quantized-lab 0.8.0__py3-none-any.whl

quantized/calc/electrical.py

@@ -0,0 +1,248 @@
+r"""Electrical transport calculators (DiraCulator ``buildElectricalTab`` +
+``+calc/+electrical``).
+
+Pure calc layer — closed-form scalars in, result dicts out. No fastapi /
+pydantic imports. Ports the seven MATLAB ``calc.electrical`` functions verbatim:
+
+.. math::
+
+    \rho = R_s\,t \qquad R_s = \rho / t \qquad \sigma = 1/\rho \\
+    \mu = \frac{1}{q\,n\,\rho} \qquad J = I / A \\
+    R_H = \frac{V_H\,t}{I\,B} \qquad n = \frac{1}{|R_H|\,q} \qquad
+    \kappa_e = \frac{L_0\,T}{\rho}
+
+Units follow the MATLAB toolbox (the behavioural reference): resistivity in
+Ω·cm, sheet resistance in Ω/sq, thickness in cm, carrier density in cm⁻³,
+mobility in cm²/(V·s), current density in A/cm², Hall coefficient in cm³/C.
+Sign convention for the Hall coefficient: ``R_H > 0`` → holes (p-type),
+``R_H < 0`` → electrons (n-type).
+
+Reference values (frozen from ``quantized_matlab``):
+  - ``resistivity(500, 2e-5) -> rho = 0.01`` Ω·cm
+  - ``sheet_resistance(1e-3, 2e-5) -> Rs = 50`` Ω/sq
+  - ``conductivity(1e-3) -> sigma = 1000`` S/cm
+  - ``mobility(1e-2, 1e18) -> mu ≈ 624.15`` cm²/(V·s)
+  - ``wiedemann_franz(300, 1.72e-6) -> kappa_e ≈ 4.26`` W/(cm·K)
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+import numpy as np
+
+from quantized.calc.constants import constants
+
+__all__ = [
+    "conductivity",
+    "current_density",
+    "hall_analysis",
+    "hall_single_point",
+    "mobility",
+    "resistivity",
+    "sheet_resistance",
+    "wiedemann_franz",
+]
+
+# Lorenz number (Sommerfeld value): L0 = pi^2 kB^2 / (3 e^2) = 2.44e-8 W*Ohm/K^2
+_LORENZ = 2.44e-8  # W*Ohm/K^2
+
+
+def _carrier_type(r_h: float) -> str:
+    """Carrier type from the sign of the Hall coefficient (+ holes, - electrons)."""
+    if r_h > 0:
+        return "hole"
+    if r_h < 0:
+        return "electron"
+    return "unknown"
+
+
+def resistivity(rs: float, t: float) -> dict[str, float]:
+    """Bulk resistivity ρ = R_s·t (Ω·cm) from sheet resistance and thickness.
+
+    Args:
+        rs: sheet resistance (Ω/sq), > 0.
+        t: film thickness (cm), > 0.
+
+    >>> round(resistivity(500.0, 2e-5)["rho"], 12)
+    0.01
+    """
+    if rs <= 0 or t <= 0:
+        raise ValueError("Rs and t must be positive")
+    return {"rho": rs * t, "Rs": rs, "t": t}
+
+
+def sheet_resistance(rho: float, t: float) -> dict[str, float]:
+    """Sheet resistance R_s = ρ/t (Ω/sq) from bulk resistivity and thickness.
+
+    >>> round(sheet_resistance(1e-3, 2e-5)["Rs"], 9)
+    50.0
+    """
+    if rho <= 0 or t <= 0:
+        raise ValueError("rho and t must be positive")
+    return {"Rs": rho / t, "rho": rho, "t": t}
+
+
+def conductivity(rho: float) -> dict[str, float]:
+    """Electrical conductivity σ = 1/ρ (S/cm) from resistivity (Ω·cm).
+
+    >>> conductivity(1e-3)["sigma"]
+    1000.0
+    """
+    if rho <= 0:
+        raise ValueError("rho must be positive")
+    return {"sigma": 1.0 / rho, "rho": rho}
+
+
+def mobility(rho: float, n: float) -> dict[str, float]:
+    """Carrier mobility μ = 1/(q·n·ρ) (cm²/V·s).
