universal-physics-tensor 10.0.0 → 12.0.0

package/dist/cases/brownian-sphere.js

@@ -1,354 +0,0 @@
-/**
- * Applied case: a Brownian sphere tracked in a fluid — the diffusion
- * coefficient and mean-square displacement from the particle's radius and the
- * fluid's viscosity and temperature, with the regime checks that make the
- * Stokes–Einstein scalar applicable.
- *
- * The atlas bridge `ab-stokes-einstein` derives D = k_BT/(6πηa) from the
- * Langevin model and Stokes drag, with Re ≤ 0.1 and m/(γt) ≤ 0.01. This case
- * evaluates it for a named geometry (radius, or diameter through an exact
- * alternate) and fluid, computes Re from the particle's own velocity scales,
- * includes the displaced-fluid added mass in the momentum relaxation time, and
- * evaluates the hydrodynamic memory (the Basset force) that the bridge does not
- * check: the full MSD with fluid inertia, and the correction it makes at t.
- * Given a distance to a plane wall, it applies the wall's drag corrections to D.
- *
- * `CE-stokes-einstein` is encoded only up to its 6π (scalar-up-to-constant);
- * the 6π here comes from Stokes drag, not from that entry.
- *
- * @module cases/brownian-sphere
- */
-import { K_B_SI } from '../core/constants.js';
-import { adaptiveSimpson } from './quadrature.js';
-import { check, requirePositive, signedRelativeDifference } from './types.js';
-const ID = 'case-brownian-sphere';
-/** Standard gravity (CGPM 1901), for the sedimentation speed. @internal */
-export const G_STANDARD = 9.80665;
-/** The thresholds `ab-stokes-einstein` states: Re ≤ 0.1 and τ_p/t ≤ 0.01. @internal */
-export const MAX_RE = 0.1;
-export const MAX_TAU_P_RATIO = 0.01;
-/** Ceiling on the memory term's own share of the MSD, |MSD_H/MSD_OU − 1|. @internal */
-export const MAX_MEMORY_CORRECTION = 0.01;
-/** (v_s t)²/(2Dt) ceiling along gravity when the vertical axis is tracked. @internal */
-export const MAX_DRIFT_RATIO = 0.01;
-/** Ceiling on |MSD/MSD_wall − 1|: the wall's correction to the tracked MSD is negligible. @internal */
-export const MAX_WALL_CORRECTION = 0.01;
-/** Ceiling on the last retained Faxén term (a/h)⁵/16 over the series' value. @internal */
-export const MAX_FAXEN_LAST_TERM = 0.01;
-/** Ceiling on √(2 D_⊥ t)/(h − a): the height, and so D_∥ and D_⊥, barely change over t. @internal */
-export const MAX_WALL_EXCURSION = 0.1;
-/** t − τ(1 − e^{−t/τ}) in units of τ, i.e. x − (1 − e^{−x}), without its cancellation at small x. @internal */
-export function ballisticDeficit(x) {
-    return x < 1e-3 ? x * x * (1 / 2 - x / 6 + (x * x) / 24 - (x * x * x) / 120) : x + Math.expm1(-x);
-}
-/**
- * MSD/(2Dt) per axis for a sphere with fluid inertia: added mass and the Basset
- * memory force, in an unbounded incompressible fluid, velocities in equilibrium.
- *
- * The velocity autocorrelation has the Laplace transform
- * Ĉ(s) = k_BT/(M s + γ(1 + √(s τ_f))), M = m + m_f/2, from the frequency-dependent
- * Stokes drag γ(1 + √(sτ_f)) + s m_f/2 (Stokes 1851; the Basset 1888 term is its
- * √s part; Hinch 1975, J. Fluid Mech. 72, 499; Clercx & Schram 1992, Phys. Rev.
- * A 46, 1942). Its poles in √s both have negative real part, so Ĉ has none on the
- * principal sheet and C(t) is the branch-cut integral
- * C(t) = (k_BT/πγ) ∫₀^∞ e^{−ut} √(τ_f u)/((1 − τ_p u)² + τ_f u) du, τ_p = M/γ.
- * Then ⟨Δx²⟩ = 2∫₀ᵗ (t − s) C(s) ds, and with v = ut,
- * MSD/(2Dt) = (1/π) ∫₀^∞ √(βv) (v − 1 + e^{−v}) / (v² ((1 − αv)² + βv)) dv, α = τ_p/t, β = τ_f/t,
- * integrated here over ln v by adaptive Simpson, split at v = 1, 1/β and around
- * the near-resonance at v = 1/α (width √(β/α) in ln v; β/α ≤ 9 for any densities).
- *
- * Limits: → 1 − 2√(τ_f/(πt)) + (τ_f − τ_p)/t for t ≫ τ_p, τ_f (expanding Ĉ in √s),
- * whose second derivative is the VACF tail k_BT/(12 ρ_f (πνt)^{3/2}); → t/(2τ_p)
- * for t ≪ τ_p, i.e. ⟨Δx²⟩ → (k_BT/M) t². Requires β > 0: without memory the
- * poles reach the principal sheet and this integral no longer holds them.
- * @internal
- */
-export function hydrodynamicMsdRatio(alpha, beta) {
-    const f = (y) => {
-        const v = Math.exp(y);
-        const lag = 1 - alpha * v;
-        return (Math.sqrt(beta * v) * (ballisticDeficit(v) / v)) / (lag * lag + beta * v);
-    };
-    const peak = -Math.log(alpha);
-    const w = Math.min(1, Math.sqrt(beta / alpha));
-    const points = [0, -Math.log(beta), peak, ...[1, 2, 4].flatMap((k) => [peak - k * w, peak + k * w])].sort((x, y) => x - y);
-    // The integrand falls as v^{3/2} below and v^{−3/2} above the breakpoints: e^{−75} at ±50 in ln v.
-    const edges = [points[0] - 50, ...points, points[points.length - 1] + 50];
-    let sum = 0;
-    for (let k = 1; k < edges.length; k++)
-        if (edges[k] > edges[k - 1])
-            sum += adaptiveSimpson(f, edges[k - 1], edges[k], 1e-12);
-    return sum / Math.PI;
-}
-/**
- * D_∥/D₀ for a sphere translating parallel to a plane wall, centre at h:
- * 1 − (9/16)ξ + (1/8)ξ³ − (45/256)ξ⁴ − (1/16)ξ⁵, ξ = a/h (Faxén 1923, method of
- * reflections, as quoted in Happel & Brenner 1965, Low Reynolds Number
- * Hydrodynamics, ch. 7). A series in a/h, truncated:
- * its error is not bounded here, and near contact it misses the logarithmic
- * lubrication divergence of the drag.
- * @internal
- */
-export function faxenParallel(aOverH) {
-    const x = aOverH;
-    return 1 - (9 / 16) * x + (1 / 8) * x ** 3 - (45 / 256) * x ** 4 - (1 / 16) * x ** 5;
-}
-/**
- * λ = F/(6πηaU) for a sphere approaching a plane wall head-on, centre at h > a,
- * exact in Stokes flow (Brenner 1961, Chem. Eng. Sci. 16, 242, bispherical coordinates):
- * λ = (4/3) sinh α Σₙ n(n+1)/((2n−1)(2n+3)) · [(2 sinh(2n+1)α + (2n+1) sinh 2α) /
- * (4 sinh²(n+½)α − (2n+1)² sinh²α) − 1], cosh α = h/a. D_⊥ = D₀/λ.
