driftlet 0.12.0 → 0.14.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +48 -76
- package/docs/device.md +61 -26
- package/docs/kit.md +71 -4
- package/docs/logo-dark.svg +3 -2
- package/docs/logo.svg +3 -2
- package/docs/reliability.md +60 -3
- package/docs/statistics.md +10 -0
- package/llms.txt +622 -391
- package/package.json +1 -1
- package/src/channels.js +27 -4
- package/src/checks.js +5 -1
- package/src/describe.js +1 -1
- package/src/device.js +112 -14
- package/src/index.js +6 -1
- package/src/kit.js +1 -0
- package/src/particles.js +331 -0
- package/src/solution.js +42 -4
- package/src/solver.js +181 -50
- package/src/stack.js +6 -4
- package/src/types.js +2 -1
- package/types/channels.d.ts +14 -3
- package/types/checks.d.ts +2 -1
- package/types/kit.d.ts +1 -0
- package/types/particles.d.ts +42 -0
- package/types/solution.d.ts +1 -0
- package/types/solver.d.ts +8 -2
- package/types/stack.d.ts +6 -5
- package/types/types.d.ts +5 -0
package/llms.txt
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# driftlet: a guide for agents
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driftlet is a dependency-free JavaScript library that solves 1D drift–diffusion–reaction
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(Poisson–Nernst–Planck) problems fast enough for live web demos
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electrochemical cells,
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(Poisson–Nernst–Planck) problems fast enough for live web demos. Semiconductor junctions, solar
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cells, electrochemical cells, batteries, membranes and nerves are one problem with different
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casts of species (electrons, holes, ions, neutral molecules), each moving down its own
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electrochemical potential μ̄, coupled by Poisson's equation, reactions and interfaces. So a
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device in any field is built the same way, from the same pieces. It runs in a browser, a Web
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Worker or Node, from npm or a CDN.
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Every code block below runs in the test suite and prints its closed-form check. Skim the next
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two sections, then go to the template nearest your device:
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- semiconductors: a pn junction (with an I–V sweep), a live page with a slider, a solar cell, a
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MOS capacitor, a Schottky diode, a thin-film transistor, a pulse drifting along a bar (under
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Transients);
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- electrochemistry: a cell, an electrode in a stirred solution (a potential step, and a cyclic
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voltammogram), corrosion;
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- physiology: a cell membrane (a resting potential), a voltage clamp, an action potential, one
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travelling along an axon.
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The references are in docs/: device.md (the definition), kit.md (the helpers), conventions.md
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(signs and levels), visualization.md, alignment.md (band offsets), statistics.md (non-ideal
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materials, insertion hosts), data.md and reliability.md (what's validated, and the limits).
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## Imports
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From a CDN, pin the version:
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From a CDN, pin the version you tested against:
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```js nocheck
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import { Device, units } from 'https://cdn.jsdelivr.net/npm/driftlet@0.
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import { build, layer, ohmic, semiconductor, live } from 'https://cdn.jsdelivr.net/npm/driftlet@0.
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import { bandDiagram } from 'https://cdn.jsdelivr.net/npm/driftlet@0.
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import { Device, units } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/index.js';
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import { build, layer, ohmic, semiconductor, live } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/kit.js';
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import { bandDiagram } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/plot.js';
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```
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From npm: `driftlet`, `driftlet/kit`, `driftlet/plot`.
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From npm: `driftlet`, `driftlet/kit`, `driftlet/plot`. Every export is listed at the end.
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## What to know first
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- **Units are SI**: m, mol/m³ (1 M = 1000 mol/m³), J/mol, m²/s,
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`units`
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`units.eV(1.12)`
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- **Units are SI**: m, mol/m³ (1 M = 1000 mol/m³; 1e16 cm⁻³ is only 0.0166 mol/m³), J/mol, m²/s,
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V, A/m², F/m², S/m². `units` converts in (`units.um(1)`, `units.perCm3(1e17)` for per cm³ or
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per cm³·s, `units.eV(1.12)` to J/mol, `units.cm2PerS(36)`, `units.molar(0.1)`) and back
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(`units.toPerCm3`, `toEV`, `toMolar`, `toUm`, …). Physiology: 1 mS/cm² = 10 S/m², 1 µF/cm² =
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0.01 F/m², 1 µA/cm² = 0.01 A/m², mM = mol/m³.
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- **Everything you set or read is an electrochemical potential μ̄** (or a voltage made from one). A
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terminal's `V` is the level of its terminal species (`terminal`, which the kit's contacts set):
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for an electron contact V = −μ̄_e/F, what a voltmeter reads. φ is bookkeeping, per material, and
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never a control.
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- **Solutions** are plain objects of `Float64Array`s: `x`, `phi`, and per species `c`, `mu` (μ̄),
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`V` (the species voltage μ̄/(zF): a quasi-Fermi level for e⁻ and h⁺) and `Vstd` (the standard
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level: a band edge; in volts, E = −V, so E_c is the lower line). `NaN` marks a value
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that doesn't exist (a species absent from a material, `V` of a neutral one, `c` in a metal).
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- **Currents.** `sol.terminals[name]` gives each terminal's `{ V, current }`, its current into
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the device; a current drive `{ I }` is the same way round (electrons fed in are I < 0).
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`sol.current` is the right contact's toward +x, so a forward diode with its p side on the right
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carries a negative one (with ports, read each contact from `sol.terminals`). Everything is per
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m² of a planar device; with a `geometry` (shells, or any cross-section A(x)) it's a total.
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- **What isn't defaulted**: an alignment between different materials, a φ law where a metal
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meets a dielectric, and the amount of anything a contact doesn't feed (`c0`). The error names
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the path and says what to give. (Kinetic details are defaulted: listed in docs/device.md.)
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- **Check before trusting.** `sol.converged` must be true; read `sol.warnings`, where a failed
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solve always says why. `describe(def)` (kit) summarises a definition and flags likely unit
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slips. Once a device works, log `check(dev, sol).text` (kit) once: each species' ledger,
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conservation in transients, and a steady state on a grid twice as fine (a FAIL means refine;
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a transient you rerun on a finer grid yourself).
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## How a device is written
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- **`build({ T, library, stack, bulkReactions, ports, grid, geometry })`** (kit) reads a stack
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left to right: its first and last items are the contacts, `layer(material, length, opts)`s
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are regions (give one a `name` to refer to it), and any other object between two layers is
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the face between them. `ohmic()`, `bath()` and the like write contacts; a plain object works.