+
+    Args:
+        rho: resistivity (Ω·cm), > 0.
+        n: carrier concentration (cm⁻³), > 0.
+
+    >>> round(mobility(1e-2, 1e18)["mu"], 3)
+    624.151
+    """
+    if rho <= 0 or n <= 0:
+        raise ValueError("rho and n must be positive")
+    q = constants()["e"]
+    return {"mu": 1.0 / (q * n * rho), "rho": rho, "n": n}
+
+
+def current_density(i: float, area: float) -> dict[str, float]:
+    """Current density J = I/A (A/cm²).
+
+    >>> current_density(0.01, 0.04)["J"]
+    0.25
+    """
+    if area <= 0:
+        raise ValueError("area must be positive")
+    return {"J": i / area, "I": i, "area": area}
+
+
+def hall_single_point(v_h: float, i: float, b: float, t: float) -> dict[str, Any]:
+    """Single-point Hall analysis (DiraCulator ``doHallEffect``).
+
+    From one Hall-voltage measurement: ``R_H = V_H·t/(I·B)`` (cm³/C, with ``t``
+    in cm), majority carrier density ``n = 1/(|R_H|·q)`` (cm⁻³), and carrier
+    type from ``sign(R_H)``.
+
+    Args:
+        v_h: Hall voltage (V); sign carries the carrier type.
+        i: longitudinal current (A), non-zero.
+        b: magnetic field (T), non-zero.
+        t: sample thickness (cm), > 0.
+
+    >>> r = hall_single_point(1e-3, 1e-3, 1.0, 1e-5)
+    >>> round(r["r_h"], 8)
+    1e-05
+    >>> r["carrier_type"]
+    'hole'
+    """
+    if i == 0 or b == 0:
+        raise ValueError("Current I and field B must be non-zero")
+    if t <= 0:
+        raise ValueError("thickness t must be positive")
+    r_h = v_h * t / (i * b)  # cm^3/C
+    q = constants()["e"]
+    n_abs = float("inf") if r_h == 0 else abs(1.0 / (r_h * q))
+    return {
+        "r_h": r_h,
+        "carrier_density": n_abs,
+        "carrier_type": _carrier_type(r_h),
+    }
+
+
+def hall_analysis(
+    field: list[float],
+    hall_resistance: list[float],
+    *,
+    thickness: float | None = None,
+    field_unit: str = "T",
+    sigma: float | None = None,
+) -> dict[str, Any]:
+    """Single-carrier Hall analysis from an R_xy vs H sweep (``hallAnalysis.m``).
+
+    Linear-fits ``R_xy = R_H·H + offset`` (normal equations, no toolbox), then
+    converts the slope to a Hall coefficient in cm³/C, deduces carrier type and
+    density, and — if σ is supplied — the Hall mobility ``μ_H = |R_H|·σ``.
+
+    Args:
+        field: magnetic field vector (T, or Oe if ``field_unit='Oe'``).
+        hall_resistance: transverse resistance/resistivity R_xy.
+        thickness: sample thickness (cm); needed for a bulk R_H / carrier density.
+        field_unit: ``'T'`` (default) or ``'Oe'`` (converted via 1 Oe = 1e-4 T).
+        sigma: longitudinal conductivity σ (S/cm) for the Hall mobility.
+
+    Returns a dict with ``r_h`` (cm³/C), ``carrier_density`` (cm⁻³),
+    ``carrier_type``, ``mobility`` (cm²/V·s), and ``fit_r2``.