- *
- * The bracket is rewritten over 4 sinh²(n+½)α so that no sinh overflows; its
- * terms fall as e^{−(2n+1)α}, so near contact (α → 0) the sum needs ~40/α terms,
- * and the low-n denominators lose ~α⁻² of relative precision to cancellation.
- * Limits: λ → 1 + (9/8)(a/h) far away (Lorentz 1907); λ → a/δ + (1/5) ln(a/δ) +
- * 0.971 as the gap δ = h − a → 0 (Cox & Brenner 1967, Chem. Eng. Sci. 22, 1753).
- * @throws Error if h/a ≤ 1.
- * @internal
- */
-export function brennerPerpendicular(hOverA) {
-    if (!(hOverA > 1))
-        throw new Error(`brennerPerpendicular: need h/a > 1 (got ${hOverA})`);
-    const al = Math.acosh(hOverA);
-    const s = Math.sinh(al);
-    const s2a = Math.sinh(2 * al);
-    let sum = 0;
-    for (let n = 1;; n++) {
-        const x = (n + 0.5) * al;
-        const k = 2 * n + 1;
-        const inv4Sinh2 = Math.exp(-2 * x) / Math.expm1(-2 * x) ** 2;
-        const cothMinus1 = 2 / Math.expm1(2 * x);
-        const bracket = (cothMinus1 + k * s2a * inv4Sinh2 + k * k * s * s * inv4Sinh2) / (1 - k * k * s * s * inv4Sinh2);
-        const term = ((n * (n + 1)) / ((2 * n - 1) * (2 * n + 3))) * bracket;
-        sum += term;
-        if (term < 1e-17 * sum)
-            break;
-        if (n > 1e7)
-            throw new Error(`brennerPerpendicular: no convergence at h/a = ${hOverA}`);
-    }
-    return (4 / 3) * s * sum;
-}
-export const BROWNIAN_SPHERE_CASE = {
-    id: ID,
-    title: 'Brownian sphere in a fluid (particle geometry, fluid conditions)',
-    parameters: [
-        { key: 'T_K', quantity: 'temperature', symbol: 'T', unit: 'K', meaning: 'absolute temperature of the fluid, > 0 K', temperature: 'absolute' },
-        { key: 'eta_Pa_s', quantity: 'dynamic viscosity', symbol: 'η', unit: 'Pa*s', meaning: 'viscosity of the fluid at T (water at 20 °C ≈ 1.0e-3 Pa·s), > 0' },
-        {
-            key: 'a_m',
-            quantity: 'particle radius',
-            symbol: 'a',
-            unit: 'm',
-            meaning: 'hydrodynamic radius of the sphere, > 0',
-            geometry: 'radius',
-            alternates: [{ key: 'diameter_m', meaning: 'the diameter 2a of the sphere', toKey: 0.5 }],
-        },
-        { key: 'rho_p_kg_per_m3', quantity: 'particle density', symbol: 'ρ_p', unit: 'kg/m^3', meaning: 'mass density of the sphere (silica ≈ 2000), > 0' },
-        { key: 'rho_f_kg_per_m3', quantity: 'fluid density', symbol: 'ρ_f', unit: 'kg/m^3', meaning: 'mass density of the fluid (water ≈ 998), > 0' },
-        { key: 't_s', quantity: 'lag time', symbol: 't', unit: 's', meaning: 'the time over which the displacement is measured, > 0' },
-        { key: 'd', quantity: 'tracked dimensions', symbol: 'd', unit: '', meaning: 'number of Cartesian axes tracked: 1, 2 (a microscope image plane, horizontal) or 3' },
-        {
-            key: 'h_m',
-            quantity: 'distance to a wall',
-            symbol: 'h',
-            unit: 'm',
-            meaning: "distance from the sphere's centre to one plane horizontal wall (a coverslip), > a; leave out when no wall is within many radii",
-            geometry: 'separation',
-            optional: true,
-        },
-    ],
-    governing: {
-        parent: [
-            'm dv/dt = −γ v + ξ(t),  ⟨ξ_i(t) ξ_j(t′)⟩ = 2γ k_BT δ_ij δ(t − t′)   (Langevin, a 3-vector equation; model-langevin)',
-            'η ∇²u = ∇p,  ∇·u = 0,  u = v on the sphere (no slip), u → 0 far away   (Stokes creeping flow, a field; model-stokes-drag) ⇒ γ = 6πηa',
-            'm dv/dt = −γ v − (m_f/2) dv/dt − 6a²√(πηρ_f) ∫_{−∞}^t v′(s)/√(t − s) ds + ξ(t), ξ coloured by the same kernel   ' +
-                '(unsteady Stokes flow: added mass and the Basset memory force; Hinch 1975)',
-        ],
-        scalar: [
-            'D = k_BT/(6πηa)   (Stokes–Einstein; ab-stokes-einstein)',
-            '⟨|Δr|²⟩ = 2 d D t  over the d tracked axes',
-        ],
-        distinction: 'The parents are a vector stochastic equation for the velocity and a field equation for the flow around the sphere; ' +
-            'the scalar keeps one isotropic number D and a mean-square displacement linear in t. Dropped: the velocity as a ' +
-            'state (the ballistic regime t ≲ τ_p), the flow field (and with it the hydrodynamic memory for t ≲ τ_f), the shape ' +
-            'beyond the radius, and every anisotropy.',
-    },
-    observable: 'MSD_m2',
-    outputs: [
-        { key: 'gamma_kg_per_s', symbol: 'γ', unit: 'kg/s', meaning: 'Stokes drag coefficient 6πηa' },
-        { key: 'D_m2_per_s', symbol: 'D', unit: 'm^2/s', meaning: 'diffusion coefficient k_BT/(6πηa)' },
-        { key: 'MSD_m2', symbol: '⟨|Δr|²⟩', unit: 'm^2', meaning: 'mean-square displacement 2dDt over the tracked axes' },
-        { key: 'rms_displacement_m', symbol: '√⟨|Δr|²⟩', unit: 'm', meaning: 'root-mean-square displacement over the tracked axes' },
-        { key: 'm_kg', symbol: 'm', unit: 'kg', meaning: 'particle mass (4/3)πa³ρ_p' },
-        { key: 'tau_p_s', symbol: 'τ_p', unit: 's', meaning: 'momentum relaxation time (m + m_f/2)/γ, with the displaced-fluid added mass m_f/2' },
-        { key: 'tau_f_s', symbol: 'τ_f', unit: 's', meaning: 'vorticity diffusion time ρ_f a²/η over one radius (hydrodynamic memory)' },
-        { key: 'v_sed_m_per_s', symbol: 'v_s', unit: 'm/s', meaning: 'Stokes sedimentation speed (2/9)(ρ_p − ρ_f) g a²/η; negative means the sphere rises' },
-        { key: 'Re', symbol: 'Re', unit: '', meaning: 'ρ_f a max(√(k_BT/m), |v_s|)/η — radius-based; a diameter-based Re is twice this' },
-        { key: 'MSD_langevin_m2', symbol: '⟨|Δr|²⟩_L', unit: 'm^2', meaning: 'the Langevin parent: 2dD[t − τ(1 − e^{−t/τ})], τ = m/γ (bare mass)' },
-        { key: 'langevin_deviation', symbol: 'MSD/MSD_L − 1', unit: '', meaning: signedRelativeDifference('diffusive MSD', 'Langevin one') },
-        {
-            key: 'MSD_hydro_m2',
-            symbol: '⟨|Δr|²⟩_H',