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- **The library** is pieces with `species` and `materials`: `semiconductor('Si')` (Si, Ge, GaAs, at
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300 K), `aqueous(names)` (H⁺ Li⁺ Na⁺ K⁺ Ag⁺ Cu²⁺ Zn²⁺ Fe²⁺ Fe³⁺ OH⁻ Cl⁻ NO₃⁻ SO₄²⁻ in water, at 25
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°C; `{ epsr: 0 }` makes it strictly neutral, with no double layers), `metal('Ag')` (Ag Cu Au Al Zn
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Li Pt). A semiconductor's textbook numbers are in `SEMICONDUCTORS.Si` (`Eg` and `chi` in eV, `Nc`
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and `Nv` in cm⁻³, `mun` and `mup` in cm²/(V·s), `epsr`); in the material, e⁻'s and h⁺'s `cRef` are
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N_c and N_v in mol/m³ and h⁺'s `mu0` is the gap (e⁻'s is 0), so n_i = √(N_c N_v) e^(−E_g/2RT),
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6.7e9 cm⁻³ for Si. A species it lacks is pushed into both lists (`z: 0` for a neutral one):
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`lib.species.push({ name: 'A-', z: -1, cRef: 1000 })`, `lib.materials.water.species['A-'] = { D,
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mu0 }`. Only μ° differences within a reaction matter: for a redox couple μ°_red − μ°_ox = −F·E°
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(against SHE, the library's μ°_H⁺ being 0). An insulator is a material with no species: `{
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species: [], materials: { SiO2: { epsr: 3.9, species: {} } } }`.
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- **Faces.** Between two different non-metals, give an alignment, `{ dipole }` or `{ step: {
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species: 'e-', value } }` (J/mol), or `phi: 'neutral'`. `vacuumDipole(def, { material, anchor:
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'e-', offset: χ }, …)` estimates a dipole from electron affinities (Anderson's rule); it reads
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only the materials, so build with `{ dipole: 0 }`, then put its value in (docs/alignment.md). Next
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to a metal, a face takes no alignment, but needs a φ law if the other side has ε > 0: `{ phi: {
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type: 'capacitive', C }, zeroCharge }` or `phi: 'neutral'`, where `zeroCharge` is the metal's V −
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φ at its edge when the face holds no charge (a work-function difference, a potential of zero
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charge, a Schottky barrier). A face's reactions label sides: `'Li+(left) = Li+(right)'`.
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- **Ports** are terminals attached sideways to a window inside a region (`from`, `to`, m from its
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left end): a source or drain, an injector, a reference electrode (`I: 0`), an electrode spread
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through a film (`reactions`, `area`), a gate along a channel or a membrane along an axon
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(`capacitance`, `gates`). A BJT's base contact is a port on a narrow window of the base,
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`{ region: 'base', from, to, V, terminal: 'h+', species: { 'h+': 'equilibrium' } }`.
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- **Drives.** A terminal is held at a voltage `V`, driven by a current `I` (open circuit is
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`I: 0`), or behind a resistance `{ V, R }`. Either can be a waveform: a table `{ t, values }`
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(piecewise linear; a step is two points at one time), or the kit's `pulse({ start, width,
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amplitude, rise, base })`, `square({ high, low, period, duty })`, `ramp({ from, to, duration,
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start })` or `triangle({ from, to, period })` (out and back each period from t = 0: a cyclic
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voltammogram, in terminal volts). `dev.set({ contacts: { right: { V } } })` changes a drive
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and keeps the state as a warm start; ports are patched by name, `{ ports: { gate: { V } } }`.
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- **Reactions** are equations: `{ equation: 'e- + h+ = 0', kf: { Si: 1e8 } }`, a coefficient
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written with its space (`2 e-`). A participant that isn't a species (solid silver) is fixed by
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its μ: `fixed: { 'Ag(s)': 0 }`. A bulk reaction's forward rate is `kf · Π c_reactants`
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(mol/(m³·s)); the backward one follows from the μ°.
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- **Recombination and light.** Band-to-band `e- + h+ = 0` gives a minority lifetime τ =
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1/(kf·N), N the majority density in mol/m³ (`kf: 1e8` is 0.6 µs at 1e16 cm⁻³); being
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bimolecular, as is the kit's `recombination()`, it shortens at high injection. SRH is `srh: { Si:
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{ tauN, tauP } }` in place of `kf` (s), or at a face `{ equation: 'e-(left) + h+(right) = 0',
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srh: { vn, vp } }` (m/s); with τ_N ≪ τ_p it gives n-type silicon's holes a lifetime τ_p at any
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injection. Light is a reaction from a reservoir (`photon = e- + h+`, uniform), or absorbed as
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it goes in,
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`photogeneration({ material, flux, alpha, mu: units.eV(3), from, to })`.
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- **Electrode kinetics.** A face reaction's `k0` (mol/(m²·s)) is its rate with every participant
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at cRef: i₀ = nF·k0 there, and k0 = k°·cRef for a textbook k° in m/s (1 cm/s at 1 M is
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`k0: 10`).
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- **Grids** grade geometrically from `hmin` at each region's ends up to `hmax`, neighbouring cells
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differing by at most `ratio` (1.2): put `hmin` below the shortest length that matters (a Debye
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length, a depletion edge). `check()` says whether it's fine enough.
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`build()` is the usual way in. It writes a plain definition for `new Device()`, which some
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templates below write by hand (where a port spans a region, or no stack fits):
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```js
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import { Device, FARADAY, GAS_CONSTANT } from 'driftlet';
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// A concentration cell: 100 mM KCl against 10 mM through a gap, read by Ag/AgCl electrodes.
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const D = { 'K+': 1.957e-9, 'Cl-': 2.032e-9 };
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const dev = new Device({
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T: 298.15,
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species: [{ name: 'K+', z: 1, cRef: 1000 }, { name: 'Cl-', z: -1, cRef: 1000 }], // cRef: the standard state, mol/m³
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materials: { water: { epsr: 0, species: { 'K+': { D: D['K+'], mu0: -283.27e3 }, 'Cl-': { D: D['Cl-'], mu0: -131.23e3 } } } },
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regions: [{ name: 'gap', material: 'water', length: 100e-6, c0: { 'K+': 10, 'Cl-': 10 } }], // left to right
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// (interfaces: [...] would hold the faces between regions, one fewer than the regions)
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contacts: {
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left: { V: 0, bath: { c: { 'K+': 100, 'Cl-': 100 }, reference: 'Cl-' } }, // V is Cl⁻'s level: an Ag/AgCl electrode's
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right: { I: 0, bath: { c: { 'K+': 10, 'Cl-': 10 }, reference: 'Cl-' } }, // open circuit
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},
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grid: { hmin: 0.1e-6, hmax: 5e-6 },
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});
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const sol = dev.solve();
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const tK = D['K+'] / (D['K+'] + D['Cl-']), VT = (GAS_CONSTANT * 298.15) / FARADAY;
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console.log(`EMF ${(sol.terminals.right.V * 1e3).toFixed(3)} mV, 2t₊V_T ln 10 = ${(2 * tK * VT * Math.log(10) * 1e3).toFixed(3)} mV`); // 58.048, 58.047
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```
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## Template: a semiconductor junction
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```
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## Template:
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## Template: a live page with a slider
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`live()` warm-starts each solve, merges slider moves made during one, and keeps the last good
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solution (on a failure, `info.failed` and `info.error` are set). It returns `{ set, solution, ready,
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close }`; `set()` and `ready` (the first solve) are promises of `{ solution, info }`.
