npm - driftlet - Versions diffs - 0.12.0 → 0.14.0 - Mend

driftlet 0.12.0 → 0.14.0

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package/README.md CHANGED Viewed

@@ -8,21 +8,33 @@
 [![test](https://github.com/markblundeberg/driftlet/actions/workflows/test.yml/badge.svg)](https://github.com/markblundeberg/driftlet/actions/workflows/test.yml)
 [![npm](https://img.shields.io/npm/v/driftlet)](https://www.npmjs.com/package/driftlet)
-**driftlet is a fast, pure-JavaScript solver for 1D drift–diffusion–reaction problems**, built
-to be the engine of live, thermodynamically honest web demos of charge transport: in
-semiconductors, electrochemical cells, membranes and solid ionic conductors. It handles any mix
-of charged and neutral species, Poisson electrostatics (or strict neutrality), bulk and
-interfacial reactions, heterointerfaces, metals and external circuits, in steady state, in time
-and as small-signal impedance. It's small enough to run in a web page: no dependencies,
-millisecond solves.
+**driftlet simulates charged species moving through one-dimensional devices**: semiconductor
+junctions and solar cells, electrochemical cells and batteries, double layers, membranes and
+nerves. It's a small JavaScript library with no dependencies, fast enough to solve live in a
+web page as you drag a slider.
 [Live demos](https://markblundeberg.github.io/driftlet/demos/) · [npm](https://www.npmjs.com/package/driftlet) ·
 [reading level diagrams](docs/visualization.md) · [device reference](docs/device.md) ·
 [agent guide](llms.txt)
+**One kind of physics.** Those look like different subjects, but underneath they're the same
+one. Each is a cast of species (electrons, holes, ions, neutral molecules) that drift and
+diffuse, each down its own electrochemical potential; their charge sets the electric field,
+reactions turn one into another, and at interfaces they pass from one material to the next or
+are stopped. A pn junction is electrons and holes in silicon. A silver electrode is Ag⁺ and NO₃⁻
+in water, with Ag⁺ trading places with the metal's electrons at its surface. A nerve is Na⁺ and
+K⁺ on either side of a membrane, crossing it through channels that open with voltage, and the
+impulse travels along the fibre on the current those same ions carry inside it. Even the levels
+each field draws are one quantity: a quasi-Fermi level, an electrode potential and a Nernst
+potential are each a species' electrochemical potential. driftlet solves that one problem, in
+steady state, in time and as small-signal impedance, so a new field is mostly a new cast, and
+the work that makes it reliable in one field makes it reliable in the others.
 **Built to be relied on.** A drift–diffusion solver that handles a textbook pn junction is a
-weekend's work; one that keeps working on the devices people actually build is not. driftlet is
-tested two ways: every physics feature against an analytic result or an independent code, and
+weekend's work; one that keeps working on the devices people actually build is not. In real
+devices concentrations span 30 orders of magnitude and double layers are a millionth of the
+device's length, and there a plain Newton solver fails or, worse, quietly converges to a wrong
+answer. driftlet is tested two ways: every physics feature against an analytic result or an independent code, and
 thousands of randomly generated devices (junctions, MOS capacitors, solar cells, electrolyte
 cells, electrodes) put through cold solves, sweeps, transients and impedance, every result
 checked. A solve that fails reports it, with what went wrong where it can tell.
@@ -44,7 +56,7 @@ import { bandDiagram } from 'driftlet/plot';    // a level diagram as an SVG str
 ```
 Or straight from a CDN in a page, pinned to a version:
-`https://cdn.jsdelivr.net/npm/driftlet@0.12.0/src/index.js` (and `src/kit.js`, `src/plot.js`).
+`https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/index.js` (and `src/kit.js`, `src/plot.js`).
 TypeScript declarations ship in the package. Writing a demo with an LLM agent? Point it at
 [`llms.txt`](llms.txt).
@@ -149,19 +161,19 @@ them locally, serve the repository root (e.g. `python3 -m http.server`) and open
 The same equations go by different names in different fields. If your problem is one-dimensional
 (planar, or radial: spheres and cylinders, or any cross-section varying along x), it's probably here:
-| If you work on | you may call it | start from | checked against |
-|---|---|---|---|
-| Semiconductor devices | drift–diffusion, van Roosbroeck, quasi-Fermi levels, Scharfetter–Gummel; pn, Schottky, MOS, heterojunctions; thin-film transistors (gradual channel, in the [saturation demo](https://markblundeberg.github.io/driftlet/demos/saturation.html#transistor)) | [first example](#a-semiconductor-junction), [pn](https://markblundeberg.github.io/driftlet/demos/pn.html) and [MOS](https://markblundeberg.github.io/driftlet/demos/mos.html) demos, [`contacts`](test/contacts.test.js), [`metal`](test/metal.test.js) tests | exact built-in potential, Shockley J–V, depletion charge, MOS C–V |
-| Solar cells | photogeneration, radiative and SRH recombination | [solar](https://markblundeberg.github.io/driftlet/demos/solar.html) [organic (excitons)](https://markblundeberg.github.io/driftlet/demos/organic.html) and [perovskite (mobile ions)](https://markblundeberg.github.io/driftlet/demos/perovskite.html) demos, [`ionmonger`](test/ionmonger.test.js), [`reactions`](test/reactions.test.js) and [`generation`](test/generation.test.js) tests: generation is a reaction from a photon reservoir (uniform, or Beer–Lambert with `photogeneration()`), SRH as a rate law, in the bulk and at faces | `J_sc = qG(L_n + L_p + W)`; J_sc under Beer–Lambert against collection theory; Shockley J–V in the dark |