+    """
+    h = np.asarray(field, dtype=float)
+    ry = np.asarray(hall_resistance, dtype=float)
+    if h.size != ry.size:
+        raise ValueError("field and hall_resistance must have the same length")
+    if h.size < 2:
+        raise ValueError("at least 2 data points are required for a linear fit")
+
+    unit = field_unit.upper()
+    if unit not in ("T", "OE"):
+        raise ValueError("field_unit must be 'T' or 'Oe'")
+    if unit == "OE":
+        h = h * 1e-4  # CGS -> SI
+
+    hm = float(h.mean())
+    rm = float(ry.mean())
+    sxx = float(np.sum((h - hm) ** 2))
+    sxy = float(np.sum((h - hm) * (ry - rm)))
+    if sxx < np.finfo(float).eps:
+        raise ValueError("field range is effectively zero; cannot compute Hall slope")
+
+    slope = sxy / sxx  # Ohm/T (or Ohm*cm/T)
+    intercept = rm - slope * hm
+    ry_fit = slope * h + intercept
+    ss_tot = float(np.sum((ry - rm) ** 2))
+    ss_res = float(np.sum((ry - ry_fit) ** 2))
+    fit_r2 = 1.0 if ss_tot < np.finfo(float).eps else 1.0 - ss_res / ss_tot
+
+    # R_H [cm^3/C] = slope [Ohm/T] * t_cm * 1e4; t=1 cm placeholder when absent.
+    r_h = slope * thickness * 1e4 if thickness is not None else slope * 1e4
+
+    q = constants()["e"]
+    if thickness is not None and abs(r_h) > 0:
+        carrier_density: float = 1.0 / (abs(r_h) * q)
+    else:
+        carrier_density = float("nan")
+    mu = abs(r_h) * sigma if sigma is not None else float("nan")
+
+    return {
+        "r_h": r_h,
+        "carrier_density": carrier_density,
+        "carrier_type": _carrier_type(r_h),
+        "mobility": mu,
+        "fit_r2": fit_r2,
+    }
+
+
+def wiedemann_franz(
+    temperature: float | list[float], resistivity_ohm_cm: float | list[float]
+) -> dict[str, Any]:
+    """Electronic thermal conductivity κ_e = L₀·T/ρ (W/(cm·K)).
+
+    L₀ = 2.44e-8 W·Ω/K² is the Sommerfeld Lorenz number. Scalars broadcast; a
+    list T with a scalar ρ (and vice versa) is supported.
+
+    >>> round(wiedemann_franz(300.0, 1.72e-6)["kappa"][0], 4)
+    4.2558
+    """
+    t = np.atleast_1d(np.asarray(temperature, dtype=float))
+    rho = np.atleast_1d(np.asarray(resistivity_ohm_cm, dtype=float))
+    if t.size == 1 and rho.size > 1:
+        t = np.full(rho.shape, t[0])
+    if rho.size == 1 and t.size > 1:
+        rho = np.full(t.shape, rho[0])
+    if t.size != rho.size:
+        raise ValueError("temperature and resistivity must be the same size, or one scalar")
+    with np.errstate(divide="ignore", invalid="ignore"):
+        kappa = _LORENZ * t / rho
+    return {"kappa": kappa.tolist(), "temperature": t.tolist(), "lorenz": _LORENZ}

quantized/calc/electrochemistry.py

@@ -0,0 +1,176 @@
+r"""Electrochemistry calculators (DiraCulator ``buildElectrochemistryTab`` +
+``+calc/+electrochemistry``).
+
+Pure calc layer — closed-form scalars in, result dicts out. No fastapi /
+pydantic imports. Ports the five MATLAB ``calc.electrochemistry`` functions
+verbatim:
+
+.. math::
+
+    E = E^0 - \frac{R\,T}{n\,F}\,\ln Q \\
+    j = j_0\!\left[e^{\alpha F\eta/RT} - e^{-(1-\alpha)F\eta/RT}\right] \\
+    b = \frac{2.303\,R\,T}{\alpha\,F} \qquad V_{IR} = I\,R \\
+    C = \frac{\varepsilon_0\,\varepsilon_r\,A}{d}
+
+Units follow the MATLAB toolbox (the behavioural reference): potentials in V,
+current density in A/cm², Tafel slope in V/decade (and mV/decade), resistance
+in Ω, double-layer thickness ``d`` in nm, electrode area ``A`` in cm²,
+capacitance in F (plus µF, pF, and F/cm² specific). Temperatures default to
+298.15 K (25 °C). The MATLAB ``latex`` result field is intentionally omitted.
