diff-grok 1.2.0 → 1.3.0

package/src/solver-tools/cvode/cvode_adams.js.map

@@ -1 +0,0 @@
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package/src/solver-tools/cvode/cvode_adams.ts

@@ -1,142 +0,0 @@
-/**
- * TypeScript port of SUNDIALS CVODE v7.5.0 (https://github.com/LLNL/sundials)
- *
- * Copyright (c) 2025, Lawrence Livermore National Security, University of
- *   Maryland Baltimore County, and the SUNDIALS contributors.
- * Copyright (c) 2013-2025, Lawrence Livermore National Security and
- *   Southern Methodist University.
- * Copyright (c) 2002-2013, Lawrence Livermore National Security.
- * Copyright (c) 2026 Datagrok.
- *
- * Licensed under the BSD-3-Clause License. See THIRD_PARTY_LICENSES
- * for the full license text and provenance chain of the original code.
- */
-
-import {CvodeMem, L_MAX} from './common';
-
-/**
- * cvAltSum - Alternating sum: sum_{i=0}^{iend} (-1)^i * a[i] / (i + k)
- */
-function cvAltSum(iend: number, a: Float64Array, k: number): number {
-  if (iend < 0) return 0.0;
-  let sum = 0.0;
-  let sign = 1;
-  for (let i = 0; i <= iend; i++) {
-    sum += sign * (a[i] / (i + k));
-    sign = -sign;
-  }
-  return sum;
-}
-
-/**
- * cvAdamsStart - Generate product polynomial coefficients for Adams method
- * Returns hsum.
- */
-function cvAdamsStart(mem: CvodeMem, m: Float64Array): number {
-  let hsum = mem.cv_h;
-  m[0] = 1.0;
-  for (let i = 1; i <= mem.cv_q; i++) m[i] = 0.0;
-
-  for (let j = 1; j < mem.cv_q; j++) {
-    if (j === mem.cv_q - 1 && mem.cv_qwait === 1) {
-      const sum = cvAltSum(mem.cv_q - 2, m, 2);
-      mem.cv_tq[1] = mem.cv_q * sum / m[mem.cv_q - 2];
-    }
-    const xi_inv = mem.cv_h / hsum;
-    for (let i = j; i >= 1; i--)
-      m[i] += m[i - 1] * xi_inv;
-
-    hsum += mem.cv_tau[j];
-  }
-  return hsum;
-}
-
-/**
- * cvAdamsFinish - Complete Adams l and tq computation
- */
-function cvAdamsFinish(mem: CvodeMem, m: Float64Array, M: Float64Array, hsum: number): void {
-  const M0_inv = 1.0 / M[0];
-
-  mem.cv_l[0] = 1.0;
-  for (let i = 1; i <= mem.cv_q; i++)
-    mem.cv_l[i] = M0_inv * (m[i - 1] / i);
-
-
-  const xi = hsum / mem.cv_h;
-  const xi_inv = 1.0 / xi;
-
-  mem.cv_tq[2] = M[1] * M0_inv / xi;
-  mem.cv_tq[5] = xi / mem.cv_l[mem.cv_q];
-
-  if (mem.cv_qwait === 1) {
-    for (let i = mem.cv_q; i >= 1; i--)
-      m[i] += m[i - 1] * xi_inv;
-
-    M[2] = cvAltSum(mem.cv_q, m, 2);
-    mem.cv_tq[3] = M[2] * M0_inv / mem.cv_L;
-  }
-
-  mem.cv_tq[4] = mem.cv_nlscoef / mem.cv_tq[2];
-}
-
-/**
- * cvSetAdams - Compute Adams method coefficients l[] and tq[]
- */
-export function cvSetAdams(mem: CvodeMem): void {
-  const m = new Float64Array(L_MAX);
-  const M = new Float64Array(3);
-
-  if (mem.cv_q === 1) {
-    mem.cv_l[0] = 1.0;
-    mem.cv_l[1] = 1.0;
-    mem.cv_tq[1] = 1.0;
-    mem.cv_tq[5] = 1.0;
-    mem.cv_tq[2] = 0.5;
-    mem.cv_tq[3] = 1.0 / 12.0;
-    mem.cv_tq[4] = mem.cv_nlscoef / mem.cv_tq[2];
-    return;
-  }
-
-  const hsum = cvAdamsStart(mem, m);
-  M[0] = cvAltSum(mem.cv_q - 1, m, 1);
-  M[1] = cvAltSum(mem.cv_q - 1, m, 2);
-  cvAdamsFinish(mem, m, M, hsum);
-}
-
-/**
- * cvAdjustAdams - Adjust history array for Adams order change
- */
-export function cvAdjustAdams(mem: CvodeMem, deltaq: number): void {
-  const N = mem.cv_N;
-
-  if (deltaq === 1) {
-    // On order increase, set new column of zn to zero
-    mem.cv_zn[mem.cv_L].fill(0.0, 0, N);
-    return;
-  }
-
-  // Order decrease: adjust zn[j] by multiples of zn[q]
-  for (let i = 0; i <= mem.cv_qmax; i++) mem.cv_l[i] = 0.0;
-  mem.cv_l[1] = 1.0;
-  let hsum = 0.0;
-
-  for (let j = 1; j <= mem.cv_q - 2; j++) {
-    hsum += mem.cv_tau[j];
-    const xi = hsum / mem.cv_hscale;
-    for (let i = j + 1; i >= 1; i--)
-      mem.cv_l[i] = mem.cv_l[i] * xi + mem.cv_l[i - 1];
-  }
-
-  for (let j = 1; j <= mem.cv_q - 2; j++)
-    mem.cv_l[j + 1] = mem.cv_q * (mem.cv_l[j] / (j + 1));
-
-
-  if (mem.cv_q > 2) {
-    const znq = mem.cv_zn[mem.cv_q];
-    for (let j = 2; j < mem.cv_q; j++) {
-      const c = -mem.cv_l[j];
-      const znj = mem.cv_zn[j];
-      for (let i = 0; i < N; i++) znj[i] += c * znq[i];
-    }
-  }
-}