-| Electrochemistry, corrosion | Nernst–Planck, concentration polarization, limiting current, Butler–Volmer, Warburg, cyclic voltammetry, salt bridges and liquid junctions, mixed potentials, electrodes under a film | [second example](#an-electrochemical-cell), [cyclic voltammetry](https://markblundeberg.github.io/driftlet/demos/redox.html), [Daniell cell](https://markblundeberg.github.io/driftlet/demos/daniell.html), [saturation](https://markblundeberg.github.io/driftlet/demos/saturation.html), [impedance](https://markblundeberg.github.io/driftlet/demos/impedance.html) and [liquid-junction](https://markblundeberg.github.io/driftlet/demos/junction.html) demos, [`circuit`](test/circuit.test.js), [`kinetics`](test/kinetics.test.js), [`impedance`](test/impedance.test.js), [`junction`](test/junction.test.js), [`ports`](test/ports.test.js) tests | `i_lim·tanh(V/4V_T)`, Butler–Volmer closed form, finite-length Warburg; junction potentials against Henderson, Planck, JPCalc and LJPcalc; Wagner–Traud |
-| Batteries, intercalation | OCV, insertion hosts, chemical diffusion | [insertion demo](https://markblundeberg.github.io/driftlet/demos/insertion.html), [`statistics`](test/statistics.test.js) test | composition vs OCV, π²D/4L² relaxation |
-| Double layers, colloids | Poisson–Boltzmann, Gouy–Chapman–Stern, Debye screening, crowding (Bikerman) | [double-layer demo](https://markblundeberg.github.io/driftlet/demos/double-layer.html), [`equilibrium`](test/equilibrium.test.js) test | Gouy–Chapman charge and profile, Kilic–Bazant–Ajdari |
-| Membranes, desalination | Donnan, ion exchange, liquid junctions, water dissociation | [membrane demo](https://markblundeberg.github.io/driftlet/demos/membrane.html), [`equilibrium`](test/equilibrium.test.js), [`neutral`](test/neutral.test.js) tests | Donnan partition, Planck EMF |
-| Solid-state ionics | mixed ionic–electronic conduction, defect chemistry, mobile ions | [`statistics`](test/statistics.test.js), [`reactions`](test/reactions.test.js) tests | mass action from standard potentials |
-| Biophysics, nanofluidics | charged nanochannels and pores, resting potentials, Goldman–Hodgkin–Katz, Nernst, Donnan, pumps and leaks | [charged-nanochannel](https://markblundeberg.github.io/driftlet/demos/channel.html), [resting-potential](https://markblundeberg.github.io/driftlet/demos/cell.html), [action-potential](https://markblundeberg.github.io/driftlet/demos/axon.html) and [liquid-junction](https://markblundeberg.github.io/driftlet/demos/junction.html) (a patch pipette's) demos, [`pore`](test/pore.test.js) test; a membrane as a face: a capacitor with ion permeabilities, and the Na⁺/K⁺ pump as a reaction on it ([`membrane`](test/membrane.test.js) test); voltage-gated channels with Hodgkin–Huxley kinetics, action potentials, and their propagation along an axon ([`gates`](test/gates.test.js), [`cable`](test/cable.test.js) tests) | GHK potential and current–voltage curve; a resolved lipid layer; Mullins–Noda; the pump's static head; Donnan; HH gating under voltage clamp; the space-clamped HH equations |
-The tests are worked setups, each with its analytic check, so they double as recipes. The
-[validation table](#validation) lists them all.
+| If you work on | you may call it | start from |
+|---|---|---|
+| Semiconductor devices | drift–diffusion, van Roosbroeck, quasi-Fermi levels, Scharfetter–Gummel; pn, Schottky, MOS, heterojunctions, thin-film transistors | the [first example](#a-semiconductor-junction); [pn](https://markblundeberg.github.io/driftlet/demos/pn.html), [MOS](https://markblundeberg.github.io/driftlet/demos/mos.html) and [transistor](https://markblundeberg.github.io/driftlet/demos/saturation.html#transistor) demos |
+| Solar cells | photogeneration, Beer–Lambert, radiative and SRH recombination, excitons, mobile ions | [solar](https://markblundeberg.github.io/driftlet/demos/solar.html), [organic](https://markblundeberg.github.io/driftlet/demos/organic.html) and [perovskite](https://markblundeberg.github.io/driftlet/demos/perovskite.html) demos |
+| Electrochemistry, corrosion | Nernst–Planck, concentration polarization, limiting current, Butler–Volmer, Warburg, cyclic voltammetry, salt bridges, liquid junctions, mixed potentials | the [second example](#an-electrochemical-cell); [cyclic voltammetry](https://markblundeberg.github.io/driftlet/demos/redox.html), [Daniell cell](https://markblundeberg.github.io/driftlet/demos/daniell.html), [limiting current](https://markblundeberg.github.io/driftlet/demos/saturation.html), [impedance](https://markblundeberg.github.io/driftlet/demos/impedance.html) and [liquid-junction](https://markblundeberg.github.io/driftlet/demos/junction.html) demos |
+| Batteries, intercalation | OCV, insertion hosts, chemical diffusion | [insertion](https://markblundeberg.github.io/driftlet/demos/insertion.html) demo |
+| Double layers, colloids | Poisson–Boltzmann, Gouy–Chapman–Stern, Debye screening, crowding (Bikerman) | [double-layer](https://markblundeberg.github.io/driftlet/demos/double-layer.html) demo |
+| Membranes, nanofluidics | Donnan, ion exchange, Teorell–Meyer–Sievers, charged nanochannels and pores | [membrane](https://markblundeberg.github.io/driftlet/demos/membrane.html) and [nanochannel](https://markblundeberg.github.io/driftlet/demos/channel.html) demos |
+| Solid-state ionics | mixed ionic–electronic conduction, defect chemistry, mobile ions | [`statistics`](test/statistics.test.js) and [`reactions`](test/reactions.test.js) tests |
+| Cell physiology, neuroscience | resting potential, Nernst, Goldman–Hodgkin–Katz, the Na⁺/K⁺ pump, patch pipettes, Hodgkin–Huxley, action potentials, the cable equation, myelin | [resting-potential](https://markblundeberg.github.io/driftlet/demos/cell.html), [action-potential](https://markblundeberg.github.io/driftlet/demos/axon.html), [propagation](https://markblundeberg.github.io/driftlet/demos/propagation.html) and [myelin](https://markblundeberg.github.io/driftlet/demos/myelin.html) demos |
+The tests are worked setups, each with its analytic check, so they double as recipes; the
+[validation table](docs/reliability.md#the-validation-table) lists them all.