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`bandDiagram()` returns an SVG string; a fixed `range` keeps its axis still. `worker: true` solves
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in a Web Worker, from a CDN too. A few hundred nodes solve in milliseconds; thousands, or
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transients, want a worker and `advance(t, { budgetMs })` per frame. `onsolution` may call `set()`,
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if that converges rather than oscillates. (A headless browser screenshotting a page that loads from
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a CDN needs a long virtual-time budget, 30 s.)
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```
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```html
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<!doctype html>
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<meta charset="utf-8">
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<title>pn junction</title>
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<label>bias <input id="V" type="range" min="-0.5" max="0.7" step="0.01" value="0"></label>
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<span id="readout"></span>
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<div id="figure"></div>
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<script type="module">
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import { units } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/index.js';
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import { build, layer, ohmic, semiconductor, live } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/kit.js';
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import { bandDiagram } from 'https://cdn.jsdelivr.net/npm/driftlet@0.14.0/src/plot.js';
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const silver = half('Ag+ + e- = Ag(s)', { 'Ag(s)': 0 }); // μ of the element: 0 on table conventions
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// A Stern layer at each metal face: its capacitance and the potential of zero charge are
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// properties of that interface, so they're yours to choose.
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const face = { phi: { type: 'capacitive', C: 0.2 }, zeroCharge: 0.1, reactions: [{ ...silver, k0: 1e-3, alpha: 0.5 }] };
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const def = build({
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layer('water', 20e-6, { c0: { 'H+': 1, 'Ag+': 10, 'NO3-': 11 } }),
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face,
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layer('Ag', 1e-6),
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ohmic(0.05, ['e-']),
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],
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grid: { hmin: 0.1e-9, hmax: 200e-9, ratio: 1.15 },
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T: 300,
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library: [semiconductor('Si')],
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stack: [ohmic(0), layer('Si', 1e-6, { donors: units.perCm3(1e17) }), layer('Si', 1e-6, { acceptors: units.perCm3(1e16) }), ohmic(0)],
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bulkReactions: [{ equation: 'e- + h+ = 0', kf: { Si: 1e8 } }],
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grid: { hmin: 1e-9, hmax: 20e-9 },
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});
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const
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const slider = document.getElementById('V');
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const dev = live(def, {
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onsolution(sol, info) {
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document.getElementById('figure').innerHTML = bandDiagram(sol, { energy: true, range: [-1.2, 1.7], title: `V = ${sol.terminals.right.V.toFixed(2)} V` });
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document.getElementById('readout').textContent = info.failed ? 'no solution here' : `I = ${sol.current.toExponential(2)} A/m²`;
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},
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});
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slider.addEventListener('input', () => dev.set({ contacts: { right: { V: +slider.value } } }));
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</script>
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```
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To draw in your own style, `traces(sol, opts)` (kit, the same options) gives the lines as data;
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see "Reading level diagrams" below.
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For an explainer, `particles(sol, { weight, cap })` (kit) draws a solution as dots, each `weight`
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mol/m² of a species, hopping at rates taken from the solution: on average their density is its
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concentration and their net crossing its flux. A friendly first figure for teaching, as long as
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the page says it samples the continuum solution and how much a dot is. Where a dot would be lost
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among millions (majority carriers, a bath), a cell over `cap` dots is a sea: shade it by
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`expected(name)`. Each frame: `swarm.step(dt)` in the device's time (about h²/D per hop, h a
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cell), then draw `swarm.dots` (`{ species, x }`) and `swarm.events` (`'unmade'` is a
|
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recombination; `'cross'` an ion through a membrane between two seas); on a new steady solution,
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`swarm.update(sol, { resample: true })`. A membrane's permeability (1e-8 m/s) is tiny beside
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D/h in the water (0.02 m/s for 100 nm cells), so an ion beside it hops ~1e6 times per crossing:
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a membrane page shows seas and crossing events, not walking ions.
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The pn demo's page script draws a diode's carriers on its band diagram this way, and the axon
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demo's the ions crossing its membrane (`cap: 0`, every cell a sea, so only the crossings).
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## Template: a solar cell
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`photon = e- + h+`, with the photons' μ well above the gap, generates uniformly at the rate `kf`.
|
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|
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Open circuit is `I: 0`, and the terminal's V is then V_oc. The photocurrent flows toward +x
|
|
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|
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(holes to the p side, on the right).
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240
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|
```js
|
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import { Device, units } from 'driftlet';
|
|
@@ -162,111 +263,170 @@ const oc = new Device(cell({ I: 0 })).solve(); // open circuit
|
|
|
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263
|
console.log(`J_sc = ${sc.current.toFixed(1)} A/m², V_oc = ${oc.terminals.right.V.toFixed(3)} V`);
|
|
163
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|
```
|
|
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265
|
|
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-
|
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266
|
+
For a perovskite cell, prefer the curated `perovskiteCell({ V, light, bulkSRH })`: IonMonger's
|
|
267
|
+
default cell (mobile iodide vacancies), with its J–V scans at seven rates in `PEROVSKITE_SCANS`
|
|
268
|
+
and `hysteresis(trace, turn)` to read the same figures from yours.
|
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|
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|
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## Template: a MOS capacitor
|
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membrane potential is φ_in − φ_out from `sol.phi` (a bath's terminal voltage reads its reference
|
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species' level instead, which differs from Δφ by that ion's Nernst term).
|
|
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|
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The gate is a metal layer with a capacitive face to the oxide (a metal screens within Å, so C is
|
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|
+
large) and the gate's alignment as `zeroCharge`. In 1D nothing supplies the inversion layer's
|
|
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|
+
electrons (a MOSFET's source and drain do), so a port holds their level at the surface: the
|
|
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|
+
low-frequency C–V. The gate's charge is the displacement into the oxide, `sol.interfaces[0].D`.