package/src/solver-tools/cvode/cvode_bdf.js.map

@@ -1 +0,0 @@
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package/src/solver-tools/cvode/cvode_bdf.ts

@@ -1,164 +0,0 @@
-/**
- * TypeScript port of SUNDIALS CVODE v7.5.0 (https://github.com/LLNL/sundials)
- *
- * Copyright (c) 2025, Lawrence Livermore National Security, University of
- *   Maryland Baltimore County, and the SUNDIALS contributors.
- * Copyright (c) 2013-2025, Lawrence Livermore National Security and
- *   Southern Methodist University.
- * Copyright (c) 2002-2013, Lawrence Livermore National Security.
- * Copyright (c) 2026 Datagrok.
- *
- * Licensed under the BSD-3-Clause License. See THIRD_PARTY_LICENSES
- * for the full license text and provenance chain of the original code.
- */
-
-import {CvodeMem} from './common';
-
-/**
- * cvSetBDF - Compute BDF method coefficients l[] and tq[]
- *
- * The polynomial l(x) = l_0 + l_1*x + ... + l_q*x^q is given by:
- *   Lambda(x) = (1 + x/xi*_q) * product_{i=1}^{q-1} (1 + x/xi_i)
- * where xi_i = (t_n - t_{n-i}) / h
- *
- * The tq array holds test quantities for error and convergence tests:
- *   tq[1] = coefficient for error at order q-1
- *   tq[2] = coefficient for error at order q
- *   tq[3] = coefficient for error at order q+1
- *   tq[4] = convergence test coefficient
- *   tq[5] = derivative for order q+2 vector
- */
-export function cvSetBDF(mem: CvodeMem): void {
-  let alpha0: number; let alpha0_hat: number; let xi_inv: number; let xistar_inv: number; let hsum: number;
-
-  mem.cv_l[0] = 1.0;
-  mem.cv_l[1] = 1.0;
-  xi_inv = 1.0;
-  xistar_inv = 1.0;
-  for (let i = 2; i <= mem.cv_q; i++) mem.cv_l[i] = 0.0;
-
-  alpha0 = -1.0;
-  alpha0_hat = -1.0;
-  hsum = mem.cv_h;
-
-  if (mem.cv_q > 1) {
-    for (let j = 2; j < mem.cv_q; j++) {
-      hsum += mem.cv_tau[j - 1];
-      xi_inv = mem.cv_h / hsum;
-      alpha0 -= 1.0 / j;
-      for (let i = j; i >= 1; i--)
-        mem.cv_l[i] += mem.cv_l[i - 1] * xi_inv;
-    }
-
-    // j = q
-    alpha0 -= 1.0 / mem.cv_q;
-    xistar_inv = -mem.cv_l[1] - alpha0;
-    hsum += mem.cv_tau[mem.cv_q - 1];
-    xi_inv = mem.cv_h / hsum;
-    alpha0_hat = -mem.cv_l[1] - xi_inv;
-
-    for (let i = mem.cv_q; i >= 1; i--)
-      mem.cv_l[i] += mem.cv_l[i - 1] * xistar_inv;
-  }
-
-  cvSetTqBDF(mem, hsum, alpha0, alpha0_hat, xi_inv, xistar_inv);
-}
-
-/**
- * cvSetTqBDF - Set test quantity array for BDF method
- */
-function cvSetTqBDF(mem: CvodeMem, hsum: number, alpha0: number,
-  alpha0_hat: number, xi_inv: number, xistar_inv: number): void {
-  const A1 = 1.0 - alpha0_hat + alpha0;