+
+Reference values (closed-form, see ``test_electrochemistry``):
+  - ``nernst_potential(0.77, 1, 0.01) -> E ≈ 0.8883`` V (25 °C)
+  - ``tafel_slope(0.5) -> bMv ≈ 118.3`` mV/dec (25 °C)
+  - ``ohmic_drop(1e-3, 50) -> V = 0.05`` V (50 mV)
+  - ``double_layer_capacitance(78, 0.5, 1.0) -> C ≈ 138`` µF
+"""
+
+from __future__ import annotations
+
+import math
+from typing import Any
+
+from quantized.calc.constants import constants
+
+__all__ = [
+    "butler_volmer",
+    "double_layer_capacitance",
+    "nernst_potential",
+    "ohmic_drop",
+    "tafel_slope",
+]
+
+_T_STANDARD = 298.15  # K (25 °C), MATLAB default temperature
+
+
+def nernst_potential(e0: float, n: float, q: float, *, t: float = _T_STANDARD) -> dict[str, float]:
+    """Nernst equilibrium electrode potential E = E⁰ − (R·T)/(n·F)·ln(Q) (V).
+
+    Args:
+        e0: standard electrode potential E⁰ (V).
+        n: number of electrons transferred (> 0).
+        q: reaction quotient (dimensionless, > 0).
+        t: temperature (K, > 0); default 298.15.
+
+    >>> round(nernst_potential(0.77, 1, 0.01)["E"], 4)
+    0.8883
+    """
+    if n <= 0:
+        raise ValueError("n must be positive")
+    if q <= 0:
+        raise ValueError("Q must be positive")
+    if t <= 0:
+        raise ValueError("T must be positive")
+    c = constants()
+    e = e0 - (c["R"] * t) / (n * c["F"]) * math.log(q)
+    return {"E": e, "E0": e0, "n": n, "Q": q, "T": t}
+
+
+def butler_volmer(
+    j0: float, eta: float, *, alpha: float = 0.5, t: float = _T_STANDARD
+) -> dict[str, float]:
+    """Butler-Volmer electrode current density (A/cm²).
+
+    j = j₀·[exp(α·F·η/RT) − exp(−(1−α)·F·η/RT)], with anodic/cathodic partials
+    and the large-overpotential Tafel approximation jTafel = j₀·exp(α·F·η/RT).
+
+    Args:
+        j0: exchange current density (A/cm², > 0).
+        eta: overpotential (V); positive = anodic.
+        alpha: transfer coefficient (0 < α < 1); default 0.5.
+        t: temperature (K, > 0); default 298.15.
+
+    >>> round(butler_volmer(1e-3, 0.0)["j"], 12)
+    0.0
+    """
+    if j0 <= 0:
+        raise ValueError("j0 must be positive")
+    if not (0 < alpha < 1):
+        raise ValueError("alpha must satisfy 0 < alpha < 1")
+    if t <= 0:
+        raise ValueError("T must be positive")
+    c = constants()
+    f_over_rt = c["F"] / (c["R"] * t)
+    try:
+        j_anodic = j0 * math.exp(alpha * f_over_rt * eta)
+        j_cathodic = -j0 * math.exp(-(1.0 - alpha) * f_over_rt * eta)
+        j = j_anodic + j_cathodic
+        j_tafel = j0 * math.exp(alpha * f_over_rt * eta)
+    except OverflowError as exc:
+        raise ValueError(
+            "overpotential eta is too large: the Butler-Volmer exponential "
+            "overflows (use a physical |eta|, well under ~30 V)"
+        ) from exc
+    return {
+        "j": j,
+        "jAnodic": j_anodic,
+        "jCathodic": j_cathodic,
+        "jTafel": j_tafel,
+    }
+
+
+def tafel_slope(alpha: float, *, t: float = _T_STANDARD) -> dict[str, float]:
+    """Tafel slope b = 2.303·R·T/(α·F) (V/decade and mV/decade).
+
+    Args:
+        alpha: transfer coefficient (0 < α < 1).
+        t: temperature (K, > 0); default 298.15.