 ## How to think about it
@@ -180,10 +192,12 @@ driftlet insists on thermodynamically honest concepts ([conventions](docs/conven
 - The species voltage `V_i = μ̄_i / (z_i F)` and standard level `V°_i` are available as views,
   alongside redox levels: [reading level diagrams](docs/visualization.md) explains them.
+## What it does
 A device is a line of **regions** (each a **material** plus a length, fixed charge and
 initial composition), joined at **interfaces**, with a **contact** at each end. The contacts
 and any internal **ports** are its **terminals**, each held at a voltage or driven by a
-current. Supported physics:
+current. Within that:
 - any mix of charged and neutral species; per-material diffusivities and standard potentials;
   species absent from some materials;
@@ -196,11 +210,15 @@ current. Supported physics:
   conductivity: Schottky and MOS gates as regions, electrodes with reactions at their faces,
   bipolar electrodes;
 - contacts as outside phases with known levels, joined by the same laws as internal faces:
-  ohmic contacts, reversible electrodes, baths, pinned barriers, conductance links, gates and
+  ohmic contacts, reversible electrodes, baths, pinned barriers, conductance links, surface
+  velocities (thermionic emission over a Schottky barrier, surface recombination), gates and
   Stern layers;
 - interfaces with explicit alignment, blocking, interface resistance, and Butler–Volmer
   reactions with participants on either side (electrode reactions, ion and electron transfer,
   mixed potentials), and a choice of electrostatic law (pinned, neutral, Helmholtz);
+- membranes as capacitive faces with ion permeabilities (Goldman–Hodgkin–Katz), pumps as
+  reactions on them and voltage-gated channels with Hodgkin–Huxley kinetics; or spread along a
+  region through a port, as an axon's wall;
 - bulk reactions with thermodynamically consistent mass action (recombination, water
   autoionisation, …);
 - imposed flow (advection) and current-free eddy mixing;
@@ -235,57 +253,11 @@ How it works numerically is in [numerics](docs/numerics.md).
 ## Validation
-Every physics feature is tested against analytic results (`npm test`, node's built-in runner).
-| What | Checked against | Tolerance |
-|---|---|---|
-| Equilibrium of any device | μ̄ of every species flat; zero current | 1e-9 RT or better |
-| Gouy–Chapman double layer | analytic charge and full nonlinear profile | 2e-3 |
-| Debye screening (linear limit) | gate in series with `ε/λ_D` | 1e-3 |
-| Donnan potential | analytic partition, between floating layers and real baths | 1e-8 |
-| Heterointerfaces with unequal dipoles (A \| B \| A) | per-face analytic double-layer split | 3e-3 |
-| Floating island | Gauss's law; conserved amounts through gate sweeps | 1e-12 |
-| pn junction | exact built-in potential; depletion charge; short-diode J–V | 1e-12; 1%; 2e-3 |
-| Long pn diode with recombination | Shockley J–V incl. depletion recombination | 2e-3 |
-| Haynes–Shockley pulse | an injected hole packet's drift, spread and decay at the ambipolar μ*, D*, 1/τ*; nothing lost while it goes in | 2e-4; 1e-2; 2e-3 |
-| A packet laid down as a `c0` profile | the same rates from a Gaussian at t = 0: μ*E t, σ₀² + 2D*t, e^(−t/τ*) | 3e-4; 1e-2; 1e-3 |
-| Beer–Lambert photogeneration in an n⁺p cell | J_sc = qΦ∫αe^(−αx)η(x)dx with the emitter's, depletion layer's and base's collection, α from 1e3 to 1e7 /m on one coarse grid | 5e-4 (3e-3 in the emitter) |
-| Organic bilayer: excitons | J_sc from excitons diffusing to the donor/acceptor interface (Beer–Lambert, a blocking anode, the splitting reaction's finite velocity); V_oc from charge-transfer detailed balance | 5e-4; 1e-6 V |
-| SRH recombination | bulk: G = R_SRH(n, p) with n = N_D + p, midgap and shallow traps, low to high injection; at a face: zero in the dark, the law between the two edge nodes, every pair collected or recombined | 1e-6; 1e-9 |
-| Perovskite J–V hysteresis, against IonMonger | an independent code (finite elements, Octave): mobile iodide vacancies, interface SRH, scans from 1 mV/s to 1 kV/s — hysteresis index, P_max, V_oc, the whole loop (as current where it's gentle, as a voltage offset near V_oc, where it falls at up to 1100 mA/cm² per volt) | 1.5e-3; 0.05 mW/cm²; 2 mV; 0.03 mA/cm² and 1 mV (0.010 and 0.31 mV found) |
-| Illuminated long pn diode | `J_sc = qG(L_n + L_p + W)` from a cold start; superposition at low injection | 5e-3; 1e-2 |
-| Schottky barrier (metal region \| n-Si) | surface density from the alignment; depletion charge | 5e-3; 2% |
-| Charged pore or nanochannel (resolved Donnan layers at each mouth) | conductance against salt, down to its plateau, as Teorell–Meyer–Sievers in a long pore (short ones short by end layers ∝ 1/L); the zero-current voltage across a salt gradient; a symmetric pore's I–V odd, rectification with charge on one side or bipolar | 1%; 5e-3 to 1e-4; 1e-9 |
-| Cell membrane (a capacitive face with permeabilities) | GHK resting potential (neutral or resolved solutions) and current–voltage curve; the same as a resolved 5 nm lipid layer; charging at I/C; with the Na⁺/K⁺ pump in a closed cell, Mullins–Noda, the static head 3Δμ̄_Na − 2Δμ̄_K = ΔG_ATP, and Donnan with the pump off | 1e-5 V; 3e-3; 2e-5 V; 1%; 1e-9 |
