diff-grok 1.2.0 → 1.3.0

package/src/tests/lsoda-lib-performance.test.js

@@ -1,95 +0,0 @@
-import { Lsoda } from '../solver-tools/lsoda';
-import { robertson, robertsonReferencePoint } from '../examples/robertson';
-import { hires, hiresReferencePoint } from '../examples/hires';
-import { vdpol, vdpolReferencePoint } from '../examples/vdpol';
-import { orego, oregoReferencePoint } from '../examples/orego';
-import { e5, e5ReferencePoint } from '../examples/e5';
-import { pollution, pollutionReferencePoint } from '../examples/pollution';
-// ─── Helpers ─────────────────────────────────────────────────────────────────
-/** Wraps an ODEs func into an OdeFunction compatible with Lsoda (returns 0). */
-function wrapFunc(ode) {
-    return (t, y, ydot) => {
-        ode.func(t, y, ydot);
-        return 0;
-    };
-}
-/** Solves a benchmark problem, checks accuracy against the reference point, and verifies solver health. */
-function solveBenchmarkAndCheck(ode, referencePoint, relTol, absTol, opts) {
-    var _a, _b;
-    const neq = ode.initial.length;
-    const tol = ode.tolerance;
-    const rtol = (_a = opts === null || opts === void 0 ? void 0 : opts.rtol) !== null && _a !== void 0 ? _a : new Float64Array(neq).fill(tol);
-    const atol = (_b = opts === null || opts === void 0 ? void 0 : opts.atol) !== null && _b !== void 0 ? _b : new Float64Array(neq).fill(tol);
-    const solver = new Lsoda(wrapFunc(ode), neq, Object.assign(Object.assign({ rtol, atol, itask: 1 }, ((opts === null || opts === void 0 ? void 0 : opts.mxstep) ? { mxstep: opts.mxstep } : {})), ((opts === null || opts === void 0 ? void 0 : opts.hmax) ? { hmax: opts.hmax } : {})));
-    let y = [...ode.initial];
-    let t = ode.arg.start;
-    const step = ode.arg.step;
-    const finish = ode.arg.finish;
-    // Warmup phase: bootstrap very stiff problems with a small initial tout
-    if ((opts === null || opts === void 0 ? void 0 : opts.warmupTout) !== undefined) {
-        const result = solver.solve(y, t, opts.warmupTout);
-        y = result.y;
-        t = result.t;
-        expect(solver.state).toBeGreaterThan(0);
-    }
-    let tout = t + step;
-    while (tout <= finish + step / 2) {
-        const result = solver.solve(y, t, tout);
-        y = result.y;
-        t = result.t;
-        if (solver.state <= 0)
-            throw new Error(`${ode.name}: solver failed at t=${t} with state=${solver.state}, error: ${solver.error}`);
-        tout += step;
-    }
-    // Check final solution against reference point
-    for (let j = 0; j < neq; j++) {
-        const absErr = Math.abs(y[j] - referencePoint[j]);
-        const allowed = relTol * Math.abs(referencePoint[j]) + absTol;
-        expect(absErr).toBeLessThan(allowed);
-    }
-}
-// ─── Performance tests ──────────────────────────────────────────────────────
-// Robertson: components span many orders of magnitude; use component-wise atol
-describe('Robertson', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(robertson, robertsonReferencePoint, 1e-2, 1e-7, {
-            mxstep: 50000,
-            atol: new Float64Array([1e-8, 1e-14, 1e-8]),
-            rtol: new Float64Array([1e-7, 1e-7, 1e-7]),
-        });
-    }, 60000);
-});
-describe('HIRES', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(hires, hiresReferencePoint, 1e-3, 1e-12);
-    }, 60000);
-});
-// Van der Pol (mu=1000): very stiff, needs many internal steps
-describe('van der Pol', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(vdpol, vdpolReferencePoint, 1e-3, 1e-6, {
-            mxstep: 50000,
-        });
-    }, 60000);
-});
-describe('OREGO', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(orego, oregoReferencePoint, 1e-2, 1e-6);
-    }, 60000);
-});
-// E5: extremely stiff (rate constants span 20 orders), needs warmup and many steps.
-// Reference values are near-zero (y1~1e-290, y2~1e-22), so absTol must be generous.
-describe('E5', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(e5, e5ReferencePoint, 1, 1e-6, {
-            mxstep: 50000,
-            warmupTout: 1e-5,
-        });
-    }, 60000);
-});
-describe('Pollution', () => {
-    it('should solve correctly', () => {
-        solveBenchmarkAndCheck(pollution, pollutionReferencePoint, 1e-2, 1e-10);
-    }, 60000);
-});
-//# sourceMappingURL=lsoda-lib-performance.test.js.map

