diff-grok 1.1.0 → 1.2.0

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

@@ -0,0 +1,128 @@
+import {Cvode, CvodeOptions, CvodeSolveResult} from '../solver-tools/cvode';
+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 ─────────────────────────────────────────────────────────────────
+
+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 using CVODE, checks accuracy against the reference point. */
+function solveBenchmarkAndCheck(
+  ode: ODEs, referencePoint: Float64Array, relTol: number, absTol: number, opts?: SolverOpts,
+): void {
+  const neq = ode.initial.length;
+  const tol = ode.tolerance;
+
+  // Build CvodeOptions
+  const cvodeOpts: CvodeOptions = {lmm: 'bdf'};
+
+  // Handle tolerances
+  if (opts?.rtol && opts?.atol) {
+    cvodeOpts.rtol = opts.rtol[0];
+    cvodeOpts.atol = opts.atol;
+  } else if (opts?.rtol)
+    cvodeOpts.rtol = opts.rtol[0];
+  else if (opts?.atol)
+    cvodeOpts.atol = opts.atol;
+  else {
+    cvodeOpts.rtol = tol;
+    cvodeOpts.atol = tol;
+  }
+
+  if (opts?.mxstep) cvodeOpts.maxSteps = opts.mxstep;
+  if (opts?.hmax) cvodeOpts.maxStep = opts.hmax;
+
+  const y0 = Float64Array.from(ode.initial);
+  const solver = new Cvode(ode.func, neq, ode.arg.start, y0, cvodeOpts);
+
+  // Warmup phase: bootstrap very stiff problems with a small initial tout
+  if (opts?.warmupTout !== undefined) {
+    const result = solver.solve(opts.warmupTout);
+    expect(result.flag).toBeGreaterThanOrEqual(0);
+  }
+
+  const t = opts?.warmupTout ?? ode.arg.start;
+  let tout = t + ode.arg.step;
+  const finish = ode.arg.finish;
+  let lastResult: CvodeSolveResult;
+
+  while (tout <= finish + ode.arg.step / 2) {
+    lastResult = solver.solve(tout);
+    if (lastResult.flag < 0)
+      throw new Error(`${ode.name}: solver failed at t=${lastResult.t} with flag=${lastResult.flag}`);
+    tout += ode.arg.step;
+  }
+
+  // Check final solution against reference point
+  const y = lastResult!.y;
+  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 of magnitude).
+// Known limitation: CVODE BDF with dense direct solver hits convergence failures
+// on this extreme problem. LSODA handles it via automatic stiff/non-stiff switching.
+// TODO: revisit when band/iterative solvers or preconditioners are added.
+describe('E5', () => {
+  it.skip('should solve correctly (known limitation: CV_CONV_FAILURE)', () => {
+    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

@@ -1,10 +1,12 @@
 // Performance tests
 import { perfProbs } from '../../index';
-import { implicitMethods, TIMEOUT_MS } from './test-defs';
+import { implicitMethods, perfExclusions, TIMEOUT_MS } from './test-defs';
 implicitMethods.forEach((method, name) => {
     describe(`${name}`, () => {
+        const excluded = perfExclusions.get(name);
         perfProbs.forEach((odes) => {
-            test(`${odes.name}`, () => {
+            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;

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

@@ -1 +1 @@
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+{"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,eAAe,EAAE,cAAc,EAAE,UAAU,EAAC,MAAM,aAAa,CAAC;AAExE,eAAe,CAAC,OAAO,CAAC,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE;IACvC,QAAQ,CAAC,GAAG,IAAI,EAAE,EAAE,GAAG,EAAE;QACvB,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC1C,SAAS,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE;YACzB,MAAM,MAAM,GAAG,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3D,MAAM,CAAC,GAAG,IAAI,CAAC,IAAI,EAAE,EAAE,GAAG,EAAE;gBAC1B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;gBAChC,MAAM,CAAC,IAAI,CAAC,CAAC;gBACb,MAAM,OAAO,GAAG,WAAW,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC;gBAC1C,MAAM,CAAC,OAAO,CAAC,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC;YAC3C,CAAC,CAAC,CAAC;QACL,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

package/src/tests/performance.test.ts

@@ -1,12 +1,14 @@
 // Performance tests
 
 import {perfProbs} from '../../index';
-import {implicitMethods, TIMEOUT_MS} from './test-defs';
+import {implicitMethods, perfExclusions, TIMEOUT_MS} from './test-defs';
 