-| Voltage-gated channels (Hodgkin–Huxley gates on a membrane face) | each gate at α/(α + β) under a voltage clamp, and relaxing at α + β after a step; a squid axon's action potential against the space-clamped HH equations with GHK currents; its impedance at rest (inductive, resonant) against the linearised equations | 1e-12; 2e-4; 1 mV; 5e-4 |
-| A propagating action potential (a squid axon along x: gated membrane port, ions drifting in the axoplasm) | rest at HH's −65 mV and gate values; conduction velocity against the cable equation solved directly, and HH's 18.8 m/s; a myelinated axon's saltatory conduction, node by node, against a compartmental cable | 0.01 mV, 1e-4; 2e-3; 1%; 1 µs of ~25 per node |
-| Liquid junctions in mixtures | Henderson's formula against JPCalc's published values; driftlet's steady junction against Planck by shooting and the stationary Nernst–Planck codes LJPcalc and JLJP, a patch pipette's K-gluconate among them; a free-diffusion junction constant in time, between the two | 0.015 mV; 2e-4 and 0.02 mV; 5e-3 mV |
-| Liquid junction, open circuit | cell EMF 2t₊(RT/F) ln(c₁/c₂); Planck diffusion potential | 1e-4 |
-| Salt diffusion mode from a `c0` profile | c̄ + a·sin(πx/2L) decaying at π²D/4L², D = 2D₊D₋/(D₊ + D₋) | 2e-5 |
-| Concentration polarization | `i = i_lim tanh(V/4V_T)`, incl. galvanostatic and load modes | 2e-4 |
-| Butler–Volmer electrode | Nernst equilibrium; mixed kinetic/diffusion closed form | 5e-4 |
-| Redox couple between inert electrodes | Nernst level of Fe³⁺/Fe²⁺; the couple's total conserved at equilibrium and under current | 1e-9; 1e-10 |
-| Interface conductance and ion transfer | series 1/G; BV rate law at the interface state | 1e-4; 1e-8 |
-| Mass action | `c(H⁺)c(OH⁻) = K_w` from standard potentials; moiety conservation | 1e-9 |
-| Second law | free energy in through the terminals (Σ N μ̄ over every species) equals the dissipation, every term ≥ 0: a pn diode, an open-circuit junction running on chemical input alone, electrodes with a bipolar plate, a port and a contact behind conductances | 1e-10 |
-| Transients | RC charging of a gated island; water relaxation rate | 1%; 2e-3 |
-| Time integration | BE first order, BDF2 second order; adaptive error control | ratios 2, 4 |
-| Advection and eddy mixing | exact convection–diffusion profile; `D + D_mix`; junction EMF unchanged by mixing | 1e-12; 1e-12; 1e-5 |
-| Metal regions | ohmic; Schottky face and MOS gate equal their contact forms; Ag \| AgNO₃ \| Ag with metal electrodes; bipolar electrode at V/2 | 1e-12; 1e-9; 1e-9; 1e-9 |
-| Internal ports | transmission line σV tanh(L/λ)/λ (O(h²)); held level; MOS low-frequency C–V with a grounded channel, and without one the same equilibrium, and a gate step filling the inversion layer to it | 1e-4; 1e-9; 2e-3; 1e-6; 1e-3 |
-| Cross-sections (spherical, cylindrical, any A(x)) | steady diffusion to a sphere and a cylinder (exact on any grid); Cottrell with the spherical term; uptake by a sphere filling from its surface; Debye–Hückel around a charged sphere, potential and charge | 1e-10; 3e-4; 2e-4; 1e-3, 3e-4 |
-| A capacitance through a port | a thin-film transistor against the charge-sheet model (below threshold to saturation, second order); de Levie impedance; gate impedance against dQ/dV | 5e-4; 1e-3; 1e-6 |
-| Electrode surfaces (coverage) | Langmuir isotherm against potential; the charge to fill a surface; the active–passive curve, blocking exactly (1 − θ) | 1e-9; 1e-3; 1e-9 |
-| Electrodes spread through a port | transmission line with the reaction's linear kinetics as the conductance (O(h²)), rates along it; Wagner–Traud mixed potential of two Butler–Volmer couples, floating | 1e-4, 2e-3; 1e-6 V |
-| Impedance | Macdonald blocking-electrode spectrum, 100 Hz–1 GHz; finite-length Warburg (Ag \| AgNO₃ \| Ag); DC limit = differential resistance; a p⁺n⁺ junction without recombination, Re Y → dI/dV and C = dQ/dV; a redox electrode against a bath at its open circuit, Re Y → dI/dV | 3e-4; 3e-5; 1e-6; 1e-4, 1e-6; 1e-4 |
-| Conservation | per step, and against time-integrated contact fluxes | 1e-11 relative |
-| Strictly neutral limit (ε = 0) | Planck EMF; polarization with no overlimiting; Donnan at neutral faces | 1e-5; 1e-4; 1e-9 |
-| Fermi–Dirac statistics | `𝓕_{±1/2}` vs quadrature; degenerate bulk; accumulation charge via `𝓕_{3/2}` | 1e-13; 1e-12; 1e-3 |
-| Crowded double layer (lattice gas) | Kilic–Bazant–Ajdari charge, up to `ψ = 40 V_T`; custom function reproduces it | 5e-4; 1e-10 |
-| Non-ideal transport | steady flux −(D/L)ΔP of the grand potential (lattice exact, Redlich–Kister O(h²)) | 1e-12; 1e-4 |
-| Debye–Hückel | junction EMF 2t₊(RT/F) ln(a₁/a₂) with activities | 1e-6 |
-| Data library | ion μ° against the electrochemical series and `K_w`; D against limiting conductivities; band data against `n_i` | 10 mV; 0.5%; 15% |
-| Intercalation host (OCV) | composition vs table and isotherm; chemical diffusion flux and relaxation rate | 1e-12; 1e-5; 1e-4 |
+Every physics feature lands with a test against an analytic result, or against an independent
+code where there isn't one: over 300 tests (`npm test`), from Shockley's diode equation and the
+Gouy–Chapman double layer to Hodgkin and Huxley's conduction velocity, and against IonMonger,
+JPCalc, LJPcalc and JLJP. [How far to trust it](docs/reliability.md) lists every check with its
+tolerance, alongside the random-device stress tests and the known limits.