|
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276
|
|
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277
|
```js
|
|
175
|
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import { Device, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
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|
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import { build, layer,
|
|
278
|
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import { Device, units, EPS0, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
279
|
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import { build, layer, ohmic, semiconductor, metal, vacuumZeroCharge } from 'driftlet/kit';
|
|
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280
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|
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const
|
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const
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const
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190
|
-
|
|
281
|
+
const oxide = { species: [], materials: { SiO2: { epsr: 3.9, species: {} } } };
|
|
282
|
+
const tox = units.nm(10), Cox = (3.9 * EPS0) / tox, NA = units.perCm3(1e17);
|
|
283
|
+
const mos = (Vg, zeroCharge) =>
|
|
284
|
+
build({
|
|
285
|
+
T: 300,
|
|
286
|
+
library: [semiconductor('Si'), metal('Al'), oxide],
|
|
287
|
+
stack: [
|
|
288
|
+
ohmic(Vg, ['e-']), // the gate's terminal: the aluminium's electrons
|
|
289
|
+
layer('Al', units.nm(20)),
|
|
290
|
+
{ phi: { type: 'capacitive', C: 10 }, zeroCharge }, // the gate's face
|
|
291
|
+
layer('SiO2', tox),
|
|
292
|
+
{ dipole: 0 }, // the oxide holds no species, so this alignment changes nothing
|
|
293
|
+
layer('Si', units.um(1), { name: 'Si', acceptors: NA }),
|
|
294
|
+
ohmic(0),
|
|
295
|
+
],
|
|
296
|
+
ports: [{ name: 'channel', region: 'Si', from: 0, to: units.nm(1), V: 0, terminal: 'e-', species: { 'e-': 'equilibrium' } }],
|
|
297
|
+
grid: { hmin: units.nm(0.25), hmax: units.nm(50), ratio: 1.15 },
|
|
298
|
+
});
|
|
299
|
+
// The gate's alignment from vacuum levels: Al's work function 4.1 eV, Si's electron affinity 4.05 eV.
|
|
300
|
+
const zc = vacuumZeroCharge(mos(0, 0), 4.1, { material: 'Si', anchor: 'e-', offset: 4.05 });
|
|
301
|
+
const dev = new Device(mos(0, zc));
|
|
302
|
+
const Q = (Vg) => {
|
|
303
|
+
dev.set({ contacts: { left: { V: Vg } } });
|
|
304
|
+
return dev.solve().interfaces[0].D;
|
|
191
305
|
};
|
|
192
|
-
const
|
|
193
|
-
|
|
194
|
-
|
|
195
|
-
|
|
196
|
-
|
|
197
|
-
|
|
198
|
-
|
|
199
|
-
|
|
200
|
-
|
|
201
|
-
|
|
202
|
-
|
|
306
|
+
for (const Vg of [-2, -0.95, 0, 0.4, 2]) {
|
|
307
|
+
const C = (Q(Vg + 0.01) - Q(Vg - 0.01)) / 0.02;
|
|
308
|
+
console.log(`V_G ${Vg} V: C/C_ox ${(C / Cox).toFixed(3)}`); // 0.949, 0.701 (flat band), 0.267, 0.375, 0.973
|
|
309
|
+
}
|
|
310
|
+
// At flat band the silicon is a capacitor of ε/L_D, its Debye length's.
|
|
311
|
+
const LD = Math.sqrt((11.7 * EPS0 * GAS_CONSTANT * 300) / (FARADAY * FARADAY * NA));
|
|
312
|
+
console.log(`flat band, theory: ${(1 / (1 + (Cox * LD) / (11.7 * EPS0))).toFixed(3)}`); // 0.699
|
|
313
|
+
```
|
|
314
|
+
|
|
315
|
+
`dev.impedance([f], { terminal: 'left' })` gives the same C at low frequency. Draw it with
|
|
316
|
+
`bandDiagram(sol, { energy: true, phi: ['SiO2'] })`: across an insulator φ is the line to draw.
|
|
317
|
+
|
|
318
|
+
## Template: a Schottky diode
|
|
319
|
+
|
|
320
|
+
A barrier pinned at the metal (`phi: 'pinned'`, `zeroCharge` the barrier height for Si, whose
|
|
321
|
+
μ°_e⁻ is 0), crossed at the emission velocity: a `velocity` link, N_in = v (c_eq − c). With
|
|
322
|
+
`'equilibrium'` links (infinite velocity) it's diffusion theory instead, 20 times the current here.
|
|
323
|
+
|
|
324
|
+
```js
|
|
325
|
+
import { Device, units, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
326
|
+
import { build, layer, ohmic, semiconductor } from 'driftlet/kit';
|
|
327
|
+
|
|
328
|
+
const T = 300, VT = (GAS_CONSTANT * T) / FARADAY, Si = semiconductor('Si');
|
|
329
|
+
const phiB = 0.85, A = 1.12e6; // the barrier (V); Richardson's constant for n-Si, A/(m²K²)
|
|
330
|
+
const v = (A * T * T) / (FARADAY * Si.materials.Si.species['e-'].cRef); // Bethe's emission velocity, 2.2e4 m/s (cRef is N_c)
|
|
331
|
+
const schottky = (V) => ({
|
|
332
|
+
V,
|
|
333
|
+
terminal: 'e-',
|
|
334
|
+
species: { 'e-': { type: 'velocity', v }, 'h+': { type: 'velocity', v, offset: 0 } },
|
|
335
|
+
phi: 'pinned',
|
|
336
|
+
zeroCharge: phiB, // E_c − E_F at the metal
|
|
203
337
|
});
|
|
204
|
-
const dev = new Device(
|
|
205
|
-
const
|
|
206
|
-
|
|
207
|
-
const
|
|
208
|
-
console.log(
|
|
209
|
-
|
|
338
|
+
const dev = new Device(build({ T, library: [Si], stack: [schottky(0), layer('Si', units.um(2), { donors: units.perCm3(1e16) }), ohmic(0)], grid: { hmin: units.nm(1), hmax: units.nm(20) } }));
|
|
339
|
+
for (const V of [0.1, 0.2, 0.3]) {
|
|
340
|
+
dev.set({ contacts: { left: { V } } }); // the metal positive: forward
|
|
341
|
+
const J = dev.solve().current, te = A * T * T * Math.exp(-phiB / VT) * Math.expm1(V / VT);
|
|
342
|
+
console.log(`${V} V: J ${J.toExponential(3)} A/m², thermionic emission ${te.toExponential(3)}`); // about 4% below: the depletion region in series
|
|
343
|
+
}
|
|
210
344
|
```
|
|
211
345
|
|
|
212
|
-
|
|
213
|
-
current), V_m is GHK. Without the pump, a closed cell runs down to Donnan equilibrium.