-  const A2 = 1.0 + mem.cv_q * A1;
-  mem.cv_tq[2] = Math.abs(A1 / (alpha0 * A2));
-  mem.cv_tq[5] = Math.abs(A2 * xistar_inv / (mem.cv_l[mem.cv_q] * xi_inv));
-
-  if (mem.cv_qwait === 1) {
-    if (mem.cv_q > 1) {
-      const C = xistar_inv / mem.cv_l[mem.cv_q];
-      const A3 = alpha0 + 1.0 / mem.cv_q;
-      const A4 = alpha0_hat + xi_inv;
-      const Cpinv = (1.0 - A4 + A3) / A3;
-      mem.cv_tq[1] = Math.abs(C * Cpinv);
-    } else
-      mem.cv_tq[1] = 1.0;
-
-    hsum += mem.cv_tau[mem.cv_q];
-    const xi_inv2 = mem.cv_h / hsum;
-    const A5 = alpha0 - 1.0 / (mem.cv_q + 1);
-    const A6 = alpha0_hat - xi_inv2;
-    const Cppinv = (1.0 - A6 + A5) / A2;
-    mem.cv_tq[3] = Math.abs(Cppinv / (xi_inv2 * (mem.cv_q + 2) * A5));
-  }
-  mem.cv_tq[4] = mem.cv_nlscoef / mem.cv_tq[2];
-}
-
-/**
- * cvIncreaseBDF - Adjust history array for BDF order increase
- */
-export function cvIncreaseBDF(mem: CvodeMem): void {
-  const N = mem.cv_N;
-
-  for (let i = 0; i <= mem.cv_qmax; i++) mem.cv_l[i] = 0.0;
-  mem.cv_l[2] = 1.0;
-  let alpha1 = 1.0;
-  let prod = 1.0;
-  let xiold = 1.0;
-  let alpha0 = -1.0;
-  let hsum = mem.cv_hscale;
-
-  if (mem.cv_q > 1) {
-    for (let j = 1; j < mem.cv_q; j++) {
-      hsum += mem.cv_tau[j + 1];
-      const xi = hsum / mem.cv_hscale;
-      prod *= xi;
-      alpha0 -= 1.0 / (j + 1);
-      alpha1 += 1.0 / xi;
-      for (let i = j + 2; i >= 2; i--)
-        mem.cv_l[i] = mem.cv_l[i] * xiold + mem.cv_l[i - 1];
-
-      xiold = xi;
-    }
-  }
-
-  const A1 = (-alpha0 - alpha1) / prod;
-  const znL = mem.cv_zn[mem.cv_L];
-  const znSaved = mem.cv_zn[mem.cv_indx_acor];
-  for (let i = 0; i < N; i++) znL[i] = A1 * znSaved[i];
-
-  if (mem.cv_q > 1) {
-    for (let j = 2; j <= mem.cv_q; j++) {
-      const c = mem.cv_l[j];
-      const znj = mem.cv_zn[j];
-      for (let i = 0; i < N; i++) znj[i] += c * znL[i];
-    }
-  }
-}
-
-/**
- * cvDecreaseBDF - Adjust history array for BDF order decrease
- */
-export function cvDecreaseBDF(mem: CvodeMem): void {
-  const N = mem.cv_N;
-
-  for (let i = 0; i <= mem.cv_qmax; i++) mem.cv_l[i] = 0.0;
-  mem.cv_l[2] = 1.0;
-  let hsum = 0.0;
-
-  for (let j = 1; j <= mem.cv_q - 2; j++) {
-    hsum += mem.cv_tau[j];
-    const xi = hsum / mem.cv_hscale;
-    for (let i = j + 2; i >= 2; i--)
-      mem.cv_l[i] = mem.cv_l[i] * xi + mem.cv_l[i - 1];
-  }
-
-  if (mem.cv_q > 2) {
-    const znq = mem.cv_zn[mem.cv_q];
-    for (let j = 2; j < mem.cv_q; j++) {
-      const c = -mem.cv_l[j];
-      const znj = mem.cv_zn[j];
-      for (let i = 0; i < N; i++) znj[i] += c * znq[i];
-    }
-  }
-}