 ## Performance

package/docs/device.md CHANGED Viewed

@@ -114,7 +114,10 @@ regions: [
   injected hole packet); what the cold start leaves unbalanced settles within the first steps.
   That fill-in is right in a quasi-neutral bulk (it's what dielectric relaxation would do), not
   where the rest state carries charge: a packet laid into a junction starts with the junction
-  itself unformed.
+  itself unformed. The grid isn't refined to fit a profile: where it's steeper than the cells
+  under it, the start is the profile sampled at the nodes, something else, and every solution
+  warns of it with the cells that would resolve it (grade toward it, or put a region boundary
+  there).
   For a spectator, the profile's integral is the amount it conserves. Where nothing else sets
   $`\phi`$ at the start, a region beside an electrode starts with the electrode's first reaction at
   equilibrium (the electrode at its open-circuit level); otherwise $`\phi`$ carries over from the
@@ -275,7 +278,9 @@ Na⁺/K⁺-ATPase between the outside (left) and the cytoplasm (right):
 together). Membrane potentials are $`\phi`$ differences between the two solutions, $`\phi_{\mathrm{in}} - \phi_{\mathrm{out}}`$,
 read from `sol.phi` (or a `'phi'` probe in a transient). A bath contact's terminal voltage is
 its reference species' level instead, what an electrode reversible to that species would read,
-so between two different solutions it differs from $`\Delta\phi`$ by that species' Nernst term.
+so between two different solutions it differs from $`\Delta\phi`$ by that species' Nernst term;
+a bath given no reference has its $`\phi`$ as its terminal voltage, and between two of those the
+terminals read $`\Delta\phi`$ itself.
 ### Voltage-gated channels
@@ -329,7 +334,12 @@ Two things differ from the textbook equations. The currents are GHK's, which rec
 conductance depends on the voltage, so a permeability matches a conductance $`g`$ at one voltage
 only (above, the chord conductances at rest, −65 mV, for Hodgkin and Huxley's 120, 36 and 0.3
 mS/cm²; matched at the reversal potentials instead, the rest depolarises itself and the axon
-fires on its own). And a cell without a pump has no resting steady state: `solve()` finds its
+fires on its own). Their own linear channels are conductance links: $`G\,(V_{i,L} - V_{i,R})`$
+toward +x is $`g\,(E_i - V)`$, with $`E_i`$ the Nernst potential at the edge concentrations, so
+`{ type: 'conductance', G: 360, gates: { n: 4 } }` is their K⁺ channel exactly
+(`hodgkinHuxley({ T, linear: true })` writes all three). Between two baths whose terminal
+voltage is their $`\phi`$, a held step is their voltage clamp, and the K⁺ current at its end is
+$`g_K n_\infty^4 (V - E_K)`$ to 2e-3. And a cell without a pump has no resting steady state: `solve()` finds its
 Donnan equilibrium, every permeant ion level across the membrane, which the real cell reaches
 only over hours. Start a transient from the concentrations given (it settles to rest within
 milliseconds), or keep the gradients with the Na⁺/K⁺ pump on the same face. Started from the
@@ -447,13 +457,22 @@ contacts: {
   at $`V + \mathtt{offset}`$, $`J = G \cdot (V_{\mathrm{out}} - V_i)`$, G in S/m².
 - `{ type: 'exchange', k, mu }` (neutral species):
   $`N_{\mathrm{in}} = k \cdot (\mu_{\mathrm{out}} - \mu)/RT`$, k in mol/(m²·s).
+- `{ type: 'velocity', v, offset }` (or `mu`, for a neutral species): a surface velocity,
+  $`N_{\mathrm{in}} = v\,(c_{\mathrm{eq}} - c)`$ with v in m/s and $`c_{\mathrm{eq}}`$ the end node's
+  concentration in equilibrium with the outside level, i.e.
+  $`v\,c\,(e^{(\bar\mu_{\mathrm{out}} - \bar\mu)/RT} - 1)`$, which keeps the flux's sign that of the
+  level difference whatever the statistics. It lies between `'blocked'` (v → 0) and
+  `'equilibrium'` (v → ∞): a contact's surface recombination velocity, or thermionic emission
+  over a Schottky barrier (below).
 - `'blocked'`: no flux.
 **`bath`** (instead of `species` and `phi`): the outside phase is a neutral composition `c`
 held in place by a charged `reference` species (as for a reversible reference electrode, e.g.
 Cl⁻ for Ag/AgCl), which is the terminal. Every bath species is in equilibrium at the level its
 composition implies, and the $`\phi`$ law is `'bulk'`. An optional `offset` places the reference
-species relative to V.
+species relative to V. Without a `reference`, V is the bath's own $`\phi`$: an ideal salt bridge
+(no junction potential), the convention by which membrane potentials are $`\phi`$ differences.
+Between two such baths, a held $`V_{\mathrm{right}} - V_{\mathrm{left}}`$ is a voltage clamp.
 **`phi`**, required whenever any species or reaction connects at the contact (default
 `'neutral'`):
@@ -471,6 +490,18 @@ species relative to V.
   means. For example, a Schottky barrier $`\phi_B`$ on n-type material with
   $`\mu^\circ_{\mathrm{e}^-} = 0`$ is `zeroCharge: φ_B`.