|
|
346
|
+
The same `velocity` link at an ohmic contact is its surface recombination velocity.
|
|
214
347
|
|
|
215
|
-
## Template:
|
|
348
|
+
## Template: a thin-film transistor (a capacitance along a channel)
|
|
216
349
|
|
|
217
|
-
|
|
218
|
-
|
|
219
|
-
|
|
220
|
-
|
|
221
|
-
(`solve()` finds Donnan), so start the transient from the concentrations given: the membrane
|
|
222
|
-
settles within milliseconds.
|
|
350
|
+
A **port with a `capacitance`** holds charge σ = C (V − zeroCharge − φ) per area of electrode
|
|
351
|
+
along its window, balanced by the region's: a gate along a channel, a porous electrode's double
|
|
352
|
+
layer. Here x runs from source to drain with the gate spread along it: the gradual-channel
|
|
353
|
+
approximation, exact for a thin film until it pinches off.
|
|
223
354
|
|
|
224
355
|
```js
|
|
225
|
-
import { Device } from 'driftlet';
|
|
226
|
-
import { build, layer, bath, aqueous, injector, pulse, hodgkinHuxley } from 'driftlet/kit';
|
|
356
|
+
import { Device, GAS_CONSTANT, FARADAY } from 'driftlet';
|
|
227
357
|
|
|
228
|
-
const T =
|
|
229
|
-
const
|
|
230
|
-
const
|
|
231
|
-
|
|
232
|
-
water.materials.water.species['A-'] = { D: 0.5e-9, mu0: 0 };
|
|
233
|
-
const hh = hodgkinHuxley({ inside, outside: out, T }); // outside on the left
|
|
234
|
-
const axon = new Device(
|
|
235
|
-
build({
|
|
358
|
+
const T = 300, VT = (GAS_CONSTANT * T) / FARADAY;
|
|
359
|
+
const t = 20e-9, L = 10e-6, W = 100e-6, C = 1e-3, mu = 1e-3; // film, length, width (m); F/m² of gate; m²/(V·s)
|
|
360
|
+
const tft = (Vg, Vd) =>
|
|
361
|
+
new Device({
|
|
236
362
|
T,
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
|
|
242
|
-
|
|
243
|
-
|
|
244
|
-
],
|
|
245
|
-
|
|
246
|
-
|
|
247
|
-
|
|
248
|
-
|
|
249
|
-
);
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
const sol = axon.advance(k * 1e-4); // 0.1 ms at a time
|
|
253
|
-
peak = Math.max(peak, sol.interfaces[0].V); // V_m, and sol.interfaces[0].gates = { m, h, n }
|
|
363
|
+
species: [{ name: 'e-', z: -1, cRef: 46 }], // an undoped film's electrons (N_c 2.8e19 cm⁻³)
|
|
364
|
+
materials: { film: { epsr: 0, species: { 'e-': { D: mu * VT, mu0: 0 } } } }, // ε = 0: F·n·t balances σ
|
|
365
|
+
regions: [{ name: 'channel', material: 'film', length: L }],
|
|
366
|
+
contacts: {
|
|
367
|
+
left: { V: 0, terminal: 'e-', species: { 'e-': 'equilibrium' }, phi: 'neutral' }, // source
|
|
368
|
+
right: { V: Vd, terminal: 'e-', species: { 'e-': 'equilibrium' }, phi: 'neutral' }, // drain
|
|
369
|
+
},
|
|
370
|
+
ports: [{ name: 'gate', region: 'channel', V: Vg, area: 1 / t, capacitance: { C, zeroCharge: 0.3 } }],
|
|
371
|
+
grid: { hmin: L / 2000, hmax: L / 100, ratio: 1.05 }, // fine at the drain, where it pinches off
|
|
372
|
+
});
|
|
373
|
+
// The output characteristic at V_G = 2 V: linear, then saturating past V_D ≈ V_G − 0.3 V.
|
|
374
|
+
for (const Vd of [0.1, 0.5, 1, 1.5, 2, 3]) {
|
|
375
|
+
const sol = tft(2, Vd).solve();
|
|
376
|
+
const I = -sol.current * t * W; // sol.current is per m² of the film's section
|
|
377
|
+
console.log(`V_D ${Vd.toFixed(1)} V: I_D ${(I * 1e6).toFixed(2)} µA, σ at the drain ${(sol.ports[0].sigma.at(-1) * 1e3).toFixed(3)} mC/m²`);
|
|
254
378
|
}
|
|
255
|
-
console.log(`peak ${(peak * 1e3).toFixed(1)} mV`); // ~ +12 mV: GHK's Na⁺ current is limited by the 50 mM inside
|
|
256
379
|
```
|
|
257
380
|
|
|
258
|
-
|
|
381
|
+
To sweep the gate on one device instead, patch the port: `dev.set({ ports: { gate: { V } } })`.
|
|
382
|
+
An organic electrochemical transistor is the same with a volumetric capacitance C*:
|
|
383
|
+
`area: 1 / t, capacitance: { C: Cstar * t }`.
|
|
384
|
+
|
|
385
|
+
## Template: an electrochemical cell
|
|
386
|
+
|
|
387
|
+
An electrode is a metal layer with the reaction at its face, behind a contact holding the
|
|
388
|
+
metal's electrons (`ohmic(V, ['e-'])`).
|
|
389
|
+
|
|
390
|
+
```js
|
|
391
|
+
import { Device } from 'driftlet';
|
|
392
|
+
import { build, layer, ohmic, half, level, SHE, aqueous, metal } from 'driftlet/kit';
|
|
393
|
+
|
|
394
|
+
const silver = half('Ag+ + e- = Ag(s)', { 'Ag(s)': 0 }); // μ of the element: 0 on table conventions
|
|
395
|
+
// A Stern layer at each metal face: its capacitance and the potential of zero charge are
|
|
396
|
+
// properties of that interface, so they're yours to choose.
