diff-grok 1.0.8 → 1.0.10

package/src/solver-tools/solver-defs.ts

@@ -2,17 +2,87 @@
 
 import {Callback} from './callbacks/callback-base';
 
-/** Right-hand side of IVP */
+/**
+ * Represents the right-hand side function **F(t, y)** of an ODE system.
+ *
+ * @param t - The independent variable.
+ * @param y - The current values of the system's state variables.
+ * @param output - A preallocated array where the computed derivatives
+ *   should be written. This approach avoids unnecessary memory allocations
+ *   and improves performance.
+ */
 export type Func = (t: number, y: Float64Array, output: Float64Array) => void;
 
-/** Solver optional settings */
+/**
+ * Optional configuration settings of the numerical solver of an initial value problem (ODE).
+ *
+ * @property maxIterations - The maximum number of iterations allowed.
+ * @property maxTimeMs - The maximum time in milliseconds allowed for the solver.
+ * @property method - The name of the numerical method to use.
+ */
 export type SolverOptions = {
   maxIterations: number,
   maxTimeMs: number,
   method: string,
 };
 
-/** Initial Value Problem (IVP) type */
+/**
+ * Specifies a single-stage ODE model.
+ *
+ * @property name - The name of the model.
+ * @property initial - The initial values of the state variables. Can be
+ *   an array or typed array.
+ * @property solutionColNames - Names of the columns in the model's output.
+ * @property tolerance - Tolerance for the numerical solver.
+ * @property func - The function representing the right-hand side F(t, y)
+ *   of the ODE system.
+ * @property arg - Specification of the independent variable:
+ *   - name: the variable's name
+ *   - start: starting value
+ *   - finish: ending value
+ *   - step: step size for the grid
+ * * Example: Solve a simple initial value problem (IVP)
+ *
+ * @example
+ * // Example. Solve the following initial value problem:
+ * //   dx/dt = x + y - t
+ * //   dy/dt = x * y + t
+ * //   x(0) = 1
+ * //   y(0) = -1
+ * // on [0, 2] with the step 0.01.
+ * import { ODEs, mrt } from 'diff-grok';
+ *
+ * const task: ODEs = {
+ *   name: 'Example', // name of your model
+ *   arg: {
+ *       name: 't',  // name of the argument
+ *       start: 0,   // initial value of the argument
+ *       finish: 2,  // final value of the argument
+ *       step: 0.01, // solution grid step
+ *   },
+ *   initial: [1, -1], // initial values
+ *   func: (t: number, y: Float64Array, output: Float64Array) => { // right-hand side of the system
+ *     output[0] = y[0] + y[1] - t; // 1-st equation
+ *     output[1] = y[0] * y[1] + t; // 2-nd equation
+ *   },
+ *   tolerance: 1e-7, // tolerance
+ *   solutionColNames: ['x', 'y'], // names of solution functions
+ * };
+ *
+ * try {
+ *   // Solve the problem using the MRT method
+ *   const solution = mrt(task);
+ *
+ *   // Print a table with the results
+ *   console.log(task.arg.name, task.solutionColNames[0], task.solutionColNames[1]);
+ *   const length = solution[0].length;
+ *   for (let i = 0; i < length; ++i)
+ *     console.log(solution[0][i], solution[1][i], solution[2][i]);
+ * } catch (err) {
+ *   console.log('Solver failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+ * }
+ * ```
+ */
 export type ODEs = {
   name: string,
   arg: {
@@ -76,25 +146,33 @@ export function jacobian(t: number, y: Float64Array, f: Func, eps: number,
   }
 }
 
-/** Error messeges */
+/** Error messeges
+ * @internal
+*/
 export enum ERROR_MSG {
   MRT_FAILS = 'The modified Rosenbrock triple method fails',
   ROS3PRW_FAILS = 'The ROS3PRw method fails',
   ROS34PRW_FAILS = 'The ROS34PRw method fails',
 };
 
-/** Callback action */
+/** Callback action
+ * @internal
+ */
 export class CallbackAction extends Error {
   constructor(msg: string) {
     super(msg);
   }
 }
 
