * rX - lambda * X
+  dO/dt = Kla * (Cod - O) - delta * rX - phi * X
+  dP/dt = alpha * rX + beta * X
+
+#expressions:
+  mu = muM * S / (Ks + S) * O / (Ko + O)
+  rX = mu * X
+
+#argument: t, 1-st stage
+  _t0 = 0 {units: h; caption: initial; category: Misc} [Start of the process]
+  _t1 = 60 {units: h; caption: 1-st stage; category: Durations; min: 20; max: 80} [Duration of the 1-st stage]
+  step = 0.1 {units: h; caption: step; category: Misc; min: 0.01; max: 1} [Time step of simulation]
+
+#update: 2-nd stage
+  duration = overall - _t1
+  S += 70
+
+#inits:  
+  X = 5 {units: kg/m³; caption: biomass; category: Initial concentrations; min: 1; max: 10} [Aspergillus niger biomass]
+  S = 150 {units: kg/m³; caption: glucose; category: Initial concentrations; min: 50; max: 200} [Glucose]
+  O = 7 {units: kg/m³; caption: oxygen; category: Initial concentrations; min: 1; max: 10} [Dissolved oxygen]
+  P = 0 {units: kg/m³; caption: acid; category: Initial concentrations; min: 0; max: 0.1} [Gluconic acid]
+
+#output:
+  t {caption: time}
+  X {caption: biomass}
+  S {caption: glucose}
+  O {caption: oxygen}
+  P {caption: acid}
+
+#parameters:
+  overall = 100 {units: h; category: Durations; min: 100; max: 140} [Overall duration]
+  muM = 0.668 {units: 1/h; category: Parameters} [Monod type model parameter]
+  alpha = 2.92 {category: Parameters} [Monod type model parameter]
+  beta = 0.131 {units: 1/h; category: Parameters} [Monod type model parameter]
+  gamma = 2.12 {category: Parameters} [Monod type model parameter]
+  lambda = 0.232 {units: 1/h; category: Parameters} [Monod type model parameter]
+  delta = 0.278 {category: Parameters} [Monod type model parameter]
+  phi = 4.87e-3 {units: 1/h; category: Parameters} [Monod type model parameter]
+  Ks = 1.309e2 {units: g/L; category: Parameters} [Monod type model parameter]
+  Ko = 3.63e-4 {units: g/L; category: Parameters} [Monod type model parameter]
+  Kla = 1.7e-2 {units: 1/s; category: Parameters} [Volumetric mass transfer coefficient]
+  Cod = 15 {units: kg/m³; category: Parameters} [Liquid phase dissolved oxygen saturation concentration]
+  
+#tolerance: 1e-9`;
+/** 2. Generate IVP-objects: for the main thread & for computations in webworkers */
+const ivp = DGL.getIVP(model);
+const ivpWW = DGL.getIvp2WebWorker(ivp);
+/** 3. Perform computations */
+try {
+    // 3.1) Extract names of outputs
+    const outputNames = DGL.getOutputNames(ivp);
+    const outSize = outputNames.length;
+    // 3.2) Set model inputs
+    const inputs = {
+        _t0: 0,
+        _t1: 60,
+        _h: 1,
+        X: 5,
+        S: 150,
+        O: 7,
+        P: 0,
+        overall: 100,
+        muM: 0.668,
+        alpha: 2.92,
+        beta: 0.131,
+        gamma: 2.12,
+        lambda: 0.232,
+        delta: 0.278,
+        phi: 4.87e-3,
+        Ks: 1.309e2,
+        Ko: 3.63e-4,
+        Kla: 1.7e-2,
+        Cod: 15,
+    };
+    const inputVector = DGL.getInputVector(inputs, ivp);
+    // 3.3) Create a pipeline
+    const creator = DGL.getPipelineCreator(ivp);
+    const pipeline = creator.getPipeline(inputVector);
+    // 3.4) Apply pipeline to perform computations
+    const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+    // 3.5) Print results
+    // 3.5.1) Table header
+    let line = '     ';
+    outputNames.forEach((name) => line += name + '         ');
+    console.log(line);
+    // 3.5.2) Table with solution
+    const length = solution[0].length;
+    for (let i = 0; i < length; ++i) {
+        line = '';
+        for (let j = 0; j < outSize; ++j)
+            line += solution[j][i].toFixed(8) + '     ';
+        console.log(line);
+    }
+}
+catch (err) {
+    console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+}
+//# sourceMappingURL=model-updates.js.map

package/docs/media/model-updates.js.map

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package/docs/media/model-updates.ts