|
|
397
|
+
const face = { phi: { type: 'capacitive', C: 0.2 }, zeroCharge: 0.1, reactions: [{ ...silver, k0: 1e-3, alpha: 0.5 }] };
|
|
398
|
+
const def = build({
|
|
399
|
+
library: [aqueous(['H+', 'Ag+', 'NO3-']), metal('Ag')],
|
|
400
|
+
stack: [
|
|
401
|
+
ohmic(0, ['e-']),
|
|
402
|
+
layer('Ag', 1e-6),
|
|
403
|
+
face,
|
|
404
|
+
layer('water', 20e-6, { c0: { 'H+': 1, 'Ag+': 10, 'NO3-': 11 } }),
|
|
405
|
+
face,
|
|
406
|
+
layer('Ag', 1e-6),
|
|
407
|
+
ohmic(0.05, ['e-']),
|
|
408
|
+
],
|
|
409
|
+
grid: { hmin: 0.1e-9, hmax: 200e-9, ratio: 1.15 },
|
|
410
|
+
});
|
|
411
|
+
const sol = new Device(def).solve();
|
|
412
|
+
const mid = sol.x.length >> 1;
|
|
413
|
+
console.log(`I = ${sol.current.toFixed(2)} A/m²`);
|
|
414
|
+
// The silver couple's redox level, and the SHE level, mid-cell (electron voltages).
|
|
415
|
+
console.log(level(sol, silver)[mid] - level(sol, SHE, { standard: true })[mid]); // ≈ 0.80 + (RT/F) ln(c/1 M)
|
|
416
|
+
```
|
|
417
|
+
|
|
418
|
+
## Template: an electrode in a stirred solution, and a potential step
|
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259
419
|
|
|
260
|
-
|
|
261
|
-
|
|
262
|
-
|
|
263
|
-
|
|
264
|
-
|
|
265
|
-
|
|
420
|
+
A working electrode, a stagnant layer, and the stirred bulk as a bath whose terminal is its
|
|
421
|
+
reference species (Cl⁻: an Ag/AgCl reference). An electrode's potential against SHE is its
|
|
422
|
+
electrons' V minus φ in the bulk (with the library's μ°). The working electrode's current is
|
|
423
|
+
positive when oxidising. The layer's resistance is in series (uncompensated IR: keep it thin, or
|
|
424
|
+
the supporting salt strong); a 100:1 excess of salt still leaves the limiting current about 1%
|
|
425
|
+
off pure diffusion.
|
|
266
426
|
|
|
267
427
|
```js
|
|
268
428
|
import { Device, GAS_CONSTANT, FARADAY } from 'driftlet';
|
|
269
|
-
import { build, layer, ohmic, bath, half, aqueous, metal } from 'driftlet/kit';
|
|
429
|
+
import { build, layer, ohmic, bath, half, aqueous, metal, IONS } from 'driftlet/kit';
|
|
270
430
|
|
|
271
431
|
const iron = half('Fe3+ + e- = Fe2+');
|
|
272
432
|
const electrode = (drive) =>
|
|
@@ -275,7 +435,7 @@ const electrode = (drive) =>
|
|
|
275
435
|
stack: [
|
|
276
436
|
ohmic(drive, ['e-']), // the working electrode's terminal: the platinum's electrons
|
|
277
437
|
layer('Pt', 1e-6),
|
|
278
|
-
{ reactions: [{ ...iron, k0: 1e-3 }] },
|
|
438
|
+
{ reactions: [{ ...iron, k0: 1e-3 }] }, // i₀ = F·k0 ≈ 96 A/m² at 1 M each; about 1 A/m² at these mM
|
|
279
439
|
layer('water', 20e-6), // the stagnant layer
|
|
280
440
|
bath({ 'K+': 500, 'Cl-': 535, 'Fe3+': 5, 'Fe2+': 10 }, 'Cl-'), // the stirred bulk (neutral)
|
|
281
441
|
],
|
|
@@ -283,27 +443,42 @@ const electrode = (drive) =>
|
|
|
283
443
|
});
|
|
284
444
|
// At rest (no current), the electrode sits at the couple's Nernst potential.
|
|
285
445
|
const rest = new Device(electrode({ I: 0 })).solve();
|
|
286
|
-
const
|
|
287
|
-
const VT = (GAS_CONSTANT * 298.15) / FARADAY;
|
|
288
|
-
console.log(`rest
|
|
289
|
-
|
|
290
|
-
|
|
291
|
-
|
|
446
|
+
const vsSHE = (sol) => sol.V['e-'][0] - sol.phi.at(-1);
|
|
447
|
+
const VT = (GAS_CONSTANT * 298.15) / FARADAY, Erest = vsSHE(rest);
|
|
448
|
+
console.log(`rest ${Erest.toFixed(4)} V vs SHE; E° + V_T ln(c₃/c₂) = ${(0.769 + VT * Math.log(5 / 10)).toFixed(4)} V`);
|
|
449
|
+
const drive = (E) => E - Erest + rest.terminals.left.V; // the terminal voltage for E vs SHE
|
|
450
|
+
// Steady, 0.2 V positive of rest: oxidising Fe²⁺. Its limiting current F·D·c/L is 35 A/m²; the
|
|
451
|
+
// kinetics (i₀ ≈ 1 A/m²) still hold it to about half here.
|
|
452
|
+
console.log(`anodic ${new Device(electrode(drive(Erest + 0.2))).solve().terminals.left.current.toFixed(2)} A/m²`); // 16.81
|
|
453
|
+
// A potential step from rest to 0.5 V positive: at first Fe²⁺ is depleted as at a plane,
|
|
454
|
+
// Cottrell's F·c·√(D/πt), until the stagnant layer is crossed (L²/D ≈ 0.5 s).
|
|
455
|
+
const dev = new Device(electrode(drive(Erest)));
|
|
456
|
+
dev.solve();
|
|
457
|
+
dev.set({ contacts: { left: { V: drive(Erest + 0.5) } } });
|
|
458
|
+
const run = dev.advance(0.03, { dtMax: 1e-3 }); // run.trace: this call's accepted steps
|
|
459
|
+
for (const t of [3e-3, 1e-2, 3e-2]) {
|
|
460
|
+
const k = run.trace.t.findIndex((tk) => tk >= t);
|
|
461
|
+
// (trace.current is the right contact's toward +x: positive for an anodic electrode on the left)
|
|
462
|
+
console.log(`${t * 1e3} ms: ${run.trace.current[k].toFixed(2)} A/m², Cottrell ${(FARADAY * 10 * Math.sqrt(IONS['Fe2+'].D / (Math.PI * run.trace.t[k]))).toFixed(2)}`);
|
|
463
|
+
}
|
|
292
464
|
```
|
|
293
465
|
|
|
466
|
+
A cyclic voltammogram is this electrode driven by `triangle({ from, to, period })`, the period
|
|
467
|
+
being 2|to − from| over the scan rate: `solve()` it at `from` first, since the scan starts there
|
|
468
|
+
at t = 0, then `advance()`. Its potential against the bath's terminal is −`trace.voltage` (that
|
|
469
|
+
is V_right − V_left), and `trace.current` is anodic positive.