-/** Default options of the solver */
+/** Default options of the solver
+ * @internal
+ */
 export enum DEFAULT_OPTIONS {
   SCRIPTING = '{maxIterations: 1}',
   NO_CHECKS = '{ }',
 }
 
-/** IVP solving method */
+/** IVP solving method
+ * @internal
+ */
 export type SolverMethod = (odes: ODEs, callback?: Callback) => Float64Array[];

package/src/tests/correctness.test.js

@@ -0,0 +1,13 @@
+// Correctness tests
+import { corrProbs } from '../../index';
+import { getError } from './test-utils';
+import { methods, MAX_MAD } from './test-defs';
+methods.forEach((method, name) => {
+    corrProbs.forEach((problem) => {
+        test(`Correctness: method - ${name}, problem - ${problem.odes.name}`, () => {
+            const error = getError(method, problem);
+            expect(error).toBeLessThan(MAX_MAD);
+        });
+    });
+});
+//# sourceMappingURL=correctness.test.js.map

package/src/tests/correctness.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"correctness.test.js","sourceRoot":"","sources":["correctness.test.ts"],"names":[],"mappings":"AAAA,oBAAoB;AAEpB,OAAO,EAAC,SAAS,EAAC,MAAM,aAAa,CAAC;AACtC,OAAO,EAAC,QAAQ,EAAC,MAAM,cAAc,CAAC;AACtC,OAAO,EAAC,OAAO,EAAE,OAAO,EAAC,MAAM,aAAa,CAAC;AAE7C,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;IAC/B,SAAS,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QAC5B,IAAI,CAAC,yBAAyB,IAAI,eAAe,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,EAAE,GAAG,EAAE;YACzE,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;YACxC,MAAM,CAAC,KAAK,CAAC,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC;QACtC,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/src/tests/correctness.test.ts

@@ -0,0 +1,14 @@
+// Correctness tests
+
+import {corrProbs} from '../../index';
+import {getError} from './test-utils';
+import {methods, MAX_MAD} from './test-defs';
+
+methods.forEach((method, name) => {
+  corrProbs.forEach((problem) => {
+    test(`Correctness: method - ${name}, problem - ${problem.odes.name}`, () => {
+      const error = getError(method, problem);
+      expect(error).toBeLessThan(MAX_MAD);
+    });
+  });
+});

package/src/tests/performance.test.js

@@ -0,0 +1,14 @@
+// Performance tests
+import { perfProbs } from '../../index';
+import { methods, TIMEOUT_MS } from './test-defs';
+methods.forEach((method, name) => {
+    perfProbs.forEach((odes) => {
+        test(`Performance: method - ${name}, problem - ${odes.name}`, () => {
+            const start = performance.now();
+            method(odes);
+            const elapsed = performance.now() - start;
+            expect(elapsed).toBeLessThan(TIMEOUT_MS);
+        });
+    });
+});
+//# sourceMappingURL=performance.test.js.map

package/src/tests/performance.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"performance.test.js","sourceRoot":"","sources":["performance.test.ts"],"names":[],"mappings":"AAAA,oBAAoB;AAEpB,OAAO,EAAC,SAAS,EAAC,MAAM,aAAa,CAAC;AACtC,OAAO,EAAC,OAAO,EAAE,UAAU,EAAC,MAAM,aAAa,CAAC;AAEhD,OAAO,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;IAC/B,SAAS,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE;QACzB,IAAI,CAAC,yBAAyB,IAAI,eAAe,IAAI,CAAC,IAAI,EAAE,EAAE,GAAG,EAAE;YACjE,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;YAChC,MAAM,CAAC,IAAI,CAAC,CAAC;YACb,MAAM,OAAO,GAAG,WAAW,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC;YAC1C,MAAM,CAAC,OAAO,CAAC,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;QAC3C,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/src/tests/performance.test.ts