+A Schottky contact is that pinned barrier with its carriers passing at their emission velocities:
+`{ V, terminal: 'e-', species: { 'e-': { type: 'velocity', v }, 'h+': { type: 'velocity', v: vp, offset: 0 } }, phi: 'pinned', zeroCharge: φ_B }`,
+with Bethe's thermionic-emission velocity $`v = A^* T^2/(F N_c)`$ ($`N_c`$ in mol/m³, the data
+library's `cRef` for e⁻; about $`2 \times 10^4`$ m/s in n-Si with $`A^*`$ = 112 A/(cm²K²)). The
+forward current is then thermionic emission's, $`J = A^* T^2 e^{-\phi_B/V_T}(e^{V/V_T} - 1)`$,
+lowered where the drift–diffusion through the depletion region can't keep up (Crowell and Sze's
+combination): 4–6% short of it for a 0.85 eV barrier on 1e16 cm⁻³ n-Si from 0.1 to 0.4 V
+([`contacts`](../test/contacts.test.js) test). With `'equilibrium'` links instead (an infinite
+velocity) the barrier passes whatever the semiconductor brings to it, which is the diffusion
+theory of the Schottky diode: there, 17 to 27 times more current. Neither has image-force
+lowering or tunnelling.
 Like every alignment, `zeroCharge` is a property of that interface. To estimate it from vacuum
 levels, `vacuumZeroCharge(def, W, inside)` from `driftlet/kit` takes the work function W of the
 conductor at the terminal voltage and the inside material's anchor and offset (see the
@@ -688,22 +719,22 @@ its window, each gate is a fraction open with Hodgkin–Huxley kinetics in the v
 port's capacitance there, $`V_m = \phi - (V - \mathtt{zeroCharge})`$, and its conductance links name
 the gates that scale them (`G × m³h`). That's a membrane all along a region, between it and an
 outside held by the port: an axon's, with x running along the axon. Per volume of axoplasm, a
-cylinder of radius a has $`2/a`$ of membrane (`area`); held at `V: 0` with `zeroCharge: 0`, the port's
-V is the outside's $`\phi`$, and a charged species' `offset` is its level there against that,
-$`(\mu^\circ + RT\ln(c_{out}/c_{\mathrm{ref}}))/(zF)`$. A conductance link's current is then
-$`G\,(V_{i,out} - V_i)`$, which is $`g\,a_m (E_i - V_m)`$: Hodgkin and Huxley's linear channel, with $`E_i`$ the
-Nernst potential at the inside's concentration there.
+cylinder of radius a has $`2/a`$ of membrane (`area`). Give the port the outside's composition as a
+`bath`: its V is then the outside's $`\phi`$ (held at 0, with `zeroCharge: 0`), and each linked ion's
+level there follows from the composition, $`(\mu^\circ + RT\ln(c_{out}/c_{\mathrm{ref}}))/(zF)`$ against
+it, as an `offset` would give it. (Only the linked ions' levels are taken, so the bath needn't list
+or balance the rest.) A conductance link's current is then $`G\,(V_{i,out} - V_i)`$, which is
+$`g\,a_m (E_i - V_m)`$: Hodgkin and Huxley's linear channel, with $`E_i`$ the Nernst potential at the
+inside's concentration there. The kit's `hodgkinHuxley({ T, area })` writes their links so:
 ```js nocheck
+const hh = hodgkinHuxley({ T, area: 2 / 238e-6 }); // a squid giant axon, radius 238 µm
 ports: [{
-  name: 'membrane', region: 'axon', V: 0, terminal: 'K+', area: 2 / 238e-6, // a squid giant axon
+  name: 'membrane', region: 'axon', V: 0, area: 2 / 238e-6,
   capacitance: { C: 0.01, zeroCharge: 0 },
-  gates: hodgkinHuxley({ /* … */ T }).gates,
-  species: {
-    'Na+': { type: 'conductance', G: 1200 * 2 / 238e-6, offset: offsetNa, gates: { m: 3, h: 1 } },
-    'K+': { type: 'conductance', G: 360 * 2 / 238e-6, offset: offsetK, gates: { n: 4 } },
-    'Cl-': { type: 'conductance', G: 3 * 2 / 238e-6, offset: offsetCl }, // the leak
-  },
+  bath: { c: { 'Na+': 367, 'K+': 18.6, 'Cl-': 459 } }, // sea water, as far as the channels go
+  gates: hh.gates,
+  species: hh.species, // Na⁺ (G × m³h), K⁺ (G × n⁴), and the leak (Cl⁻), G = g × area
 }]
 ```
@@ -841,12 +872,14 @@ const now = dev.solution();                   // snapshot of the current state
 - `solve()` finds the steady state from the current state without advancing time. If every
   species is fed by a contact, it solves the steady equations directly. Otherwise conserved
   amounts (blocked species, reactive moieties) are kept exactly. If a direct solve fails at a
-  bias (a cold start far from equilibrium), it solves with both terminals level and ramps the
-  right terminal's voltage to its target; with generation reactions (below), it ramps their
-  rates up from nearly nothing. A terminal driven by a current (open circuit, say) is held at a
-  voltage instead, the voltage marched until the current crosses its target, and floated from
-  there. If 20 V either way brings no crossing (a current beyond the limiting one), the solve
-  fails with a warning giving the range of currents the held voltages passed.
+  bias, it ramps the contacts' voltages from where they were last solved (the left one first,
+  where it moved), or from level terminals on a cold start; with generation reactions (below),
+  it ramps their rates up from nearly nothing. A terminal driven by a current (open circuit,
+  say) is held at a voltage instead, the voltage marched until the current crosses its target,
+  and floated from there. If 20 V either way brings no crossing (a current beyond the limiting
+  one, or a device that only stores what comes in, which has no steady state at a current), the
+  solve fails with a warning giving the range of currents the held voltages passed. A solve that
+  fails reports the state it failed in, then leaves the device as it was before it.
 - `step(dt, { method })` advances the transient by dt seconds, halving internally where Newton
   needs it. `method` is `'be'` (backward Euler, the default) or `'bdf2'`.