-            unit: 'm^2',
-            meaning: 'the Langevin–Basset parent: added mass and hydrodynamic memory, unbounded incompressible fluid (branch-cut integral of its Laplace-domain VACF)',
-        },
-        { key: 'hydro_correction_m2', symbol: '⟨|Δr|²⟩_H − ⟨|Δr|²⟩', unit: 'm^2', meaning: 'what inertia and memory change in the MSD at t; ≈ −4dD√(τ_f t/π) at t ≫ τ_f' },
-        { key: 'hydro_deviation', symbol: 'MSD/MSD_H − 1', unit: '', meaning: signedRelativeDifference('diffusive MSD', 'Langevin–Basset one') },
-        {
-            key: 'memory_correction',
-            symbol: 'MSD_H/MSD_OU − 1',
-            unit: '',
-            meaning: "the memory force's own share: MSD_H against the Ornstein–Uhlenbeck MSD with the same τ_p (added mass, no memory)",
-        },
-        { key: 'D_parallel_m2_per_s', symbol: 'D_∥', unit: 'm^2/s', meaning: 'D beside the wall, parallel to it: D·(Faxén series in a/h); not defined without h_m' },
-        { key: 'D_perp_m2_per_s', symbol: 'D_⊥', unit: 'm^2/s', meaning: 'D normal to the wall: D/λ, λ from Brenner\'s exact series; not defined without h_m' },
-        { key: 'MSD_wall_m2', symbol: '⟨|Δr|²⟩_w', unit: 'm^2', meaning: '2t(d_∥ D_∥ + d_⊥ D_⊥): the tracked horizontal axes parallel to the wall, a third one normal to it; not defined without h_m' },
-        { key: 'wall_deviation', symbol: 'MSD/MSD_w − 1', unit: '', meaning: signedRelativeDifference('unbounded-fluid MSD', 'wall-corrected one', 'not defined without h_m') },
-    ],
-    comparison: {
-        reference: 'the parent Langevin model (bare mass, white noise; it has neither added mass nor hydrodynamic memory)',
-        valueKey: 'MSD_m2',
-        referenceKey: 'MSD_langevin_m2',
-        deviationKey: 'langevin_deviation',
-        method: 'closed form of the Ornstein–Uhlenbeck MSD, velocities starting in equilibrium',
-    },
-    conditions: [
-        'a rigid sphere released at r = 0; its displacement density starts as δ(r) and spreads as a Gaussian of variance 2Dt per axis',
-        'no-slip boundary on the sphere; the fluid is at rest far from it (no imposed flow; no wall within many radii, or with h_m one plane no-slip wall)',
-        'fluid in thermal equilibrium at T; one isolated particle (dilute: no hydrodynamic interaction with others)',
-    ],
-    notIncluded: [
-        'walls other than one plane: a second wall, a channel or a curved surface; and, with h_m, the spread of heights the sphere samples (D_∥, D_⊥ are taken at h)',
-        'localization error and camera motion blur of the tracking, which offset and bias the measured MSD',
-        'fluid compressibility: the incompressible memory kernel gives ⟨v²⟩ = k_BT/(m + m_f/2) at t = 0; sound restores k_BT/m over a/c_s (Zwanzig & Bixon 1970)',
-        'the memory force near a wall: MSD_hydro is the unbounded-fluid result, and a wall within √(νt) changes the memory tail',
-        'the rotational diffusion of the sphere, and any non-spherical shape',
-    ],
-    measurement: [
-        'single-particle tracking: fit ⟨|Δr|²⟩(t) over the d tracked axes, slope 2dD; compare D and MSD_m2 at the chosen lag ' +
-            '(with N independent displacements the relative scatter of the MSD is ≈ √(2/(dN)))',
-        'subtract the static localization offset 2dσ_loc² (measured on an immobilized particle) before comparing',
-        'dynamic light scattering: the field autocorrelation decays at Γ = D q², an independent route to the same D',
-    ],
-    links: [
-        { id: 'ab-stokes-einstein', role: 'the derivation D = k_BT/(6πηa) with its regime Re ≤ 0.1, m/(γt) ≤ 0.01 (`upt atlas ab-stokes-einstein`)' },
-        { id: 'ab-langevin-diffusion', role: 'the overdamped coarse-graining D = k_BT/γ and its ballistic counterexample' },
-        { id: 'model-stokes-drag', role: 'the creeping-flow drag γ = 6πηa' },
-        { id: 'CE-stokes-einstein', role: 'encoded only up to its dimensionless 6π (scalar-up-to-constant); the 6π here is from Stokes drag' },
-    ],
-    examples: {
-        valid: {
-            args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=2000', 'rho_f_kg_per_m3=998', 't_s=1', 'd=2', 'h_m=100um'],
-            note: 'a 1 µm-radius silica sphere in water at 20 °C, 100 µm above the coverslip, tracked in the image plane over 1 s',
-            fails: [],
-        },
-        failures: [
-            {
-                args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=2000', 'rho_f_kg_per_m3=998', 't_s=1us', 'd=2'],
-                note: 'the same sphere over 1 µs: still ballistic (t ≈ 2τ_p) and inside the hydrodynamic memory time',
-                fails: ['overdamped', 'memory'],
-            },
-            {
-                args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=50um', 'rho_p_kg_per_m3=7800', 'rho_f_kg_per_m3=998', 't_s=100', 'd=3'],
-                note: 'a 50 µm-radius steel sphere tracked in 3-D: it sinks at ≈ 3.7 cm/s, Re ≈ 1.9, and the drift swamps diffusion',
-                fails: ['creeping-flow', 'drift'],
-            },
-            {
-                args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=1050', 'rho_f_kg_per_m3=998', 't_s=50ms', 'd=2', 'h_m=3um'],
-                note: 'a 1 µm-radius polystyrene sphere 3 µm (centre) above the coverslip: the wall slows D_∥ by ≈ 19%',
-                fails: ['wall'],
-            },
-            {
-                args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=1050', 'rho_f_kg_per_m3=998', 't_s=50ms', 'd=2', 'h_m=1.2um'],
-                note: 'the same sphere with a 0.2 µm gap: past the range of the Faxén series, and its height changes by more than the gap allows over t',
-                fails: ['faxen-range', 'wall', 'wall-static'],
-            },
-        ],
-    },
-    /** Evaluate the Stokes-Einstein MSD and regime checks for the supplied Brownian-sphere inputs. */