@@ -0,0 +1,15 @@
+// Performance tests
+
+import {perfProbs} from '../../index';
+import {methods, TIMEOUT_MS} from './test-defs';
+
+methods.forEach((method, name) => {
+  perfProbs.forEach((odes) => {
+    test(`Performance: method - ${name}, problem - ${odes.name}`, () => {
+      const start = performance.now();
+      method(odes);
+      const elapsed = performance.now() - start;
+      expect(elapsed).toBeLessThan(TIMEOUT_MS);
+    });
+  });
+});

package/src/tests/pipeline.test.js

@@ -0,0 +1,10 @@
+// Pipeline tests
+import { problems } from './test-defs';
+import { evalModel } from './test-utils';
+problems.forEach((task, name) => {
+    test(`Pipeline: model - ${name}`, () => {
+        const solution = evalModel(task.model, task.inputs);
+        expect(solution.length).toBe(task.outputsCount);
+    });
+});
+//# sourceMappingURL=pipeline.test.js.map

package/src/tests/pipeline.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pipeline.test.js","sourceRoot":"","sources":["pipeline.test.ts"],"names":[],"mappings":"AAAA,iBAAiB;AAEjB,OAAO,EAAC,QAAQ,EAAC,MAAM,aAAa,CAAC;AACrC,OAAO,EAAC,SAAS,EAAC,MAAM,cAAc,CAAC;AAEvC,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,IAAI,EAAE,EAAE;IAC9B,IAAI,CAAC,qBAAqB,IAAI,EAAE,EAAE,GAAG,EAAE;QACrC,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC;QACpD,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;IAClD,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/src/tests/pipeline.test.ts

@@ -0,0 +1,11 @@
+// Pipeline tests
+
+import {problems} from './test-defs';
+import {evalModel} from './test-utils';
+
+problems.forEach((task, name) => {
+  test(`Pipeline: model - ${name}`, () => {
+    const solution = evalModel(task.model, task.inputs);
+    expect(solution.length).toBe(task.outputsCount);
+  });
+});

package/src/tests/test-defs.js

@@ -0,0 +1,194 @@
+/* eslint-disable max-len */
+import { mrt, ros3prw, ros34prw } from '../../index';
+export const methods = new Map([
+    ['MRT', mrt],
+    ['ROS3PRw', ros3prw],
+    ['ROS34PRw', ros34prw],
+]);
+export const MAX_MAD = 0.1;
+export const TIMEOUT_MS = 10000;
+const BASIC_MODEL = `#name: M|M|2|2
+#description: Modelling the system with two servers & two waiting places (EXPLAINED)
+#equations:  
+  dp0/dt = -la * p0 + mu * p1
+  dp1/dt = la * p0 - (la + mu) * p1 + 2 * mu * p2
+  dp2/dt = la * p1 - (la + 2 * mu) * p2 + 2 * mu * p3
+  dp3/dt = la * p2 - (la + 2 * mu) * p3 + 2 * mu * p4
+
+#expressions:
+  la = 1 / arrival
+  mu = 1 / service
+  p4 = 1 - p0 - p1 - p2 - p3
+  busy = 1 - p0 - p1
+  queue = p3 + 2 * p4
+
+#argument: t
+  _t0 = 0     {min: 0;      max: 10;   caption: start;   category: Time; units: min}  [Initial time of simulation]
+  _t1 = 60    {min: 20;     max: 100;  caption: finish;  category: Time; units: min}  [Final time of simulation]
+  _h  = 1     {min: 0.01;   max: 0.1;  caption: step;    category: Time; units: min}  [Time step of simulation] 
+
+#inits:
+  p0 = 1   {min: 0; max: 1; category: Initial state; caption: empty}   [Probability that initially there are NO customers]
+  p1 = 0   {min: 0; max: 1; category: Initial state; caption: single}  [Probability that initially there is ONE customer]
+  p2 = 0   {min: 0; max: 1; category: Initial state; caption: two}     [Probability that initially there are TWO customers]
+  p3 = 0   {min: 0; max: 1; category: Initial state; caption: three}   [Probability that initially there are THREE customers]
+
+#output:
+  t     {caption: Time, min}
+  p0    {caption: P(Empty)}
+  busy  {caption: P(Full load)}
+  queue {caption: E(Queue)}
+
+#parameters:
+  arrival = 10   {min: 1; max: 100; category: Means; caption: arrival;  units: min} [Mean arrival time]
+  service = 100  {min: 1; max: 100; category: Means; caption: service; units: min} [Mean service time]`;
+const BASIC_MODEL_INPUTS = {
+    _t0: 0,
+    _t1: 60,
+    _h: 1,
+    p0: 1,
+    p1: 0,
+    p2: 0,
+    p3: 0,
+    arrival: 10,
+    service: 100,
+};
+const BASIC_MODEL_OUTPUTS = 4;
+const CYCLIC_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`;
+const CYCLIC_MODEL_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 CYCLIC_MODEL_OUTPUTS = 5;
+const MULTISTAGE_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`;
+const MULTISTAGE_MODEL_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 MULTISTAGE_MODEL_OUTPUTS = 5;
+export const problems = new Map([
+    ['basic', { model: BASIC_MODEL, inputs: BASIC_MODEL_INPUTS, outputsCount: BASIC_MODEL_OUTPUTS }],
+    ['cyclic', { model: CYCLIC_MODEL, inputs: CYCLIC_MODEL_INPUTS, outputsCount: CYCLIC_MODEL_OUTPUTS }],
+    ['multistage', { model: MULTISTAGE_MODEL, inputs: MULTISTAGE_MODEL_INPUTS, outputsCount: MULTISTAGE_MODEL_OUTPUTS }],
+]);
+//# sourceMappingURL=test-defs.js.map