@@ -0,0 +1,122 @@
+/* eslint-disable max-len */
+/** This example shows how to apply pipelines and models with updates.
+    This approach can be used for in-webworkers analysis of models.
+
+    Here, we consider gluconic acid (GA) production by Aspergillus niger modeling.
+*/
+
+import * as DGL from '../../index';
+
+/** 1. Model specification */
+const model = `#name: GA-production
+#tags: model
+#description: Gluconic acid (GA) production by Aspergillus niger modeling
+#equations:
+  dX/dt = rX
+  dS/dt = -gamma * rX - lambda * X
+  dO/dt = Kla * (Cod - O) - delta * rX - phi * X
+  dP/dt = alpha * rX + beta * X
+
+#expressions:
+  mu = muM * S / (Ks + S) * O / (Ko + O)
+  rX = mu * X
+
+#argument: t, 1-st stage
+  _t0 = 0 {units: h; caption: initial; category: Misc} [Start of the process]
+  _t1 = 60 {units: h; caption: 1-st stage; category: Durations; min: 20; max: 80} [Duration of the 1-st stage]
+  step = 0.1 {units: h; caption: step; category: Misc; min: 0.01; max: 1} [Time step of simulation]
+
+#update: 2-nd stage
+  duration = overall - _t1
+  S += 70
+
+#inits:  
+  X = 5 {units: kg/m³; caption: biomass; category: Initial concentrations; min: 1; max: 10} [Aspergillus niger biomass]
+  S = 150 {units: kg/m³; caption: glucose; category: Initial concentrations; min: 50; max: 200} [Glucose]
+  O = 7 {units: kg/m³; caption: oxygen; category: Initial concentrations; min: 1; max: 10} [Dissolved oxygen]
+  P = 0 {units: kg/m³; caption: acid; category: Initial concentrations; min: 0; max: 0.1} [Gluconic acid]
+
+#output:
+  t {caption: time}
+  X {caption: biomass}
+  S {caption: glucose}
+  O {caption: oxygen}
+  P {caption: acid}
+
+#parameters:
+  overall = 100 {units: h; category: Durations; min: 100; max: 140} [Overall duration]
+  muM = 0.668 {units: 1/h; category: Parameters} [Monod type model parameter]
+  alpha = 2.92 {category: Parameters} [Monod type model parameter]
+  beta = 0.131 {units: 1/h; category: Parameters} [Monod type model parameter]
+  gamma = 2.12 {category: Parameters} [Monod type model parameter]
+  lambda = 0.232 {units: 1/h; category: Parameters} [Monod type model parameter]
+  delta = 0.278 {category: Parameters} [Monod type model parameter]
+  phi = 4.87e-3 {units: 1/h; category: Parameters} [Monod type model parameter]
+  Ks = 1.309e2 {units: g/L; category: Parameters} [Monod type model parameter]
+  Ko = 3.63e-4 {units: g/L; category: Parameters} [Monod type model parameter]
+  Kla = 1.7e-2 {units: 1/s; category: Parameters} [Volumetric mass transfer coefficient]
+  Cod = 15 {units: kg/m³; category: Parameters} [Liquid phase dissolved oxygen saturation concentration]
+  
+#tolerance: 1e-9`;
+
+/** 2. Generate IVP-objects: for the main thread & for computations in webworkers */
+const ivp = DGL.getIVP(model);
+const ivpWW = DGL.getIvp2WebWorker(ivp);
+
+/** 3. Perform computations */
+try {
+  // 3.1) Extract names of outputs
+  const outputNames = DGL.getOutputNames(ivp);
+  const outSize = outputNames.length;
+
+  // 3.2) Set model inputs
+  const inputs = {
+    _t0: 0,
+    _t1: 60,
+    _h: 1,
+    X: 5,
+    S: 150,
+    O: 7,
+    P: 0,
+    overall: 100,
+    muM: 0.668,
+    alpha: 2.92,
+    beta: 0.131,
+    gamma: 2.12,
+    lambda: 0.232,
+    delta: 0.278,
+    phi: 4.87e-3,
+    Ks: 1.309e2,
+    Ko: 3.63e-4,
+    Kla: 1.7e-2,
+    Cod: 15,
+  };
+  const inputVector = DGL.getInputVector(inputs, ivp);
+
+  // 3.3) Create a pipeline
+  const creator = DGL.getPipelineCreator(ivp);
+  const pipeline = creator.getPipeline(inputVector);
+
+  // 3.4) Apply pipeline to perform computations
+  const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+
+  // 3.5) Print results
+
+  // 3.5.1) Table header
+  let line = '     ';
+  outputNames.forEach((name) => line += name + '         ');
+  console.log(line);
+
+  // 3.5.2) Table with solution
+  const length = solution[0].length;
+  for (let i = 0; i < length; ++i) {
+    line = '';
+
+    for (let j = 0; j < outSize; ++j)
+      line += solution[j][i].toFixed(8) + '     ';
+
+    console.log(line);
+  }
+} catch (err) {
+  console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+}

package/docs/media/orego.js

@@ -0,0 +1,24 @@
+/** The OREGO model (see https://archimede.uniba.it/~testset/report/orego.pdf) */
+export const orego = {
+    name: 'OREGO',
+    arg: { name: 't', start: 0, finish: 360, step: 0.01 },
+    initial: [1, 2, 3],
+    func: (t, y, output) => {
+        // extract function values
+        const y1 = y[0];
+        const y2 = y[1];
+        const y3 = y[2];
+        // compute output
+        output[0] = 77.27 * (y2 - y1 * y2 + y1 - 0.000008375 * y1 * y1);
+        output[1] = 1 / 77.27 * (-y2 - y1 * y2 + y3);
+        output[2] = 0.161 * (y1 - y3);
+    },
+    tolerance: 1e-8,
+    solutionColNames: ['y1', 'y2', 'y3'],
+};
+export const oregoReferencePoint = new Float64Array([
+    1.000814870318523,
+    1228.178521549917,
+    132.0554942846706,
+]);
+//# sourceMappingURL=orego.js.map

package/docs/media/orego.js.map

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