package/src/solver-tools/cvode/cvode_class.js.map

@@ -1 +0,0 @@
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package/src/solver-tools/cvode/cvode_class.ts

@@ -1,271 +0,0 @@
-/**
- * TypeScript port of SUNDIALS CVODE v7.5.0 (https://github.com/LLNL/sundials)
- *
- * Copyright (c) 2025, Lawrence Livermore National Security, University of
- *   Maryland Baltimore County, and the SUNDIALS contributors.
- * Copyright (c) 2013-2025, Lawrence Livermore National Security and
- *   Southern Methodist University.
- * Copyright (c) 2002-2013, Lawrence Livermore National Security.
- * Copyright (c) 2026 Datagrok.
- *
- * Licensed under the BSD-3-Clause License. See THIRD_PARTY_LICENSES
- * for the full license text and provenance chain of the original code.
- */
-
-// CVODE TypeScript port - High-level Cvode class API
-// Follows the Lsoda class pattern from src/lsoda.ts
-
-import {
-  CvodeMem,
-  CvodeRhsFn,
-  CvodeJacFn,
-  CvodeRootFn,
-  cvodeGetDky,
-  CV_ADAMS, CV_BDF,
-  CV_NORMAL, CV_ONE_STEP,
-  CV_ROOT_RETURN,
-} from './common';
-
-import {cvodeCreate, cvodeInit, cvode} from './cvode';
-import {cvodeSetLinearSolver, cvodeSetJacFn} from './cvode_ls';
-import {cvodeRootInit} from './cvode_root';
-import {
-  CvodeStats,
-  cvodeGetIntegratorStats,
-  cvodeSStolerances,
-  cvodeSVtolerances,
-  cvodeSetMaxNumSteps,
-  cvodeSetMaxOrd,
-  cvodeSetMaxStep,
-  cvodeSetMinStep,
-  cvodeSetInitStep,
-  cvodeSetStopTime,
-  cvodeSetUserData,
-} from './cvode_io';
-
-// ============================================================================
-// Public types
-// ============================================================================
-
-/**
- * User ODE function: y' = f(t, y).
- * Arrays are 0-based. Return value is void; wrapping to int is done internally.
- */
-export type OdeFunction = (t: number, y: Float64Array, ydot: Float64Array) => void;
-
-/**
- * Options for the Cvode solver.
- */
-export interface CvodeOptions {
-  /** Linear multistep method: 'adams' (non-stiff) or 'bdf' (stiff). Default: 'bdf'. */
-  lmm?: 'adams' | 'bdf';
-  /** Relative tolerance. Default: 1e-4. */
-  rtol?: number;
-  /** Absolute tolerance: scalar or per-component array. Default: 1e-6. */
-  atol?: number | Float64Array;
-  /** Maximum number of internal steps per cvode() call. */
-  maxSteps?: number;
-  /** Maximum method order. */
-  maxOrder?: number;
-  /** Maximum step size (0 = no limit). */
-  maxStep?: number;
-  /** Minimum step size. */
-  minStep?: number;
-  /** Initial step size (0 = auto-select). */
-  initStep?: number;
-  /** Stop time: integration will not proceed past this value. */
-  stopTime?: number;
-  /** Root function: g(t, y, gout). */
-  rootFn?: (t: number, y: Float64Array, gout: Float64Array) => void;
-  /** Number of root functions (required when rootFn is provided). */
-  nRootFns?: number;
-  /** User-supplied Jacobian function: J = df/dy. */
-  jacFn?: (t: number, y: Float64Array, fy: Float64Array, J: Float64Array[]) => void;
-  /** Arbitrary user data (passed as context, not forwarded to callbacks). */
-  userData?: any;
-}
-
-/**
- * Result returned by solve() and step().