package/src/tests/test-defs.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"test-defs.js","sourceRoot":"","sources":["test-defs.ts"],"names":[],"mappings":"AAAA,4BAA4B;AAC5B,OAAO,EAAC,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAC,MAAM,aAAa,CAAC;AAEnD,MAAM,CAAC,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC;IAC7B,CAAC,KAAK,EAAE,GAAG,CAAC;IACZ,CAAC,SAAS,EAAE,OAAO,CAAC;IACpB,CAAC,UAAU,EAAE,QAAQ,CAAC;CACvB,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,OAAO,GAAG,GAAG,CAAC;AAC3B,MAAM,CAAC,MAAM,UAAU,GAAG,KAAK,CAAC;AAEhC,MAAM,WAAW,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;uGAkCmF,CAAC;AAExG,MAAM,kBAAkB,GAAG;IACzB,GAAG,EAAE,CAAC;IACN,GAAG,EAAE,EAAE;IACP,EAAE,EAAE,CAAC;IACL,EAAE,EAAE,CAAC;IACL,EAAE,EAAE,CAAC;IACL,EAAE,EAAE,CAAC;IACL,EAAE,EAAE,CAAC;IACL,OAAO,EAAE,EAAE;IACX,OAAO,EAAE,GAAG;CACb,CAAC;AAEF,MAAM,mBAAmB,GAAG,CAAC,CAAC;AAE9B,MAAM,YAAY,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAuCJ,CAAC;AAElB,MAAM,mBAAmB,GAAG;IAC1B,MAAM,EAAE,EAAE;IACV,GAAG,EAAE,CAAC;IACN,GAAG,EAAE,EAAE;IACP,EAAE,EAAE,CAAC;IACL,KAAK,EAAE,CAAC;IACR,KAAK,EAAE,CAAC;IACR,IAAI,EAAE,CAAC;IACP,GAAG,EAAE,GAAG;IACR,IAAI,EAAE,KAAK;IACX,EAAE,EAAE,IAAI;IACR,EAAE,EAAE,GAAG;IACP,EAAE,EAAE,IAAI;IACR,CAAC,EAAE,KAAK;IACR,EAAE,EAAE,IAAI;IACR,IAAI,EAAE,IAAI;IACV,GAAG,EAAE,KAAK;IACV,IAAI,EAAE,KAAK;CACZ,CAAC;AAEF,MAAM,oBAAoB,GAAG,CAAC,CAAC;AAE/B,MAAM,gBAAgB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAiDR,CAAC;AAElB,MAAM,uBAAuB,GAAG;IAC9B,GAAG,EAAE,CAAC;IACN,GAAG,EAAE,EAAE;IACP,EAAE,EAAE,CAAC;IACL,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,OAAO,EAAE,GAAG;IACZ,GAAG,EAAE,KAAK;IACV,KAAK,EAAE,IAAI;IACX,IAAI,EAAE,KAAK;IACX,KAAK,EAAE,IAAI;IACX,MAAM,EAAE,KAAK;IACb,KAAK,EAAE,KAAK;IACZ,GAAG,EAAE,OAAO;IACZ,EAAE,EAAE,OAAO;IACX,EAAE,EAAE,OAAO;IACX,GAAG,EAAE,MAAM;IACX,GAAG,EAAE,EAAE;CACR,CAAC;AAEF,MAAM,wBAAwB,GAAG,CAAC,CAAC;AAQnC,MAAM,CAAC,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAsB;IACnD,CAAC,OAAO,EAAE,EAAC,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,kBAAkB,EAAE,YAAY,EAAE,mBAAmB,EAAC,CAAC;IAC9F,CAAC,QAAQ,EAAE,EAAC,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,mBAAmB,EAAE,YAAY,EAAE,oBAAoB,EAAC,CAAC;IAClG,CAAC,YAAY,EAAE,EAAC,KAAK,EAAE,gBAAgB,EAAE,MAAM,EAAE,uBAAuB,EAAE,YAAY,EAAE,wBAAwB,EAAC,CAAC;CACnH,CAAC,CAAC"}