-    regimeAt(inputs, outputs) {
-        const re = outputs.Re;
-        const m = outputs.m_kg;
-        const gamma = outputs.gamma_kg_per_s;
-        const t = inputs.t_s;
-        if (re == null || m == null || gamma == null || t == null)
-            return '';
-        return `upt regime diffusion --at Re=${re} m=${m} gamma=${gamma} t=${t}`;
-    },
-    /** Compute the Stokes-Einstein diffusion, MSD and regime checks for one set of Brownian-sphere inputs. */
-    run(i) {
-        requirePositive(ID, i, ['T_K', 'eta_Pa_s', 'a_m', 'rho_p_kg_per_m3', 'rho_f_kg_per_m3', 't_s']);
-        const { T_K: T, eta_Pa_s: eta, a_m: a, rho_p_kg_per_m3: rhoP, rho_f_kg_per_m3: rhoF, t_s: t, d } = i;
-        if (d !== 1 && d !== 2 && d !== 3)
-            throw new Error(`${ID}: d must be 1, 2 or 3 (got ${d})`);
-        const kT = K_B_SI * T;
-        const gamma = 6 * Math.PI * eta * a;
-        const D = kT / gamma;
-        const msd = 2 * d * D * t;
-        const volume = (4 / 3) * Math.PI * a ** 3;
-        const m = volume * rhoP;
-        const tauP = (m + 0.5 * volume * rhoF) / gamma;
-        const tauF = (rhoF * a * a) / eta;
-        const vSed = ((2 / 9) * (rhoP - rhoF) * G_STANDARD * a * a) / eta;
-        const re = (rhoF * a * Math.max(Math.sqrt(kT / m), Math.abs(vSed))) / eta;
-        const tauBare = m / gamma;
-        const msdLangevin = 2 * d * D * tauBare * ballisticDeficit(t / tauBare);
-        const msdHydro = msd * hydrodynamicMsdRatio(tauP / t, tauF / t);
-        const msdAddedMass = 2 * d * D * tauP * ballisticDeficit(t / tauP);
-        const memory = msdHydro / msdAddedMass - 1;
-        const checks = [
-            check('creeping-flow', 'creeping flow around the sphere, Re ≪ 1', 'ρ_f a max(√(k_BT/m), |v_s|)/η', re, '<=', MAX_RE, "the threshold ab-stokes-einstein states: a chosen machine form of Re ≪ 1"),
-            check('overdamped', 'overdamped times t ≫ τ_p', '(m + m_f/2)/(γ t)', tauP / t, '<=', MAX_TAU_P_RATIO, "ab-stokes-einstein's m/(γt) ≤ 0.01, with the added mass m_f/2 included (stricter)"),
-            check('memory', 'past the hydrodynamic memory, t ≫ τ_f = ρ_f a²/η', '|MSD_H/MSD_OU − 1|', Math.abs(memory), '<=', MAX_MEMORY_CORRECTION, 'chosen threshold: the Basset memory changes the MSD by ≤ 1% at t (computed, not estimated; ≈ 2√(τ_f/(πt)) at t ≫ τ_f)'),
-        ];
-        const unchecked = ['the particle is a rigid sphere and a is its hydrodynamic radius (a coating or a shell changes it)'];
-        let wall = null;
-        if (i.h_m !== undefined) {
-            const h = i.h_m;
-            if (!Number.isFinite(h) || !(h > a))
-                throw new Error(`${ID}: h_m must be a finite distance > a_m, centre to wall (got ${h})`);
-            const faxen = faxenParallel(a / h);
-            const lambda = brennerPerpendicular(h / a);
-            const dPar = D * faxen;
-            const dPerp = D / lambda;
-            const msdWall = 2 * t * (Math.min(d, 2) * dPar + (d === 3 ? dPerp : 0));
-            wall = { dPar, dPerp, msdWall };
-            const excursion = Math.sqrt(2 * dPerp * t) + (Math.abs(vSed) * t) / lambda;
-            checks.push(check('faxen-range', 'the Faxén series in a/h holds for D_∥', '(a/h)⁵/16 ÷ (D_∥/D)', (a / h) ** 5 / 16 / faxen, '<=', MAX_FAXEN_LAST_TERM, 'chosen threshold: the last retained term is ≤ 1% of the series — a size estimate of the truncation, not a bound; D_⊥ (Brenner) is exact at any h > a'), check('wall', 'the wall correction to the tracked MSD is negligible', '|MSD/MSD_w − 1|', Math.abs(msd / msdWall - 1), '<=', MAX_WALL_CORRECTION, 'chosen threshold: the unbounded-fluid D is then within 1% for the tracked axes; otherwise read MSD_wall_m2'), check('wall-static', 'the height barely changes over t', '(√(2 D_⊥ t) + |v_s| t/λ)/(h − a)', excursion / (h - a), '<=', MAX_WALL_EXCURSION, 'chosen threshold: diffusion plus wall-slowed sedimentation normal to the wall move the sphere by ≤ 10% of the gap, so D_∥, D_⊥ taken at h hold over t'));
-            unchecked.push('the wall is plane, rigid, no-slip and horizontal, and the gap h − a is many molecular sizes and roughness heights (no surface forces, no lubrication-scale slip)');
-        }
-        if (d === 3) {
-            checks.push(check('drift', 'sedimentation drift negligible along gravity over t', '(v_s t)²/(2 D t)', (vSed * t) ** 2 / (2 * D * t), '<=', MAX_DRIFT_RATIO, 'chosen threshold: the vertical MSD then carries ≤ 1% from the deterministic drift'));
-        }
-        else {
-            unchecked.push(`the ${d === 1 ? 'tracked axis is' : 'tracked axes are'} horizontal, so sedimentation (${Number(Math.abs(vSed * t).toPrecision(3))} m over t) moves the sphere out of the plane but not along ${d === 1 ? 'it' : 'them'}`);
-        }
-        return {
-            outputs: {
-                gamma_kg_per_s: gamma,
-                D_m2_per_s: D,
-                MSD_m2: msd,
-                rms_displacement_m: Math.sqrt(msd),
-                m_kg: m,
-                tau_p_s: tauP,
-                tau_f_s: tauF,
-                v_sed_m_per_s: vSed,
-                Re: re,
-                MSD_langevin_m2: msdLangevin,
-                langevin_deviation: msd / msdLangevin - 1,
-                MSD_hydro_m2: msdHydro,
-                hydro_correction_m2: msdHydro - msd,
-                hydro_deviation: msd / msdHydro - 1,
-                memory_correction: memory,
-                D_parallel_m2_per_s: wall?.dPar ?? null,
-                D_perp_m2_per_s: wall?.dPerp ?? null,
-                MSD_wall_m2: wall?.msdWall ?? null,
-                wall_deviation: wall === null ? null : msd / wall.msdWall - 1,
-            },
-            checks,
-            unchecked,
-        };
-    },
-};
-//# sourceMappingURL=brownian-sphere.js.map

package/dist/cases/brownian-sphere.js.map