- */
-export interface CvodeSolveResult {
-  /** Time reached by the solver. */
-  t: number;
-  /** Solution vector at time t (0-based, copy). */
-  y: Float64Array;
-  /** Solver flag (CV_SUCCESS=0, CV_ROOT_RETURN=2, CV_TSTOP_RETURN=1, negative=error). */
-  flag: number;
-  /** Root indices found when flag === CV_ROOT_RETURN. */
-  rootsFound?: Int32Array;
-}
-
-// ============================================================================
-// Cvode class
-// ============================================================================
-
-/**
- * High-level CVODE solver class with a 0-based public interface.
- *
- * Usage:
- *   const solver = new Cvode(f, neq, t0, y0, { lmm: 'bdf', rtol: 1e-6, atol: 1e-9 });
- *   const result = solver.solve(tout);
- */
-export class Cvode {
-  private mem: CvodeMem;
-  private neq: number;
-  /** Output vector reused across calls (0-based, neq elements). */
-  private yout: Float64Array;
-  /** Wrapped RHS stored to allow re-initialization. */
-  private wrappedF: CvodeRhsFn;
-
-  constructor(
-    f: OdeFunction,
-    neq: number,
-    t0: number,
-    y0: Float64Array,
-    options?: CvodeOptions,
-  ) {
-    this.neq = neq;
-    this.yout = new Float64Array(neq);
-
-    const opts = options ?? {};
-
-    // --- 1. Create CvodeMem ---
-    const lmmValue = (opts.lmm === 'adams') ? CV_ADAMS : CV_BDF;
-    this.mem = cvodeCreate(lmmValue);
-
-    // --- 2. Wrap user's OdeFunction to CvodeRhsFn (void -> number) ---
-    this.wrappedF = (_t: number, _y: Float64Array, _ydot: Float64Array, _userData: any): number => {
-      f(_t, _y, _ydot);
-      return 0;
-    };
-
-    // --- 3. Initialize ---
-    cvodeInit(this.mem, this.wrappedF, t0, y0);
-
-    // --- 4. Set tolerances ---
-    const rtol = opts.rtol ?? 1e-4;
-    const atol = opts.atol ?? 1e-6;
-
-    if (typeof atol === 'number')
-      cvodeSStolerances(this.mem, rtol, atol);
-    else
-      cvodeSVtolerances(this.mem, rtol, atol);
-
-
-    // --- 5. Set up dense linear solver (required for BDF; optional but useful for Adams) ---
-    cvodeSetLinearSolver(this.mem);
-
-    // --- 6. Set user-supplied Jacobian if provided ---
-    if (opts.jacFn) {
-      const userJac = opts.jacFn;
-      const wrappedJacFn: CvodeJacFn = (
-        t: number, y: Float64Array, fy: Float64Array,
-        J: Float64Array[], userData: any,
-      ): number => {
-        userJac(t, y, fy, J);
-        return 0;
-      };
-      cvodeSetJacFn(this.mem, wrappedJacFn);
-    }
-
-    // --- 7. Apply optional settings ---
-    if (opts.maxSteps !== undefined) cvodeSetMaxNumSteps(this.mem, opts.maxSteps);
-    if (opts.maxOrder !== undefined) cvodeSetMaxOrd(this.mem, opts.maxOrder);
-    if (opts.maxStep !== undefined) cvodeSetMaxStep(this.mem, opts.maxStep);
-    if (opts.minStep !== undefined) cvodeSetMinStep(this.mem, opts.minStep);
-    if (opts.initStep !== undefined) cvodeSetInitStep(this.mem, opts.initStep);
-    if (opts.stopTime !== undefined) cvodeSetStopTime(this.mem, opts.stopTime);
-    if (opts.userData !== undefined) cvodeSetUserData(this.mem, opts.userData);
-
-    // --- 8. Set up rootfinding if requested ---