package/src/tests/test-defs.ts

@@ -0,0 +1,211 @@
+/* eslint-disable max-len */
+import {mrt, ros3prw, ros34prw} from '../../index';
+
+export const methods = new Map([
+  ['MRT', mrt],
+  ['ROS3PRw', ros3prw],
+  ['ROS34PRw', ros34prw],
+]);
+
+export const MAX_MAD = 0.1;
+export const TIMEOUT_MS = 10000;
+
+const BASIC_MODEL = `#name: M|M|2|2
+#description: Modelling the system with two servers & two waiting places (EXPLAINED)
+#equations:  
+  dp0/dt = -la * p0 + mu * p1
+  dp1/dt = la * p0 - (la + mu) * p1 + 2 * mu * p2
+  dp2/dt = la * p1 - (la + 2 * mu) * p2 + 2 * mu * p3
+  dp3/dt = la * p2 - (la + 2 * mu) * p3 + 2 * mu * p4
+
+#expressions:
+  la = 1 / arrival
+  mu = 1 / service
+  p4 = 1 - p0 - p1 - p2 - p3
+  busy = 1 - p0 - p1
+  queue = p3 + 2 * p4
+
+#argument: t
+  _t0 = 0     {min: 0;      max: 10;   caption: start;   category: Time; units: min}  [Initial time of simulation]
+  _t1 = 60    {min: 20;     max: 100;  caption: finish;  category: Time; units: min}  [Final time of simulation]
+  _h  = 1     {min: 0.01;   max: 0.1;  caption: step;    category: Time; units: min}  [Time step of simulation] 
+
+#inits:
+  p0 = 1   {min: 0; max: 1; category: Initial state; caption: empty}   [Probability that initially there are NO customers]
+  p1 = 0   {min: 0; max: 1; category: Initial state; caption: single}  [Probability that initially there is ONE customer]
+  p2 = 0   {min: 0; max: 1; category: Initial state; caption: two}     [Probability that initially there are TWO customers]
+  p3 = 0   {min: 0; max: 1; category: Initial state; caption: three}   [Probability that initially there are THREE customers]
+
+#output:
+  t     {caption: Time, min}
+  p0    {caption: P(Empty)}
+  busy  {caption: P(Full load)}
+  queue {caption: E(Queue)}
+
+#parameters:
+  arrival = 10   {min: 1; max: 100; category: Means; caption: arrival;  units: min} [Mean arrival time]
+  service = 100  {min: 1; max: 100; category: Means; caption: service; units: min} [Mean service time]`;
+
+const BASIC_MODEL_INPUTS = {
+  _t0: 0,
+  _t1: 60,
+  _h: 1,
+  p0: 1,
+  p1: 0,
+  p2: 0,
+  p3: 0,
+  arrival: 10,
+  service: 100,
+};
+
+const BASIC_MODEL_OUTPUTS = 4;
+
+const CYCLIC_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`;
+
+const CYCLIC_MODEL_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 CYCLIC_MODEL_OUTPUTS = 5;
+
+const MULTISTAGE_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`;
+
+const MULTISTAGE_MODEL_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 MULTISTAGE_MODEL_OUTPUTS = 5;
+
+type TestProblem = {
+  model: string,
+  inputs: Record<string, number>,
+  outputsCount: number,
+};
+
+export const problems = new Map<string, TestProblem>([
+  ['basic', {model: BASIC_MODEL, inputs: BASIC_MODEL_INPUTS, outputsCount: BASIC_MODEL_OUTPUTS}],
+  ['cyclic', {model: CYCLIC_MODEL, inputs: CYCLIC_MODEL_INPUTS, outputsCount: CYCLIC_MODEL_OUTPUTS}],
+  ['multistage', {model: MULTISTAGE_MODEL, inputs: MULTISTAGE_MODEL_INPUTS, outputsCount: MULTISTAGE_MODEL_OUTPUTS}],
+]);