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* Applied case: a Brownian sphere tracked in a fluid — the diffusion\n * coefficient and mean-square displacement from the particle's radius and the\n * fluid's viscosity and temperature, with the regime checks that make the\n * Stokes–Einstein scalar applicable.\n *\n * The atlas bridge `ab-stokes-einstein` derives D = k_BT/(6πηa) from the\n * Langevin model and Stokes drag, with Re ≤ 0.1 and m/(γt) ≤ 0.01. This case\n * evaluates it for a named geometry (radius, or diameter through an exact\n * alternate) and fluid, computes Re from the particle's own velocity scales,\n * includes the displaced-fluid added mass in the momentum relaxation time, and\n * evaluates the hydrodynamic memory (the Basset force) that the bridge does not\n * check: the full MSD with fluid inertia, and the correction it makes at t.\n * Given a distance to a plane wall, it applies the wall's drag corrections to D.\n *\n * `CE-stokes-einstein` is encoded only up to its 6π (scalar-up-to-constant);\n * the 6π here comes from Stokes drag, not from that entry.\n *\n * @module cases/brownian-sphere\n */\nimport { K_B_SI } from '../core/constants.js';\nimport { adaptiveSimpson } from './quadrature.js';\nimport { check, requirePositive, signedRelativeDifference, type AppliedCase } from './types.js';\n\nconst ID = 'case-brownian-sphere';\n\n/** Standard gravity (CGPM 1901), for the sedimentation speed. @internal */\nexport const G_STANDARD = 9.80665;\n\n/** The thresholds `ab-stokes-einstein` states: Re ≤ 0.1 and τ_p/t ≤ 0.01. @internal */\nexport const MAX_RE = 0.1;\nexport const MAX_TAU_P_RATIO = 0.01;\n\n/** Ceiling on the memory term's own share of the MSD, |MSD_H/MSD_OU − 1|. @internal */\nexport const MAX_MEMORY_CORRECTION = 0.01;\n\n/** (v_s t)²/(2Dt) ceiling along gravity when the vertical axis is tracked. @internal */\nexport const MAX_DRIFT_RATIO = 0.01;\n\n/** Ceiling on |MSD/MSD_wall − 1|: the wall's correction to the tracked MSD is negligible. @internal */\nexport const MAX_WALL_CORRECTION = 0.01;\n\n/** Ceiling on the last retained Faxén term (a/h)⁵/16 over the series' value. @internal */\nexport const MAX_FAXEN_LAST_TERM = 0.01;\n\n/** Ceiling on √(2 D_⊥ t)/(h − a): the height, and so D_∥ and D_⊥, barely change over t. @internal */\nexport const MAX_WALL_EXCURSION = 0.1;\n\n/** t − τ(1 − e^{−t/τ}) in units of τ, i.e. x − (1 − e^{−x}), without its cancellation at small x. @internal */\nexport function ballisticDeficit(x: number): number {\n  return x < 1e-3 ? x * x * (1 / 2 - x / 6 + (x * x) / 24 - (x * x * x) / 120) : x + Math.expm1(-x);\n}\n\n/**\n * MSD/(2Dt) per axis for a sphere with fluid inertia: added mass and the Basset\n * memory force, in an unbounded incompressible fluid, velocities in equilibrium.\n *\n * The velocity autocorrelation has the Laplace transform\n * Ĉ(s) = k_BT/(M s + γ(1 + √(s τ_f))), M = m + m_f/2, from the frequency-dependent\n * Stokes drag γ(1 + √(sτ_f)) + s m_f/2 (Stokes 1851; the Basset 1888 term is its\n * √s part; Hinch 1975, J. Fluid Mech. 72, 499; Clercx & Schram 1992, Phys. Rev.\n * A 46, 1942). Its poles in √s both have negative real part, so Ĉ has none on the\n * principal sheet and C(t) is the branch-cut integral\n * C(t) = (k_BT/πγ) ∫₀^∞ e^{−ut} √(τ_f u)/((1 − τ_p u)² + τ_f u) du, τ_p = M/γ.\n * Then ⟨Δx²⟩ = 2∫₀ᵗ (t − s) C(s) ds, and with v = ut,\n * MSD/(2Dt) = (1/π) ∫₀^∞ √(βv) (v − 1 + e^{−v}) / (v² ((1 − αv)² + βv)) dv, α = τ_p/t, β = τ_f/t,\n * integrated here over ln v by adaptive Simpson, split at v = 1, 1/β and around\n * the near-resonance at v = 1/α (width √(β/α) in ln v; β/α ≤ 9 for any densities).\n *\n * Limits: → 1 − 2√(τ_f/(πt)) + (τ_f − τ_p)/t for t ≫ τ_p, τ_f (expanding Ĉ in √s),\n * whose second derivative is the VACF tail k_BT/(12 ρ_f (πνt)^{3/2}); → t/(2τ_p)\n * for t ≪ τ_p, i.e. ⟨Δx²⟩ → (k_BT/M) t². Requires β > 0: without memory the\n * poles reach the principal sheet and this integral no longer holds them.\n * @internal\n */\nexport function hydrodynamicMsdRatio(alpha: number, beta: number): number {\n  const f = (y: number) => {\n    const v = Math.exp(y);\n    const lag = 1 - alpha * v;\n    return (Math.sqrt(beta * v) * (ballisticDeficit(v) / v)) / (lag * lag + beta * v);\n  };\n  const peak = -Math.log(alpha);\n  const w = Math.min(1, Math.sqrt(beta / alpha));\n  const points = [0, -Math.log(beta), peak, ...[1, 2, 4].flatMap((k) => [peak - k * w, peak + k * w])].sort((x, y) => x - y);\n  // The integrand falls as v^{3/2} below and v^{−3/2} above the breakpoints: e^{−75} at ±50 in ln v.\n  const edges = [points[0]! - 50, ...points, points[points.length - 1]! + 50];\n  let sum = 0;\n  for (let k = 1; k < edges.length; k++) if (edges[k]! > edges[k - 1]!) sum += adaptiveSimpson(f, edges[k - 1]!, edges[k]!, 1e-12);\n  return sum / Math.PI;\n}\n\n/**\n * D_∥/D₀ for a sphere translating parallel to a plane wall, centre at h:\n * 1 − (9/16)ξ + (1/8)ξ³ − (45/256)ξ⁴ − (1/16)ξ⁵, ξ = a/h (Faxén 1923, method of\n * reflections, as quoted in Happel & Brenner 1965, Low Reynolds Number\n * Hydrodynamics, ch. 7). A series in a/h, truncated:\n * its error is not bounded here, and near contact it misses the logarithmic\n * lubrication divergence of the drag.\n * @internal\n */\nexport function faxenParallel(aOverH: number): number {\n  const x = aOverH;\n  return 1 - (9 / 16) * x + (1 / 8) * x ** 3 - (45 / 256) * x ** 4 - (1 / 16) * x ** 5;\n}\n\n/**\n * λ = F/(6πηaU) for a sphere approaching a plane wall head-on, centre at h > a,\n * exact in Stokes flow (Brenner 1961, Chem. Eng. Sci. 16, 242, bispherical coordinates):\n * λ = (4/3) sinh α Σₙ n(n+1)/((2n−1)(2n+3)) · [(2 sinh(2n+1)α + (2n+1) sinh 2α) /\n * (4 sinh²(n+½)α − (2n+1)² sinh²α) − 1], cosh α = h/a. D_⊥ = D₀/λ.\n *\n * The bracket is rewritten over 4 sinh²(n+½)α so that no sinh overflows; its\n * terms fall as e^{−(2n+1)α}, so near contact (α → 0) the sum needs ~40/α terms,\n * and the low-n denominators lose ~α⁻² of relative precision to cancellation.