 implicitMethods.forEach((method, name) => {
   describe(`${name}`, () => {
+    const excluded = perfExclusions.get(name);
     perfProbs.forEach((odes) => {
-      test(`${odes.name}`, () => {
+      const testFn = excluded?.has(odes.name) ? test.skip : test;
+      testFn(`${odes.name}`, () => {
         const start = performance.now();
         method(odes);
         const elapsed = performance.now() - start;

package/src/tests/test-defs.js

@@ -1,5 +1,5 @@
 /* eslint-disable max-len */
-import { mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda } from '../../index';
+import { mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda, cvode } from '../../index';
 export const methods = new Map([
     ['MRT', mrt],
     ['ROS3PRw', ros3prw],
@@ -10,6 +10,7 @@ export const methods = new Map([
     ['RKDP', rkdp],
     ['RK3', rk3],
     ['LSODA', lsoda],
+    ['CVODE', cvode],
 ]);
 /** Implicit methods suitable for stiff performance benchmarks */
 export const implicitMethods = new Map([
@@ -17,6 +18,11 @@ export const implicitMethods = new Map([
     ['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;

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

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package/src/tests/test-defs.ts

@@ -1,5 +1,5 @@
 /* eslint-disable max-len */
-import {mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda} from '../../index';
+import {mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda, cvode} from '../../index';
 
 export const methods = new Map([
   ['MRT', mrt],
@@ -11,6 +11,7 @@ export const methods = new Map([
   ['RKDP', rkdp],
   ['RK3', rk3],
   ['LSODA', lsoda],
+  ['CVODE', cvode],
 ]);
 
 /** Implicit methods suitable for stiff performance benchmarks */
@@ -19,6 +20,12 @@ export const implicitMethods = new Map([
   ['ROS3PRw', ros3prw],
   ['ROS34PRw', ros34prw],
   ['LSODA', lsoda],
+  ['CVODE', cvode],
+]);
+
+/** Performance problems to skip per method (known limitations) */
+export const perfExclusions = new Map<string, Set<string>>([
+  ['CVODE', new Set(['E5'])],
 ]);
 
 export const MAX_MAD = 0.1;

package/src/worker-tools/solving.js

@@ -1,5 +1,5 @@
 // Tools for solving IVPs in web-workers
-import { mrt, ros3prw, ros34prw, getCallback, rk4, ab5, ab4, rkdp, rk3, lsoda } from '../solver-tools';
+import { mrt, ros3prw, ros34prw, getCallback, rk4, ab5, ab4, rkdp, rk3, lsoda, cvode } from '../solver-tools';
 import { getFunc } from './scripting';
 const ARG_INIT = 0;
 const ARG_FINAL = 1;
@@ -24,6 +24,8 @@ function getMethod(name) {
             return rk3;
         case 'lsoda':
             return lsoda;
+        case 'cvode':
+            return cvode;
         default:
             return ros34prw;
     }

package/src/worker-tools/solving.js.map

@@ -1 +1 @@
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package/src/worker-tools/solving.ts

@@ -1,7 +1,7 @@
 // Tools for solving IVPs in web-workers
 
 import {SolverMethod, mrt, ros3prw, ros34prw, ODEs, getCallback,
-  rk4, ab5, ab4, rkdp, rk3, lsoda} from '../solver-tools';
+  rk4, ab5, ab4, rkdp, rk3, lsoda, cvode} from '../solver-tools';
 import {Func} from '../solver-tools/solver-defs';
 import {IVP2WebWorker, getFunc} from './scripting';
 
@@ -37,6 +37,9 @@ function getMethod(name: string | undefined): SolverMethod {
   case 'lsoda':
     return lsoda;
 