package/src/tests/test-utils.js

@@ -0,0 +1,28 @@
+import { getIVP, getIvp2WebWorker, getInputVector, getPipelineCreator, applyPipeline } from '../../index';
+/** Return numerical solution error: maximum absolute deviation between approximate & exact solutions */
+export function getError(method, corProb) {
+    let error = 0;
+    // Get numerical solution
+    const approxSolution = method(corProb.odes);
+    const exact = corProb.exact;
+    const arg = approxSolution[0];
+    const pointsCount = arg.length;
+    const funcsCount = approxSolution.length - 1;
+    // Compute error
+    for (let i = 0; i < pointsCount; ++i) {
+        const exactSolution = exact(arg[i]);
+        for (let j = 0; j < funcsCount; ++j)
+            error = Math.max(error, Math.abs(exactSolution[j] - approxSolution[j + 1][i]));
+    }
+    return error;
+} // getError
+/** Evaluate model  */
+export function evalModel(model, inputs) {
+    const ivp = getIVP(model);
+    const ivpWW = getIvp2WebWorker(ivp);
+    const inputVector = getInputVector(inputs, ivp);
+    const creator = getPipelineCreator(ivp);
+    const pipeline = creator.getPipeline(inputVector);
+    return applyPipeline(pipeline, ivpWW, inputVector);
+} // evalModel
+//# sourceMappingURL=test-utils.js.map

package/src/tests/test-utils.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"test-utils.js","sourceRoot":"","sources":["test-utils.ts"],"names":[],"mappings":"AAAA,OAAO,EAAoB,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,kBAAkB,EACrF,aAAa,EAAC,MAAM,aAAa,CAAC;AAEpC,wGAAwG;AACxG,MAAM,UAAU,QAAQ,CAAC,MAAsC,EAAE,OAAoB;IACnF,IAAI,KAAK,GAAG,CAAC,CAAC;IAEd,yBAAyB;IACzB,MAAM,cAAc,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAE5C,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC;IAE5B,MAAM,GAAG,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC;IAE9B,MAAM,WAAW,GAAG,GAAG,CAAC,MAAM,CAAC;IAC/B,MAAM,UAAU,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;IAE7C,gBAAgB;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,EAAE,CAAC,EAAE,CAAC;QACrC,MAAM,aAAa,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAEpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,EAAE,CAAC;YACjC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,GAAG,cAAc,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IACnF,CAAC;IAED,OAAO,KAAK,CAAC;AACf,CAAC,CAAC,WAAW;AAEb,sBAAsB;AACtB,MAAM,UAAU,SAAS,CAAC,KAAa,EAAE,MAA8B;IACrE,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAC1B,MAAM,KAAK,GAAG,gBAAgB,CAAC,GAAG,CAAC,CAAC;IACpC,MAAM,WAAW,GAAG,cAAc,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IAChD,MAAM,OAAO,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC;IACxC,MAAM,QAAQ,GAAG,OAAO,CAAC,WAAW,CAAC,WAAW,CAAC,CAAC;IAClD,OAAO,aAAa,CAAC,QAAQ,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC;AACrD,CAAC,CAAC,YAAY"}