\n * Limits: λ → 1 + (9/8)(a/h) far away (Lorentz 1907); λ → a/δ + (1/5) ln(a/δ) +\n * 0.971 as the gap δ = h − a → 0 (Cox & Brenner 1967, Chem. Eng. Sci. 22, 1753).\n * @throws Error if h/a ≤ 1.\n * @internal\n */\nexport function brennerPerpendicular(hOverA: number): number {\n  if (!(hOverA > 1)) throw new Error(`brennerPerpendicular: need h/a > 1 (got ${hOverA})`);\n  const al = Math.acosh(hOverA);\n  const s = Math.sinh(al);\n  const s2a = Math.sinh(2 * al);\n  let sum = 0;\n  for (let n = 1; ; n++) {\n    const x = (n + 0.5) * al;\n    const k = 2 * n + 1;\n    const inv4Sinh2 = Math.exp(-2 * x) / Math.expm1(-2 * x) ** 2;\n    const cothMinus1 = 2 / Math.expm1(2 * x);\n    const bracket = (cothMinus1 + k * s2a * inv4Sinh2 + k * k * s * s * inv4Sinh2) / (1 - k * k * s * s * inv4Sinh2);\n    const term = ((n * (n + 1)) / ((2 * n - 1) * (2 * n + 3))) * bracket;\n    sum += term;\n    if (term < 1e-17 * sum) break;\n    if (n > 1e7) throw new Error(`brennerPerpendicular: no convergence at h/a = ${hOverA}`);\n  }\n  return (4 / 3) * s * sum;\n}\n\nexport const BROWNIAN_SPHERE_CASE: AppliedCase = {\n  id: ID,\n  title: 'Brownian sphere in a fluid (particle geometry, fluid conditions)',\n  parameters: [\n    { key: 'T_K', quantity: 'temperature', symbol: 'T', unit: 'K', meaning: 'absolute temperature of the fluid, > 0 K', temperature: 'absolute' },\n    { key: 'eta_Pa_s', quantity: 'dynamic viscosity', symbol: 'η', unit: 'Pa*s', meaning: 'viscosity of the fluid at T (water at 20 °C ≈ 1.0e-3 Pa·s), > 0' },\n    {\n      key: 'a_m',\n      quantity: 'particle radius',\n      symbol: 'a',\n      unit: 'm',\n      meaning: 'hydrodynamic radius of the sphere, > 0',\n      geometry: 'radius',\n      alternates: [{ key: 'diameter_m', meaning: 'the diameter 2a of the sphere', toKey: 0.5 }],\n    },\n    { key: 'rho_p_kg_per_m3', quantity: 'particle density', symbol: 'ρ_p', unit: 'kg/m^3', meaning: 'mass density of the sphere (silica ≈ 2000), > 0' },\n    { key: 'rho_f_kg_per_m3', quantity: 'fluid density', symbol: 'ρ_f', unit: 'kg/m^3', meaning: 'mass density of the fluid (water ≈ 998), > 0' },\n    { key: 't_s', quantity: 'lag time', symbol: 't', unit: 's', meaning: 'the time over which the displacement is measured, > 0' },\n    { key: 'd', quantity: 'tracked dimensions', symbol: 'd', unit: '', meaning: 'number of Cartesian axes tracked: 1, 2 (a microscope image plane, horizontal) or 3' },\n    {\n      key: 'h_m',\n      quantity: 'distance to a wall',\n      symbol: 'h',\n      unit: 'm',\n      meaning: \"distance from the sphere's centre to one plane horizontal wall (a coverslip), > a; leave out when no wall is within many radii\",\n      geometry: 'separation',\n      optional: true,\n    },\n  ],\n  governing: {\n    parent: [\n      'm dv/dt = −γ v + ξ(t),  ⟨ξ_i(t) ξ_j(t′)⟩ = 2γ k_BT δ_ij δ(t − t′)   (Langevin, a 3-vector equation; model-langevin)',\n      'η ∇²u = ∇p,  ∇·u = 0,  u = v on the sphere (no slip), u → 0 far away   (Stokes creeping flow, a field; model-stokes-drag) ⇒ γ = 6πηa',\n      'm dv/dt = −γ v − (m_f/2) dv/dt − 6a²√(πηρ_f) ∫_{−∞}^t v′(s)/√(t − s) ds + ξ(t), ξ coloured by the same kernel   ' +\n        '(unsteady Stokes flow: added mass and the Basset memory force; Hinch 1975)',\n    ],\n    scalar: [\n      'D = k_BT/(6πηa)   (Stokes–Einstein; ab-stokes-einstein)',\n      '⟨|Δr|²⟩ = 2 d D t  over the d tracked axes',\n    ],\n    distinction:\n      'The parents are a vector stochastic equation for the velocity and a field equation for the flow around the sphere; ' +\n      'the scalar keeps one isotropic number D and a mean-square displacement linear in t. Dropped: the velocity as a ' +\n      'state (the ballistic regime t ≲ τ_p), the flow field (and with it the hydrodynamic memory for t ≲ τ_f), the shape ' +\n      'beyond the radius, and every anisotropy.',\n  },\n  observable: 'MSD_m2',\n  outputs: [\n    { key: 'gamma_kg_per_s', symbol: 'γ', unit: 'kg/s', meaning: 'Stokes drag coefficient 6πηa' },\n    { key: 'D_m2_per_s', symbol: 'D', unit: 'm^2/s', meaning: 'diffusion coefficient k_BT/(6πηa)' },\n    { key: 'MSD_m2', symbol: '⟨|Δr|²⟩', unit: 'm^2', meaning: 'mean-square displacement 2dDt over the tracked axes' },\n    { key: 'rms_displacement_m', symbol: '√⟨|Δr|²⟩', unit: 'm', meaning: 'root-mean-square displacement over the tracked axes' },\n    { key: 'm_kg', symbol: 'm', unit: 'kg', meaning: 'particle mass (4/3)πa³ρ_p' },\n    { key: 'tau_p_s', symbol: 'τ_p', unit: 's', meaning: 'momentum relaxation time (m + m_f/2)/γ, with the displaced-fluid added mass m_f/2' },\n    { key: 'tau_f_s', symbol: 'τ_f', unit: 's', meaning: 'vorticity diffusion time ρ_f a²/η over one radius (hydrodynamic memory)' },\n    { key: 'v_sed_m_per_s', symbol: 'v_s', unit: 'm/s', meaning: 'Stokes sedimentation speed (2/9)(ρ_p − ρ_f) g a²/η; negative means the sphere rises' },\n    { key: 'Re', symbol: 'Re', unit: '', meaning: 'ρ_f a max(√(k_BT/m), |v_s|)/η — radius-based; a diameter-based Re is twice this' },\n    { key: 'MSD_langevin_m2', symbol: '⟨|Δr|²⟩_L', unit: 'm^2', meaning: 'the Langevin parent: 2dD[t − τ(1 − e^{−t/τ})], τ = m/γ (bare mass)' },\n    { key: 'langevin_deviation', symbol: 'MSD/MSD_L − 1', unit: '', meaning: signedRelativeDifference('diffusive MSD', 'Langevin one') },\n    {\n      key: 'MSD_hydro_m2',\n      symbol: '⟨|Δr|²⟩_H',\n      unit: 'm^2',\n      meaning: 'the Langevin–Basset parent: added mass and hydrodynamic memory, unbounded incompressible fluid (branch-cut integral of its Laplace-domain VACF)',\n    },\n    { key: 'hydro_correction_m2', symbol: '⟨|Δr|²⟩_H − ⟨|Δr|²⟩', unit: 'm^2', meaning: 'what inertia and memory change in the MSD at t; ≈ −4dD√(τ_f t/π) at t ≫ τ_f' },\n    { key: 'hydro_deviation', symbol: 'MSD/MSD_H − 1', unit: '', meaning: signedRelativeDifference('diffusive MSD', 'Langevin–Basset one') },\n    {\n      key: 