 - `advance(tEnd, opts)` integrates adaptively to `tEnd` with variable-step BDF2, controlling
@@ -920,17 +953,19 @@ console.log(`${run.steps} steps; I(0.01 s) ≈ ${run.trace.current[run.trace.t.f
 | `phi` | bookkeeping $`\phi`$, V (`NaN` where undefined) |
 | `c[name]`, `mu[name]`, `muStd[name]` | concentration, $`\bar\mu`$, standard level $`\mu^\circ + zF\phi`$ (`NaN` where absent) |
 | `V[name]`, `Vstd[name]` | species voltage $`\bar\mu/(zF)`$ and standard level as a voltage (charged species) |
+| `flux[name]` | flux toward +x across each segment, between nodes `g` and `g + 1` (a face's across its pair of nodes), mol/(m²·s) (mol/s through a cross-section): the fluxes the balances add up |
+| `D[name]` | diffusivity at each node, m²/s (`NaN` where absent, or in a metal) |
 | `current`, `terminalVoltage` | current toward +x through the device (A/m², or A through a [cross-section](#geometry)) and $`V_{\mathrm{right}} - V_{\mathrm{left}}`$ |
 | `terminals[name]` | `{ V, current }` for each terminal (contacts and ports), current into the device |
-| `contacts.left/right` | `{ V, flux: {name}, D, current }` at each contact |
+| `contacts.left/right` | `{ V, flux: {name}, D, current, links: {name} }` at each contact; `links` names how each species that crosses it does (`'equilibrium'`, `'velocity'`, …) |
 | `gates.left/right` | charge on a gate or Stern plate, where the contact is capacitive |
 | `ports[k]` | `{ name, V, flux: {name}, current }`: what each internal port brings into the device; an electrode's rates, coverages and charge [as well](#what-a-solution-reports) |
-| `interfaces[f]` | `{ left, right, dipole, sheetCharge, D, N: {name}, rates }`: the names of the regions the face joins, what crosses it by its links, and each face reaction's rate (mol/(m²·s)) |
-| `bulkReactions[k]` | `{ rate, regions, total }`: each bulk reaction's forward rate at every node (mol/(m³·s), `NaN` where it doesn't run), and integrated over each region and the device (mol/(m²·s)), as the balances count it: a charge-balance check is J = F(generation − recombination), which the kit's `check()` does for every species |
+| `interfaces[f]` | `{ left, right, dipole, sheetCharge, D, N: {name}, rates, links: {name} }`: the names of the regions the face joins, what crosses it by its links, each face reaction's rate (mol/(m²·s)), and how each species that crosses it does; for those crossing by permeability, `oneWay: { name: [toward +x, toward −x] }`, the one-way fluxes whose difference is `N` (Ussing's unidirectional fluxes) |
+| `bulkReactions[k]` | `{ rate, forward, nu, regions, total }`: each bulk reaction's net forward rate at every node (mol/(m³·s), `NaN` where it doesn't run), its one-way forward rate (the backward is `forward − rate`), what one forward reaction makes of each species (`nu`, negative for what it consumes), and integrated over each region and the device (mol/(m²·s)), as the balances count it: a charge-balance check is J = F(generation − recombination), which the kit's `check()` does for every species |
 | `charge` | total charge in the device, C/m² (C through a cross-section) |
 | `conservation` | per species stretch: amount, reference, intake through contacts, drift |
 | `warnings` | e.g. unresolved double layers, conventions a statistics model relies on, and for a failed solve, where the system is nearly singular |
-| `converged`, `iterations`, `steps`, `substeps`, `history`, `time` | solver bookkeeping |
+| `converged`, `iterations`, `steps`, `substeps`, `history`, `time`, `T` | solver bookkeeping, and the temperature |
 | `steady` | whether this is a converged steady state (from `solve()`), not a transient's: what `check()` in the kit decides its checks by |
 | `done`, `rejected`, `trace` | from `advance()`: whether `tEnd` was reached; rejected steps; `{ t, current, voltage }` per accepted step |

package/docs/kit.md CHANGED Viewed

@@ -57,8 +57,12 @@ console.log(`I = ${sol.current.toFixed(1)} A/m²`);
 - **Contacts** are the first and last items. `ohmic(drive, carriers)` holds each carrier in
   equilibrium with a metal at the terminal voltage (default `['e-', 'h+']`, an
   infinite-recombination contact; `['e-']` alone is selective, and is the current collector on
-  a metal region). `bath(c, reference, drive, { offset })` is a bath (`offset` places the reference species
-  relative to the terminal voltage, e.g. to read a solution's potentials against SHE). A drive is a voltage, a waveform, or
+  a metal region). `bath(c, reference, drive, { offset })` is a bath whose terminal voltage is
+  the level of its `reference` species, as an electrode reversible to it would read (`offset`
+  places that species relative to the terminal voltage, e.g. to read a solution's potentials
+  against SHE). `bath(c, drive)`, without a reference, is a bath whose terminal voltage is its
+  φ: an ideal salt bridge, the convention of membrane potentials, so that between two such baths
+  V_right − V_left is the φ difference a voltage clamp sets. A drive is a voltage, a waveform, or
   `{ V }`, `{ I }`, `{ V, R }`.
 - **`library`** takes pieces with `species` and `materials`, merged with any given directly
   (`combine()` does the merging on its own). A species or material given twice must be given
@@ -144,7 +148,7 @@ which is the transport the full solve accounts for.
 ## Channels
-**`hodgkinHuxley({ inside, outside, T, g, leak, leakZ, at, names })`**: Hodgkin and Huxley's
+**`hodgkinHuxley({ inside, outside, T, g, leak, leakZ, at, names, linear, area })`**: Hodgkin and Huxley's
 squid-axon channels for a [membrane face](device.md#voltage-gated-channels) with the outside on its
 left: `{ gates, species }`, the face's `gates` (m, h and n, their 1952 rates at 6.3 °C scaled to
 `T` by Q₁₀ = 3) and links for Na⁺ (P·m³h), K⁺ (P·n⁴) and the leak (one ion, `leak`, of charge
@@ -152,6 +156,13 @@ left: `{ gates, species }`, the face's `gates` (m, h and n, their 1952 rates at
 whose chord conductance at `at` (−65 mV) is HH's `g` (120, 36 and 0.3 mS/cm²) at the
 concentrations given. Spread it into the face beside its $`\phi`$ law, adding the other species'
 links: `{ phi: { type: 'capacitive', C: 0.01 }, gates: hh.gates, species: { ...hh.species, 'A-': 'blocked' } }`.