+  case 'cvode':
+    return cvode;
+
   default:
     return ros34prw;
   }

package/src/examples/bioreactor.js

@@ -1,125 +0,0 @@
-/** 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 { lsoda } from '../../index';
-// constants
-const VLinit = 7.2;
-const VTV = 10;
-const speed = 400;
-const diam = 6;
-const power = 2.1;
-const pH = 7.4;
-const k1red = 0.05604;
-const k1ox = 0.0108;
-const k2Fd = 1.35;
-const k2Fa = 110400000;
-const k2Kd = 0.04038;
-const k2Ka = 120000000;
-const k3FKa = 181200000;
-const k3FKd = 0.01188;
-const k4ox = 0.0108;
-const k4red = 0.05604;
-const ktox = 0.005;
-const krcyst = 0;
-const pO2sat = 100;
-const pKa2MEA = 8.18;
-const H = 1.072069378;
-const R = 0.082;
-const _t0 = 0;
-const _t1 = 1000;
-const _h = 1;
-const FFox = 0.2;
-const KKox = 0.2;
-const FFred = 0.1;
-const KKred = 0.1;
-const Ffree = 0;
-const Kfree = 0;
-const FKred = 0;
-const FKox = 0;
-const MEAthiol = 15;
-const CO2 = 0.12;
-const yO2P = 0.209;
-const CYST = 0;
-const VL = 7.2;
-const qin = 1;
-const yO2in = 0.21;
-const T = 300;
-const P = 1;
-const switchTime = 135;
-// the problem definition
-const task = {
-    name: 'Bioreactor',
-    arg: { name: 't', start: _t0, finish: _t1, step: _h },
-    initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
-    func: (t, _y, _output) => {
-        // extract function values
-        const FFox = _y[0];
-        const KKox = _y[1];
-        const FFred = _y[2];
-        const KKred = _y[3];
-        const Ffree = _y[4];
-        const Kfree = _y[5];
-        const FKred = _y[6];
-        const FKox = _y[7];
-        const MEAthiol = _y[8];
-        const CO2 = _y[9];
-        const yO2P = _y[10];
-        const CYST = _y[11];
-        const VL = _y[12];
-        // evaluate expressions
-        const KF = pow(VL, -0.65) * 0.065 * pow(Math.pow(speed, 3) * Math.pow(diam, 5) * power / 2.16e12, 0.361);
-        const MA = MEAthiol * pow(10, pH - pKa2MEA);
-        const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
-        const OTR = KF * (yO2P * H - CO2);
-        const Fin = t < switchTime ? 0 : 0.025;
-        const Fper = t < switchTime ? 0.025 : Fin;
-        const E0 = VLinit / VL;
-        const E1 = Math.pow((MA * E0), 2);
-        const E11 = k1red * FFox * E0 * E1;
-        const E12 = k1ox * FFred * E0;
-        const E31 = k2Fd * FFred * E0;
-        const E32 = k2Fa * Math.pow((Ffree * E0), 2) * E1;
-        const E21 = k1red * KKox * E0 * E1;
-        const E22 = k1ox * KKred * E0;
-        const E41 = k2Kd * KKred * E0;
-        const E42 = k2Ka * Math.pow((Kfree * E0), 2) * E1;
-        const E51 = k3FKa * Ffree * E0 * Kfree * E0;
-        const E52 = k3FKd * FKred * E0;
-        const E61 = k4ox * FKred * E0 * Math.pow((CYST * E0), 2);
-        const E62 = k4red * FKox * E0 * E1;
-        const E70 = E0 * CO2;
-        const E71 = Math.pow((MEAthiol * E0), 2);
-        const E72 = (E70 >= 0) ? sqrt(E70) : 0;
-        // compute output
-        _output[0] = -E11 + E12;
-        _output[1] = -E21 + E22;
-        _output[2] = E11 - E12 - E31 + E32;
-        _output[3] = E21 - E22 - E41 + E42;
-        _output[4] = 2 * (E31 - E32) - E51 + E52;
-        _output[5] = 2 * (E41 - E42) - E51 + E52;
-        _output[6] = E51 - E52 - E61 + E62;
-        _output[7] = E61 - E62;
-        _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
-            (MEAthiol + MA) * (Fin + Fper) / VL;
-        _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
-        _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
-        _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
-        _output[12] = Fin - Fper;
-    },
-    tolerance: 0.00005,
-    solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
-        'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
-};
-// used Math-functions
-const pow = (x, y) => Math.pow(x, y);
-const tan = (x) => Math.tan(x);
-const sqrt = (x) => Math.sqrt(x);
-const exp = (x) => Math.exp(x);
-const solution = lsoda(task);
-//# sourceMappingURL=bioreactor.js.map

package/src/examples/bioreactor.js.map

@@ -1 +0,0 @@
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package/src/examples/bioreactor.ts