|
|
470
|
+
|
|
294
471
|
## Template: corrosion under a drop (an electrode spread through a film)
|
|
295
472
|
|
|
296
|
-
A **port with reactions** is an electrode spread through a
|
|
297
|
-
|
|
298
|
-
`area`
|
|
299
|
-
|
|
300
|
-
|
|
301
|
-
x is the radius of a drop seen from its centre, A = 2πr·h(r), and every current and amount becomes
|
|
302
|
-
a total through it (A, mol), not per m².
|
|
473
|
+
A **port with reactions** is an electrode spread through a strictly neutral region: a metal under
|
|
474
|
+
a film of water, a crevice's walls, a porous electrode. Its `terminal` is the metal's carrier,
|
|
475
|
+
`area` its area per volume (1/h under a film h thick), each reaction Butler–Volmer per area, and
|
|
476
|
+
a `capacitance` the double layer. A **`geometry`** gives the device a cross-section A(x): here x
|
|
477
|
+
is the radius of a drop, A = 2πr·h(r), and currents and amounts become totals (A, mol).
|
|
303
478
|
|
|
304
479
|
```js
|
|
305
480
|
import { Device, GAS_CONSTANT, FARADAY } from 'driftlet';
|
|
306
|
-
import { aqueous, polarization } from 'driftlet/kit';
|
|
481
|
+
import { aqueous, polarization, H2O } from 'driftlet/kit';
|
|
307
482
|
|
|
308
483
|
// Salt water on iron: a drop 3 mm across. The iron dissolves and reduces O₂, which comes in from
|
|
309
484
|
// the air through the drop's top, fastest at the thin rim: the centre corrodes, the rim doesn't.
|
|
@@ -321,7 +496,7 @@ const dev = new Device({
|
|
|
321
496
|
regions: [{ name: 'drop', material: 'water', length: R, c0: { 'Na+': 500, 'Cl-': 500 + 2e-6, 'Fe2+': 1e-6, 'OH-': 1e-4, 'H+': 1e-4, O2: cO2 } }],
|
|
322
497
|
contacts: { left: { phi: 'neutral' }, right: { phi: 'neutral' } }, // closed: the centre, and the rim
|
|
323
498
|
bulkReactions: [
|
|
324
|
-
{ equation: 'H+ + OH- = H2O', fixed: { H2O
|
|
499
|
+
{ equation: 'H+ + OH- = H2O', fixed: { H2O }, kf: { water: 1.4e8 } }, // H2O: water's μ, −237.129 kJ/mol
|
|
325
500
|
// O₂ from the air through the drop: a rate k_f (1 − c/c_sat), k_f = D c_sat/h² (not a port's
|
|
326
501
|
// exchange link, whose rate is linear in μ rather than c)
|
|
327
502
|
{ equation: 'Air = O2', fixed: { Air: 16.4e3 + RT * Math.log(cO2 / 1000) }, kf: { water: { x: r, values: h.map((y) => (D * cO2) / (y * y)) } } },
|
|
@@ -333,7 +508,7 @@ const dev = new Device({
|
|
|
333
508
|
capacitance: { C: 0.2, zeroCharge: -0.4 }, // the double layer: the potential moves continuously
|
|
334
509
|
reactions: [
|
|
335
510
|
{ equation: 'Fe2+ + 2 e- = Fe(s)', fixed: { 'Fe(s)': 0 }, k0: 5e-6, alpha: 0.5 },
|
|
336
|
-
{ equation: 'O2 + 2 H2O + 4 e- = 4 OH-', fixed: { H2O
|
|
511
|
+
{ equation: 'O2 + 2 H2O + 4 e- = 4 OH-', fixed: { H2O }, k0: 3e-9, alpha: 0.125 },
|
|
337
512
|
],
|
|
338
513
|
}],
|
|
339
514
|
grid: { hmin: 5e-6, hmax: 60e-6, ratio: 1.2 },
|
|
@@ -350,55 +525,195 @@ const evans = polarization(dev, sol, { port: 'iron', x: 0 }, levels);
|
|
|
350
525
|
for (const rx of evans.reactions) console.log(`${rx.equation}: ${Array.from(rx.current, (i) => i.toFixed(2)).join(', ')} A/m²`);
|
|
351
526
|
```
|
|
352
527
|
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
(docs/
|
|
528
|
+
Species can take an electrode's surface sites (`surface`, Langmuir coverages), and a reaction
|
|
529
|
+
with `bare: true` runs only on bare metal: a passive film (docs/device.md). A battery's insertion
|
|
530
|
+
electrode is a material described by its OCV curve (docs/statistics.md).
|
|
356
531
|
|
|
357
|
-
## Template: a
|
|
532
|
+
## Template: a cell membrane
|
|
358
533
|
|
|
359
|
-
A
|
|
360
|
-
|
|
361
|
-
|
|
362
|
-
|
|
363
|
-
|
|
534
|
+
A lipid bilayer is a face: a capacitor (1 µF/cm², 0.01 F/m²) crossed by channels with a
|
|
535
|
+
permeability (`{ type: 'permeability', P }`, m/s: Goldman–Hodgkin–Katz comes out of it) and by
|
|
536
|
+
pumps, reactions with saturating kinetics (`vmax`, `K`). The membrane potential is φ_in − φ_out,
|
|
537
|
+
read from `sol.phi` as below. (A bath's terminal V is its φ only without a reference species,
|
|
538
|
+
`bath(c, drive)`; `bath(c, 'Cl-')`'s is Cl⁻'s level, which differs by Cl⁻'s Nernst term.)