'memory_correction',\n      symbol: 'MSD_H/MSD_OU − 1',\n      unit: '',\n      meaning: \"the memory force's own share: MSD_H against the Ornstein–Uhlenbeck MSD with the same τ_p (added mass, no memory)\",\n    },\n    { key: 'D_parallel_m2_per_s', symbol: 'D_∥', unit: 'm^2/s', meaning: 'D beside the wall, parallel to it: D·(Faxén series in a/h); not defined without h_m' },\n    { key: 'D_perp_m2_per_s', symbol: 'D_⊥', unit: 'm^2/s', meaning: 'D normal to the wall: D/λ, λ from Brenner\\'s exact series; not defined without h_m' },\n    { key: 'MSD_wall_m2', symbol: '⟨|Δr|²⟩_w', unit: 'm^2', meaning: '2t(d_∥ D_∥ + d_⊥ D_⊥): the tracked horizontal axes parallel to the wall, a third one normal to it; not defined without h_m' },\n    { key: 'wall_deviation', symbol: 'MSD/MSD_w − 1', unit: '', meaning: signedRelativeDifference('unbounded-fluid MSD', 'wall-corrected one', 'not defined without h_m') },\n  ],\n  comparison: {\n    reference: 'the parent Langevin model (bare mass, white noise; it has neither added mass nor hydrodynamic memory)',\n    valueKey: 'MSD_m2',\n    referenceKey: 'MSD_langevin_m2',\n    deviationKey: 'langevin_deviation',\n    method: 'closed form of the Ornstein–Uhlenbeck MSD, velocities starting in equilibrium',\n  },\n  conditions: [\n    'a rigid sphere released at r = 0; its displacement density starts as δ(r) and spreads as a Gaussian of variance 2Dt per axis',\n    'no-slip boundary on the sphere; the fluid is at rest far from it (no imposed flow; no wall within many radii, or with h_m one plane no-slip wall)',\n    'fluid in thermal equilibrium at T; one isolated particle (dilute: no hydrodynamic interaction with others)',\n  ],\n  notIncluded: [\n    'walls other than one plane: a second wall, a channel or a curved surface; and, with h_m, the spread of heights the sphere samples (D_∥, D_⊥ are taken at h)',\n    'localization error and camera motion blur of the tracking, which offset and bias the measured MSD',\n    'fluid compressibility: the incompressible memory kernel gives ⟨v²⟩ = k_BT/(m + m_f/2) at t = 0; sound restores k_BT/m over a/c_s (Zwanzig & Bixon 1970)',\n    'the memory force near a wall: MSD_hydro is the unbounded-fluid result, and a wall within √(νt) changes the memory tail',\n    'the rotational diffusion of the sphere, and any non-spherical shape',\n  ],\n  measurement: [\n    'single-particle tracking: fit ⟨|Δr|²⟩(t) over the d tracked axes, slope 2dD; compare D and MSD_m2 at the chosen lag ' +\n      '(with N independent displacements the relative scatter of the MSD is ≈ √(2/(dN)))',\n    'subtract the static localization offset 2dσ_loc² (measured on an immobilized particle) before comparing',\n    'dynamic light scattering: the field autocorrelation decays at Γ = D q², an independent route to the same D',\n  ],\n  links: [\n    { id: 'ab-stokes-einstein', role: 'the derivation D = k_BT/(6πηa) with its regime Re ≤ 0.1, m/(γt) ≤ 0.01 (`upt atlas ab-stokes-einstein`)' },\n    { id: 'ab-langevin-diffusion', role: 'the overdamped coarse-graining D = k_BT/γ and its ballistic counterexample' },\n    { id: 'model-stokes-drag', role: 'the creeping-flow drag γ = 6πηa' },\n    { id: 'CE-stokes-einstein', role: 'encoded only up to its dimensionless 6π (scalar-up-to-constant); the 6π here is from Stokes drag' },\n  ],\n  examples: {\n    valid: {\n      args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=2000', 'rho_f_kg_per_m3=998', 't_s=1', 'd=2', 'h_m=100um'],\n      note: 'a 1 µm-radius silica sphere in water at 20 °C, 100 µm above the coverslip, tracked in the image plane over 1 s',\n      fails: [],\n    },\n    failures: [\n      {\n        args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=2000', 'rho_f_kg_per_m3=998', 't_s=1us', 'd=2'],\n        note: 'the same sphere over 1 µs: still ballistic (t ≈ 2τ_p) and inside the hydrodynamic memory time',\n        fails: ['overdamped', 'memory'],\n      },\n      {\n        args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=50um', 'rho_p_kg_per_m3=7800', 'rho_f_kg_per_m3=998', 't_s=100', 'd=3'],\n        note: 'a 50 µm-radius steel sphere tracked in 3-D: it sinks at ≈ 3.7 cm/s, Re ≈ 1.9, and the drift swamps diffusion',\n        fails: ['creeping-flow', 'drift'],\n      },\n      {\n        args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=1050', 'rho_f_kg_per_m3=998', 't_s=50ms', 'd=2', 'h_m=3um'],\n        note: 'a 1 µm-radius polystyrene sphere 3 µm (centre) above the coverslip: the wall slows D_∥ by ≈ 19%',\n        fails: ['wall'],\n      },\n      {\n        args: ['T_K=293.15', 'eta_Pa_s=1e-3', 'a_m=1um', 'rho_p_kg_per_m3=1050', 'rho_f_kg_per_m3=998', 't_s=50ms', 'd=2', 'h_m=1.2um'],\n        note: 'the same sphere with a 0.2 µm gap: past the range of the Faxén series, and its height changes by more than the gap allows over t',\n        fails: ['faxen-range', 'wall', 'wall-static'],\n      },\n    ],\n  },\n  /** Evaluate the Stokes-Einstein MSD and regime checks for the supplied Brownian-sphere inputs. */\n  regimeAt(inputs, outputs) {\n    const re = outputs.Re;\n    const m = outputs.m_kg;\n    const gamma = outputs.gamma_kg_per_s;\n    const t = inputs.t_s;\n    if (re == null || m == null || gamma == null || t == null) return '';\n    return `upt regime diffusion --at Re=${re} m=${m} gamma=${gamma} t=${t}`;\n  },\n  /** Compute the Stokes-Einstein diffusion, MSD and regime checks for one set of Brownian-sphere inputs. */\n  run(i) {\n    requirePositive(ID, i, ['T_K', 'eta_Pa_s', 'a_m', 'rho_p_kg_per_m3', 'rho_f_kg_per_m3', 't_s']);\n    const { T_K: T, eta_Pa_s: eta, a_m: a, rho_p_kg_per_m3: rhoP, rho_f_kg_per_m3: rhoF, t_s: t, d } = i as Record<string, number>;\n    if (d !== 1 && d !== 2 && d !