package/src/tests/lsoda-lib-performance.test.js.map

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package/src/tests/lsoda-lib-performance.test.ts

@@ -1,126 +0,0 @@
-import {Lsoda} from '../solver-tools/lsoda';
-import {ODEs} from '../../index';
-import {robertson, robertsonReferencePoint} from '../examples/robertson';
-import {hires, hiresReferencePoint} from '../examples/hires';
-import {vdpol, vdpolReferencePoint} from '../examples/vdpol';
-import {orego, oregoReferencePoint} from '../examples/orego';
-import {e5, e5ReferencePoint} from '../examples/e5';
-import {pollution, pollutionReferencePoint} from '../examples/pollution';
-
-// ─── Helpers ─────────────────────────────────────────────────────────────────
-
-/** Wraps an ODEs func into an OdeFunction compatible with Lsoda (returns 0). */
-function wrapFunc(ode: ODEs): (t: number, y: Float64Array, ydot: Float64Array) => number {
-  return (t, y, ydot) => {
-    ode.func(t, y, ydot);
-    return 0;
-  };
-}
-
-interface SolverOpts {
-  mxstep?: number;
-  hmax?: number;
-  rtol?: Float64Array;
-  atol?: Float64Array;
-  /** Small initial tout to bootstrap very stiff problems before the main loop. */
-  warmupTout?: number;
-}
-
-/** Solves a benchmark problem, checks accuracy against the reference point, and verifies solver health. */
-function solveBenchmarkAndCheck(
-  ode: ODEs, referencePoint: Float64Array, relTol: number, absTol: number, opts?: SolverOpts,
-): void {
-  const neq = ode.initial.length;
-  const tol = ode.tolerance;
-  const rtol = opts?.rtol ?? new Float64Array(neq).fill(tol);
-  const atol = opts?.atol ?? new Float64Array(neq).fill(tol);
-
-  const solver = new Lsoda(wrapFunc(ode), neq, {
-    rtol, atol, itask: 1,
-    ...(opts?.mxstep ? {mxstep: opts.mxstep} : {}),
-    ...(opts?.hmax ? {hmax: opts.hmax} : {}),
-  });
-
-  let y: ArrayLike<number> = [...ode.initial];
-  let t = ode.arg.start;
-  const step = ode.arg.step;
-  const finish = ode.arg.finish;
-
-  // Warmup phase: bootstrap very stiff problems with a small initial tout
-  if (opts?.warmupTout !== undefined) {
-    const result = solver.solve(y, t, opts.warmupTout);
-    y = result.y;
-    t = result.t;
-    expect(solver.state).toBeGreaterThan(0);
-  }
-
-  let tout = t + step;
-  while (tout <= finish + step / 2) {
-    const result = solver.solve(y, t, tout);
-    y = result.y;
-    t = result.t;
-
-    if (solver.state <= 0)
-      throw new Error(`${ode.name}: solver failed at t=${t} with state=${solver.state}, error: ${solver.error}`);
-
-    tout += step;
-  }
-
-  // Check final solution against reference point
-  for (let j = 0; j < neq; j++) {
-    const absErr = Math.abs(y[j] - referencePoint[j]);
-    const allowed = relTol * Math.abs(referencePoint[j]) + absTol;
-    expect(absErr).toBeLessThan(allowed);
-  }
-}
-
-// ─── Performance tests ──────────────────────────────────────────────────────
-
-// Robertson: components span many orders of magnitude; use component-wise atol
-describe('Robertson', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(robertson, robertsonReferencePoint, 1e-2, 1e-7, {
-      mxstep: 50000,
-      atol: new Float64Array([1e-8, 1e-14, 1e-8]),
-      rtol: new Float64Array([1e-7, 1e-7, 1e-7]),
-    });
-  }, 60000);
-});
-
-describe('HIRES', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(hires, hiresReferencePoint, 1e-3, 1e-12);
-  }, 60000);
-});
-
-// Van der Pol (mu=1000): very stiff, needs many internal steps
-describe('van der Pol', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(vdpol, vdpolReferencePoint, 1e-3, 1e-6, {
-      mxstep: 50000,
-    });
-  }, 60000);
-});
-
-describe('OREGO', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(orego, oregoReferencePoint, 1e-2, 1e-6);
-  }, 60000);
-});
-
-// E5: extremely stiff (rate constants span 20 orders), needs warmup and many steps.
-// Reference values are near-zero (y1~1e-290, y2~1e-22), so absTol must be generous.
-describe('E5', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(e5, e5ReferencePoint, 1, 1e-6, {
-      mxstep: 50000,
-      warmupTout: 1e-5,
-    });
-  }, 60000);
-});
-
-describe('Pollution', () => {
-  it('should solve correctly', () => {
-    solveBenchmarkAndCheck(pollution, pollutionReferencePoint, 1e-2, 1e-10);
-  }, 60000);
-});