+With `linear: true` (and no concentrations) the face gets HH's own linear channels instead:
+conductance links, `G` = g, gated the same, whose currents are g(V − E) with E each ion's Nernst
+level at the concentrations either side; between two `bath`s without a reference species, that's
+their voltage clamp. For a [membrane port](device.md#a-membrane-through-a-window-gated-channels) along a region (an axon
+along x), give `area`, the membrane per volume (2/a for radius a), in place of `inside`, `outside`
+and `at`: the links are then their linear conductances, `G` = g × area, gated the same, each ion's
+reversal potential following from the port's `bath` and the concentrations inside.
 `ghkCurrent(z, inside, outside, V, T)` is the GHK current (outward, A/m²) at unit permeability.
 ## Sources
@@ -421,7 +432,8 @@ page can show that its numbers hold up. Pass the solution `solve()` or `advance(
   region's charge must agree to `tol` (relative; default 1e-2, about what a plot shows; a
   benchmark wants 1e-3 or less). The discretisation is second order, so the change estimates
   this grid's own error (about ¾ of it). It costs one more solve, so run it once, not on every
-  slider move.
+  slider move. In a transient it's `?`, not checked: the answer there depends on the whole run
+  (and on drives set along the way), so run it again yourself on a grid twice as fine.
 It returns `{ ok, items, text }`: `ok` when nothing failed, an item per check
 (`{ name, ok, summary, details }`, with `ok: null` for a prompt to look), and `text`, a line
@@ -497,6 +509,61 @@ const { solution, info } = await dev.set({ contacts: { right: { V: 0.5 } } });
 console.log(`I(0.5 V) = ${solution.current.toFixed(1)} A/m², in ${info.ms.toFixed(1)} ms`);
 ```
+## Particles
+`particles(sol, opts)` draws a solution as dots, each a fixed amount of one species (`weight`,
+mol/m²), hopping between the cells of a display lattice. The hops' one-way rates come from the
+solution, so on average the dots fill each cell as its concentration does and cross each
+boundary, net, at its flux: they're a sample of the solution, not a separate model. Dots are
+made and unmade by the bulk reactions' one-way rates (so in equilibrium generation and
+recombination both go on, in balance) and wherever else the flux diverges (ports, face
+reactions), and enter and leave through the contacts and any metal.
+- Across a boundary the one-way fluxes have the solution's flux as their difference and
+  Scharfetter–Gummel's exchange as their product, which gives a dot in a flat potential the
+  diffusivity D. A face crossed by permeability uses its own one-way fluxes (the solution's
+  `oneWay`), so the dots crossing each way are Ussing's unidirectional fluxes, as a tracer
+  experiment counts them.
+- Concentrations span decades, so one weight can't draw them all. A cell that would hold more
+  than `cap` dots is a **sea** instead: drawn as shading, holding no dots, exchanging them with
+  its neighbours as a contact's reservoir does. A junction then shows its majority carriers as
+  seas and its minority carriers as dots. Crossings between two seas through a membrane are
+  `events`.
+- `step(dt)` moves the dots on by dt of the device's time. `update(sol)` takes a new solution;
+  with `{ resample: true }` (a jump between steady states) each cell's dots are thinned or added
+  to by the change in what it should hold, which keeps them a Poisson sample while moving as few
+  as can be. Without it (a transient) they move on at the new rates.
+- The swarm has `dots` (`{ species, cell, x }`), `cells` (`{ x0, x1, region }`), `sea[name]`
+  (1 per sea cell), `expected(name)` (dots per cell on average), `events` from the last step
+  (`{ species, kind, x, dir }`: `'in'`, `'out'`, `'made'`, `'unmade'`, `'cross'`) and
+  `crossed[name]` (`{ up, down }` at each boundary, counts you zero when you like).
+```js
+import { Device, GAS_CONSTANT } from 'driftlet';
+import { particles } from 'driftlet/kit';
+// A species diffusing through a gel slab between two baths: c falls from 1 to 0.1 mol/m³.
+const RT = GAS_CONSTANT * 298.15;
+const sol = new Device({
+  species: [{ name: 'X', z: 0 }],
+  materials: { gel: { epsr: 0, species: { X: { D: 1e-9, mu0: 0, cRef: 1 } } } },
+  regions: [{ material: 'gel', length: 1e-4 }],
+  contacts: {
+    left: { phi: 'neutral', species: { X: { type: 'equilibrium', mu: 0 } } },
+    right: { phi: 'neutral', species: { X: { type: 'equilibrium', mu: RT * Math.log(0.1) } } },
+  },
+}).solve();
+const swarm = particles(sol, { dots: 300, cells: 20 });
+for (let i = 0; i < 100; i++) swarm.step(0.01); // 1 s of the slab's time
+console.log(`${swarm.dots.length} dots, each ${swarm.weight.X.toExponential(1)} mol/m²`);
+```
+The dots are a friendly first picture for teaching. Pages that explain driftlet itself lead with
+the fields, so the [pn demo](https://markblundeberg.github.io/driftlet/demos/pn.html) draws its
+carriers this way at the bottom, on the band diagram, and the
+[axon demo](https://markblundeberg.github.io/driftlet/demos/axon.html) the ions crossing its
+membrane in each direction, both sides seas (`cap: 0`).
 ## Alignment from vacuum levels
 `vacuumLevel`, `vacuumDipole` and `vacuumZeroCharge` turn vacuum-level estimates (electron

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