+
+    >>> round(tafel_slope(0.5)["bMv"], 1)
+    118.3
+    """
+    if not (0 < alpha < 1):
+        raise ValueError("alpha must satisfy 0 < alpha < 1")
+    if t <= 0:
+        raise ValueError("T must be positive")
+    c = constants()
+    b = 2.303 * c["R"] * t / (alpha * c["F"])
+    return {"b": b, "bMv": b * 1000.0}
+
+
+def ohmic_drop(i: float, r: float) -> dict[str, float]:
+    """Ohmic (iR) voltage drop V = I·R (V and mV).
+
+    Args:
+        i: current (A); positive = anodic.
+        r: uncompensated cell resistance (Ω, ≥ 0).
+
+    >>> ohmic_drop(1e-3, 50)["V"]
+    0.05
+    """
+    if r < 0:
+        raise ValueError("R must be non-negative")
+    v = i * r
+    return {"V": v, "VmV": v * 1000.0}
+
+
+def double_layer_capacitance(epsilon: float, d: float, area: float) -> dict[str, Any]:
+    """Parallel-plate double-layer capacitance C = ε₀·ε_r·A/d.
+
+    Internally converts d (nm → m) and A (cm² → m²); returns capacitance in F,
+    µF, pF, and the specific capacitance per unit area (F/cm²).
+
+    Args:
+        epsilon: relative permittivity ε_r (dimensionless, > 0).
+        d: layer thickness (nm, > 0).
+        area: electrode area (cm², > 0).
+
+    >>> round(double_layer_capacitance(78, 0.5, 1.0)["CuF"], 1)
+    138.1
+    """
+    if epsilon <= 0:
+        raise ValueError("epsilon must be positive")
+    if d <= 0:
+        raise ValueError("d must be positive")
+    if area <= 0:
+        raise ValueError("area must be positive")
+    c = constants()
+    d_m = d * 1e-9  # nm -> m
+    area_m2 = area * 1e-4  # cm^2 -> m^2
+    cap = c["eps0"] * epsilon * area_m2 / d_m  # F
+    return {
+        "C": cap,
+        "CuF": cap * 1e6,
+        "CpF": cap * 1e12,
+        "Cspec": cap / area,  # F/cm^2
+    }

quantized/calc/element_data.json

@@ -0,0 +1 @@
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quantized/calc/element_data.py

@@ -0,0 +1,59 @@
+"""Periodic-table data for all 118 elements. Port of calc.elementData.
+
+The element table itself lives in ``element_data.json`` (dumped verbatim from
+MATLAB ``calc.elementData()`` for exact data parity); this module just loads it
+and exposes the lookup API. Pure calc layer.
+"""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+from numpy.typing import NDArray
+
+__all__ = ["by_symbol", "by_z", "element_data", "get_property"]
+
+_DATA_PATH = Path(__file__).parent / "element_data.json"
+_ELEMENTS: list[dict[str, Any]] | None = None
+
+
+def _load() -> list[dict[str, Any]]:
+    global _ELEMENTS
+    if _ELEMENTS is None:
+        _ELEMENTS = json.loads(_DATA_PATH.read_text(encoding="utf-8"))
+    return _ELEMENTS
+
+
+def element_data() -> list[dict[str, Any]]:
+    """Return the full 118-element table (list of element dicts)."""
+    return _load()
+
+
+def by_symbol(symbol: str) -> dict[str, Any]:
+    """Look up a single element by symbol (e.g. 'Fe'). Raises if not found."""
+    for el in _load():
+        if el["symbol"] == symbol:
+            return el
+    raise ValueError(f"element symbol '{symbol}' not found")
+
+
+def by_z(z: int) -> dict[str, Any]:
+    """Look up a single element by atomic number Z (1-118)."""
+    if z < 1 or z > 118:
+        raise ValueError("Z must be between 1 and 118")
+    return _load()[z - 1]
+
+
+def get_property(name: str) -> NDArray[np.float64] | list[Any]:
+    """Return a property across all 118 elements.
+
+    Numeric properties return a float array (MATLAB NaN -> null -> nan);
+    non-numeric properties (e.g. 'symbol', 'category') return a list.
+    """
+    vals = [el[name] for el in _load()]
+    if all(v is None or (isinstance(v, int | float) and not isinstance(v, bool)) for v in vals):
+        return np.array(vals, dtype=float)
+    return vals