-    if (opts.rootFn && opts.nRootFns && opts.nRootFns > 0) {
-      const userRoot = opts.rootFn;
-      const wrappedRootFn: CvodeRootFn = (
-        t: number, y: Float64Array, gout: Float64Array, _userData: any,
-      ): number => {
-        userRoot(t, y, gout);
-        return 0;
-      };
-      cvodeRootInit(this.mem, opts.nRootFns, wrappedRootFn);
-    }
-  }
-
-  // ==========================================================================
-  // Public methods
-  // ==========================================================================
-
-  /**
-   * Integrate from the current time to tout using CV_NORMAL mode
-   * (integrator advances to tout and interpolates).
-   *
-   * @param tout - target output time
-   * @returns CvodeSolveResult with { t, y, flag, rootsFound? }
-   */
-  solve(tout: number): CvodeSolveResult {
-    const {flag, t} = cvode(this.mem, tout, this.yout, CV_NORMAL);
-    return this._buildResult(t, flag);
-  }
-
-  /**
-   * Take a single internal step using CV_ONE_STEP mode.
-   * The solver advances by one internal step of whatever size it chooses.
-   *
-   * @returns CvodeSolveResult with { t, y, flag, rootsFound? }
-   */
-  step(): CvodeSolveResult {
-    const {flag, t} = cvode(this.mem, 1e30, this.yout, CV_ONE_STEP);
-    return this._buildResult(t, flag);
-  }
-
-  /**
-   * Dense output: compute the k-th derivative of the interpolating polynomial
-   * at time t using the current Nordsieck history array.
-   *
-   * @param t - interpolation time (must be within the last step interval)
-   * @param k - derivative order (0 = solution, 1 = first derivative, ...)
-   * @returns copy of the interpolated vector (length neq)
-   */
-  getDky(t: number, k: number): Float64Array {
-    const dky = new Float64Array(this.neq);
-    const flag = cvodeGetDky(this.mem, t, k, dky);
-    if (flag !== 0)
-      throw new Error(`[Cvode] getDky failed: t=${t} out of range or k=${k} invalid`);
-
-    return dky;
-  }
-
-  /**
-   * Return current integrator statistics.
-   */
-  getStats(): CvodeStats {
-    return cvodeGetIntegratorStats(this.mem);
-  }
-
-  /**
-   * Re-initialize the solver for a new initial-value problem with the same
-   * ODE function and options. Resets internal state and counters.
-   *
-   * @param t0 - new initial time
-   * @param y0 - new initial conditions (length neq)
-   */
-  reInit(t0: number, y0: Float64Array): void {
-    cvodeInit(this.mem, this.wrappedF, t0, y0);
-  }
-
-  // ==========================================================================
-  // Private helpers
-  // ==========================================================================
-
-  private _buildResult(t: number, flag: number): CvodeSolveResult {
-    const y = new Float64Array(this.yout); // copy
-    const result: CvodeSolveResult = {t, y, flag};
-
-    if (flag === CV_ROOT_RETURN) {
-      // Return a copy of the root direction info array
-      result.rootsFound = new Int32Array(this.mem.cv_iroots);
-    }
-
-    return result;
-  }
-}

package/src/solver-tools/cvode/cvode_hin.js.map

@@ -1 +0,0 @@
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