== 3) throw new Error(`${ID}: d must be 1, 2 or 3 (got ${d})`);\n    const kT = K_B_SI * T;\n    const gamma = 6 * Math.PI * eta * a;\n    const D = kT / gamma;\n    const msd = 2 * d * D * t;\n    const volume = (4 / 3) * Math.PI * a ** 3;\n    const m = volume * rhoP;\n    const tauP = (m + 0.5 * volume * rhoF) / gamma;\n    const tauF = (rhoF * a * a) / eta;\n    const vSed = ((2 / 9) * (rhoP - rhoF) * G_STANDARD * a * a) / eta;\n    const re = (rhoF * a * Math.max(Math.sqrt(kT / m), Math.abs(vSed))) / eta;\n    const tauBare = m / gamma;\n    const msdLangevin = 2 * d * D * tauBare * ballisticDeficit(t / tauBare);\n    const msdHydro = msd * hydrodynamicMsdRatio(tauP / t, tauF / t);\n    const msdAddedMass = 2 * d * D * tauP * ballisticDeficit(t / tauP);\n    const memory = msdHydro / msdAddedMass - 1;\n    const checks = [\n      check('creeping-flow', 'creeping flow around the sphere, Re ≪ 1', 'ρ_f a max(√(k_BT/m), |v_s|)/η', re, '<=', MAX_RE,\n        \"the threshold ab-stokes-einstein states: a chosen machine form of Re ≪ 1\"),\n      check('overdamped', 'overdamped times t ≫ τ_p', '(m + m_f/2)/(γ t)', tauP / t, '<=', MAX_TAU_P_RATIO,\n        \"ab-stokes-einstein's m/(γt) ≤ 0.01, with the added mass m_f/2 included (stricter)\"),\n      check('memory', 'past the hydrodynamic memory, t ≫ τ_f = ρ_f a²/η', '|MSD_H/MSD_OU − 1|', Math.abs(memory), '<=', MAX_MEMORY_CORRECTION,\n        'chosen threshold: the Basset memory changes the MSD by ≤ 1% at t (computed, not estimated; ≈ 2√(τ_f/(πt)) at t ≫ τ_f)'),\n    ];\n    const unchecked = ['the particle is a rigid sphere and a is its hydrodynamic radius (a coating or a shell changes it)'];\n    let wall: { dPar: number; dPerp: number; msdWall: number } | null = null;\n    if (i.h_m !== undefined) {\n      const h = i.h_m;\n      if (!Number.isFinite(h) || !(h > a)) throw new Error(`${ID}: h_m must be a finite distance > a_m, centre to wall (got ${h})`);\n      const faxen = faxenParallel(a / h);\n      const lambda = brennerPerpendicular(h / a);\n      const dPar = D * faxen;\n      const dPerp = D / lambda;\n      const msdWall = 2 * t * (Math.min(d, 2) * dPar + (d === 3 ? dPerp : 0));\n      wall = { dPar, dPerp, msdWall };\n      const excursion = Math.sqrt(2 * dPerp * t) + (Math.abs(vSed) * t) / lambda;\n      checks.push(\n        check('faxen-range', 'the Faxén series in a/h holds for D_∥', '(a/h)⁵/16 ÷ (D_∥/D)', (a / h) ** 5 / 16 / faxen, '<=', MAX_FAXEN_LAST_TERM,\n          'chosen threshold: the last retained term is ≤ 1% of the series — a size estimate of the truncation, not a bound; D_⊥ (Brenner) is exact at any h > a'),\n        check('wall', 'the wall correction to the tracked MSD is negligible', '|MSD/MSD_w − 1|', Math.abs(msd / msdWall - 1), '<=', MAX_WALL_CORRECTION,\n          'chosen threshold: the unbounded-fluid D is then within 1% for the tracked axes; otherwise read MSD_wall_m2'),\n        check('wall-static', 'the height barely changes over t', '(√(2 D_⊥ t) + |v_s| t/λ)/(h − a)', excursion / (h - a), '<=', MAX_WALL_EXCURSION,\n          'chosen threshold: diffusion plus wall-slowed sedimentation normal to the wall move the sphere by ≤ 10% of the gap, so D_∥, D_⊥ taken at h hold over t'),\n      );\n      unchecked.push(\n        'the wall is plane, rigid, no-slip and horizontal, and the gap h − a is many molecular sizes and roughness heights (no surface forces, no lubrication-scale slip)',\n      );\n    }\n    if (d === 3) {\n      checks.push(\n        check('drift', 'sedimentation drift negligible along gravity over t', '(v_s t)²/(2 D t)', (vSed * t) ** 2 / (2 * D * t), '<=',\n          MAX_DRIFT_RATIO, 'chosen threshold: the vertical MSD then carries ≤ 1% from the deterministic drift'),\n      );\n    } else {\n      unchecked.push(\n        `the ${d === 1 ? 'tracked axis is' : 'tracked axes are'} horizontal, so sedimentation (${Number(Math.abs(vSed * t).toPrecision(3))} m over t) moves the sphere out of the plane but not along ${d === 1 ? 'it' : 'them'}`,\n      );\n    }\n    return {\n      outputs: {\n        gamma_kg_per_s: gamma,\n        D_m2_per_s: D,\n        MSD_m2: msd,\n        rms_displacement_m: Math.sqrt(msd),\n        m_kg: m,\n        tau_p_s: tauP,\n        tau_f_s: tauF,\n        v_sed_m_per_s: vSed,\n        Re: re,\n        MSD_langevin_m2: msdLangevin,\n        langevin_deviation: msd / msdLangevin - 1,\n        MSD_hydro_m2: msdHydro,\n        hydro_correction_m2: msdHydro - msd,\n        hydro_deviation: msd / msdHydro - 1,\n        memory_correction: memory,\n        D_parallel_m2_per_s: wall?.dPar ?? null,\n        D_perp_m2_per_s: wall?.dPerp ?? null,\n        MSD_wall_m2: wall?.msdWall ?? null,\n        wall_deviation: wall === null ? null : msd / wall.msdWall - 1,\n      },\n      checks,\n      unchecked,\n    };\n  },\n};\n"]}

package/dist/cases/damped-resonator.d.ts

@@ -1,23 +0,0 @@
-import { type AppliedCase } from './types.js';
-/** Q floor for the single-Lorentzian (near-resonance) form of the spectrum. @internal */
-export declare const MIN_Q_LORENTZIAN = 10;
-/** (1/t_obs)/linewidth ceiling: the record resolves the line. @internal */
-export declare const MAX_RESOLUTION_RATIO = 0.1;
-/**
- * √(k_BT/k)/A ceiling. Thermal motion of one mode is x = X cos ω_d t + Y sin ω_d t
- * with ⟨X²⟩ = ⟨Y²⟩ = k_BT/k (equipartition), so the envelope of the ring-down
- * plus it is Rician with ⟨A_obs²⟩ = A² + 2k_BT/k (Rice 1944); at the ceiling
- * √(1 + 2·0.01) − 1 ≈ 0.0100.
- * @internal
- */
-export declare const MAX_THERMAL_RATIO = 0.1;
-/**
- * FWHM in Hz of |∫₀ᵀ e^{−(α + iΔω)t} dt|², the near-resonance power spectrum of
- * a ring-down x0 e^{−αt} cos(ω_d t) recorded for T. The negative-frequency
- * pole is dropped, which is the Q ≫ 1 approximation. The peak is at Δω = 0:
- * the integrand is positive, so |X(Δω)| ≤ X(0).
- * @internal
- */
-export declare function windowedLinewidthHz(alpha: number, T: number): number;
-export declare const DAMPED_RESONATOR_CASE: AppliedCase;
-//# sourceMappingURL=damped-resonator.d.ts.map

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