package/src/tests/performance.test.js

@@ -1,18 +0,0 @@
-// Performance tests
-import { perfProbs } from '../../index';
-import { implicitMethods, perfExclusions, TIMEOUT_MS } from './test-defs';
-implicitMethods.forEach((method, name) => {
-    describe(`${name}`, () => {
-        const excluded = perfExclusions.get(name);
-        perfProbs.forEach((odes) => {
-            const testFn = (excluded === null || excluded === void 0 ? void 0 : excluded.has(odes.name)) ? test.skip : test;
-            testFn(`${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

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package/src/tests/performance.test.ts

@@ -1,19 +0,0 @@
-// Performance tests
-
-import {perfProbs} from '../../index';
-import {implicitMethods, perfExclusions, TIMEOUT_MS} from './test-defs';
-
-implicitMethods.forEach((method, name) => {
-  describe(`${name}`, () => {
-    const excluded = perfExclusions.get(name);
-    perfProbs.forEach((odes) => {
-      const testFn = excluded?.has(odes.name) ? test.skip : test;
-      testFn(`${odes.name}`, () => {
-        const start = performance.now();
-        method(odes);
-        const elapsed = performance.now() - start;
-        expect(elapsed).toBeLessThan(TIMEOUT_MS);
-      });
-    });
-  });
-});

package/src/tests/pipeline.test.js

@@ -1,10 +0,0 @@
-// 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

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package/src/tests/pipeline.test.ts

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

@@ -1,213 +0,0 @@
-/* eslint-disable max-len */
-import { mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda, cvode } from '../../index';
-export const methods = new Map([
-    ['MRT', mrt],
-    ['ROS3PRw', ros3prw],
-    ['ROS34PRw', ros34prw],
-    ['RK4', rk4],
-    ['AB5', ab5],
-    ['AB4', ab4],
-    ['RKDP', rkdp],
-    ['RK3', rk3],
-    ['LSODA', lsoda],
-    ['CVODE', cvode],
-]);
-/** Implicit methods suitable for stiff performance benchmarks */
-export const implicitMethods = new Map([
-    ['MRT', mrt],
-    ['ROS3PRw', ros3prw],
-    ['ROS34PRw', ros34prw],
-    ['LSODA', lsoda],
-    ['CVODE', cvode],
-]);
-/** Performance problems to skip per method (known limitations) */
-export const perfExclusions = new Map([
-    ['CVODE', new Set(['E5'])],
-]);
-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

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