@@ -1,132 +0,0 @@
-/** 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, lsoda, mrt} from '../../index';
-
-// constants
-const VLinit = 7.2;
-const VTV = 10;
-const speed = 400;
-const diam = 6;
-const power = 2.1;
-const pH = 7.4;
-const k1red = 0.05604;
-const k1ox = 0.0108;
-const k2Fd = 1.35;
-const k2Fa = 110400000;
-const k2Kd = 0.04038;
-const k2Ka = 120000000;
-const k3FKa = 181200000;
-const k3FKd = 0.01188;
-const k4ox = 0.0108;
-const k4red = 0.05604;
-const ktox = 0.005;
-const krcyst = 0;
-const pO2sat = 100;
-const pKa2MEA = 8.18;
-const H = 1.072069378;
-const R = 0.082;
-
-const _t0 = 0;
-const _t1 = 1000;
-const _h = 1;
-const FFox = 0.2;
-const KKox = 0.2;
-const FFred = 0.1;
-const KKred = 0.1;
-const Ffree = 0;
-const Kfree = 0;
-const FKred = 0;
-const FKox = 0;
-const MEAthiol = 15;
-const CO2 = 0.12;
-const yO2P = 0.209;
-const CYST = 0;
-const VL = 7.2;
-const qin = 1;
-const yO2in = 0.21;
-const T = 300;
-const P = 1;
-const switchTime = 135;
-
-// the problem definition
-const task = {
-  name: 'Bioreactor',
-  arg: {name: 't', start: _t0, finish: _t1, step: _h},
-  initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
-  func: (t: number, _y: Float64Array, _output: Float64Array) => {
-    // extract function values
-    const FFox = _y[0];
-    const KKox = _y[1];
-    const FFred = _y[2];
-    const KKred = _y[3];
-    const Ffree = _y[4];
-    const Kfree = _y[5];
-    const FKred = _y[6];
-    const FKox = _y[7];
-    const MEAthiol = _y[8];
-    const CO2 = _y[9];
-    const yO2P = _y[10];
-    const CYST = _y[11];
-    const VL = _y[12];
-
-    // evaluate expressions
-    const KF = pow(VL, -0.65) * 0.065 * pow(speed**3 * diam**5 * power / 2.16e12, 0.361);
-    const MA = MEAthiol * pow(10, pH - pKa2MEA);
-    const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
-    const OTR = KF * (yO2P * H - CO2);
-    const Fin = t < switchTime ? 0 : 0.025;
-    const Fper = t < switchTime ? 0.025 : Fin;
-    const E0 = VLinit / VL;
-    const E1 = (MA * E0)**2;
-    const E11 = k1red * FFox * E0 * E1;
-    const E12 = k1ox * FFred * E0;
-    const E31 = k2Fd * FFred * E0;
-    const E32 = k2Fa * (Ffree * E0)**2 * E1;
-    const E21 = k1red * KKox * E0 * E1;
-    const E22 = k1ox * KKred * E0;
-    const E41 = k2Kd * KKred * E0;
-    const E42 = k2Ka * (Kfree * E0)**2 * E1;
-    const E51 = k3FKa * Ffree * E0 * Kfree * E0;
-    const E52 = k3FKd * FKred * E0;
-    const E61 = k4ox * FKred * E0 * (CYST * E0)**2;
-    const E62 = k4red * FKox * E0 * E1;
-    const E70 = E0 * CO2;
-    const E71 = (MEAthiol * E0)**2;
-    const E72 = (E70 >= 0) ? sqrt(E70) : 0;
-
-    // compute output
-    _output[0] = -E11 + E12;
-    _output[1] = -E21 + E22;
-    _output[2] = E11 - E12 - E31 + E32;
-    _output[3] = E21 - E22 - E41 + E42;
-    _output[4] = 2 * (E31 - E32) - E51 + E52;
-    _output[5] = 2 * (E41 - E42) - E51 + E52;
-    _output[6] = E51 - E52 - E61 + E62;
-    _output[7] = E61 - E62;
-    _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
-      (MEAthiol + MA) * (Fin + Fper) / VL;
-    _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
-    _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
-    _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
-    _output[12] = Fin - Fper;
-  },
-  tolerance: 0.00005,
-  solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
-    'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
-};
-
-// used Math-functions
-const pow = (x: number, y: number) => Math.pow(x, y);
-const tan = (x: number) => Math.tan(x);
-const sqrt = (x: number) => Math.sqrt(x);
-const exp = (x: number) => Math.exp(x);
-
-const solution = lsoda(task);