|
|
364
539
|
|
|
365
540
|
```js
|
|
366
|
-
import { Device,
|
|
541
|
+
import { Device, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
542
|
+
import { build, layer, bath, aqueous, check } from 'driftlet/kit';
|
|
367
543
|
|
|
368
|
-
const T =
|
|
369
|
-
const
|
|
370
|
-
const
|
|
371
|
-
|
|
544
|
+
const T = 310.15, VT = (GAS_CONSTANT * T) / FARADAY;
|
|
545
|
+
const out = { 'Na+': 145, 'K+': 5, 'Cl-': 110, 'A-': 40 }; // mM = mol/m³; A⁻: anions that don't cross
|
|
546
|
+
const inside = { 'Na+': 12, 'K+': 140, 'Cl-': 10, 'A-': 142 };
|
|
547
|
+
const water = aqueous(['Na+', 'K+', 'Cl-'], { epsr: 0 }); // strictly neutral solutions
|
|
548
|
+
water.species.push({ name: 'A-', z: -1, cRef: 1000 });
|
|
549
|
+
water.materials.water.species['A-'] = { D: 0.5e-9, mu0: 0 };
|
|
550
|
+
const P = { 'K+': 1e-8, 'Na+': 0.04e-8, 'Cl-': 0.45e-8 }; // m/s, Hodgkin and Katz's ratios
|
|
551
|
+
const membrane = {
|
|
552
|
+
phi: { type: 'capacitive', C: 0.01 },
|
|
553
|
+
species: { 'K+': { type: 'permeability', P: P['K+'] }, 'Na+': { type: 'permeability', P: P['Na+'] }, 'Cl-': { type: 'permeability', P: P['Cl-'] }, 'A-': 'blocked' },
|
|
554
|
+
// The Na⁺/K⁺ pump (outside on the left): 3 Na⁺ out, 2 K⁺ in, per ATP (50 kJ/mol); vmax ≈ 3000
|
|
555
|
+
// pumps per µm² at 100 cycles/s.
|
|
556
|
+
reactions: [{ equation: '3 Na+(right) + 2 K+(left) + ATP = 3 Na+(left) + 2 K+(right) + ADP', fixed: { ATP: 50e3, ADP: 0 }, vmax: 5e-7, K: { 'Na+': 10, 'K+': 1.5 } }],
|
|
557
|
+
};
|
|
558
|
+
const cell = build({
|
|
559
|
+
T,
|
|
560
|
+
library: [water],
|
|
561
|
+
stack: [
|
|
562
|
+
bath(out, 'Cl-'), // the extracellular fluid, held
|
|
563
|
+
layer('water', 1e-6, { name: 'outside', c0: out }),
|
|
564
|
+
membrane,
|
|
565
|
+
layer('water', 5e-6, { name: 'cytoplasm', c0: inside }), // a closed cell: its contents set by leaks and the pump
|
|
566
|
+
{ species: { 'Na+': 'blocked', 'K+': 'blocked', 'Cl-': 'blocked', 'A-': 'blocked' }, phi: 'neutral' },
|
|
567
|
+
],
|
|
568
|
+
grid: { hmin: 50e-9, hmax: 200e-9 },
|
|
569
|
+
});
|
|
570
|
+
const dev = new Device(cell), sol = dev.solve();
|
|
571
|
+
const g = sol.x.length - 1, ci = (s) => sol.c[s][g], Vm = sol.phi[g] - sol.phi[0];
|
|
572
|
+
// Mullins–Noda: in steady state the pump's 3:2 sets the ratio of the Na⁺ and K⁺ leaks.
|
|
573
|
+
const mn = VT * Math.log((1.5 * P['K+'] * out['K+'] + P['Na+'] * out['Na+']) / (1.5 * P['K+'] * ci('K+') + P['Na+'] * ci('Na+')));
|
|
574
|
+
console.log(`V_m = ${(Vm * 1e3).toFixed(2)} mV (Mullins–Noda ${(mn * 1e3).toFixed(2)}), inside Na⁺ ${ci('Na+').toFixed(1)} K⁺ ${ci('K+').toFixed(1)} mM`);
|
|
575
|
+
console.log(check(dev, sol).text); // per compartment: Na⁺ leaks into the cytoplasm as fast as it's pumped out
|
|
576
|
+
```
|
|
577
|
+
|
|
578
|
+
Between two baths instead (the inside one `bath(inside, 'Cl-', { I: 0 })`: held composition, no
|
|
579
|
+
current), V_m is GHK. Without the pump, a closed cell runs down to Donnan equilibrium.
|
|
580
|
+
|
|
581
|
+
## Template: a voltage clamp
|
|
582
|
+
|
|
583
|
+
A face's `gates` (each a fraction open, dx/dt = α(V)(1 − x) − β(V)x with V = φ_right − φ_left)
|
|
584
|
+
scale its links (`gates: { m: 3, h: 1 }`). `hodgkinHuxley({ T, linear: true })` (kit) writes the
|
|
585
|
+
squid axon's as Hodgkin and Huxley had them, conductances g(V − E). Between two baths without a
|
|
586
|
+
reference species, V_right − V_left is V_m, so a held step is their voltage clamp.
|
|
587
|
+
|
|
588
|
+
```js
|
|
589
|
+
import { Device, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
590
|
+
import { build, layer, bath, aqueous, hodgkinHuxley } from 'driftlet/kit';
|
|
591
|
+
|
|
592
|
+
const T = 279.45, VT = (GAS_CONSTANT * T) / FARADAY; // HH's 6.3 °C
|
|
593
|
+
const out = { 'Na+': 440, 'K+': 20, 'Cl-': 450, 'A-': 10 }, inside = { 'Na+': 50, 'K+': 400, 'Cl-': 52, 'A-': 398 }; // squid, mM
|
|
594
|
+
const water = aqueous(['Na+', 'K+', 'Cl-'], { epsr: 0 });
|
|
595
|
+
water.species.push({ name: 'A-', z: -1, cRef: 1000 });
|
|
596
|
+
water.materials.water.species['A-'] = { D: 0.5e-9, mu0: 0 };
|
|
597
|
+
const hh = hodgkinHuxley({ T, linear: true });
|
|
598
|
+
const step = -0.01; // from −65 mV to −10 mV at 1 ms
|
|
599
|
+
const dev = new Device(
|
|
600
|
+
build({
|
|
372
601
|
T,
|
|
373
|
-
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
|
|
378
|
-
|
|
379
|
-
|
|
380
|
-
|
|
381
|
-
grid: { hmin:
|
|
382
|
-
})
|
|
383
|
-
|
|
384
|
-
|
|
385
|
-
|
|
386
|
-
|
|
387
|
-
|
|
602
|
+
library: [water],
|
|
603
|
+
stack: [
|
|
604
|
+
bath(out), // the outside, on the left
|
|
605
|
+
layer('water', 1e-6, { c0: out }),
|
|
606
|
+
{ phi: { type: 'capacitive', C: 0.01 }, gates: hh.gates, species: { ...hh.species, 'A-': 'blocked' } },
|
|
607
|
+
layer('water', 1e-6, { c0: inside }),
|
|
608
|
+
bath(inside, { t: [0, 1e-3, 1e-3, 1], values: [-0.065, -0.065, step, step] }),
|
|
609
|
+
],
|
|
610
|
+
grid: { hmin: 20e-9, hmax: 0.2e-6 },
|
|
611
|
+
}),
|
|
612
|
+
);
|
|
613
|
+
dev.solve(); // the rest at −65 mV, the gates at their values there
|
|
614
|
+
const run = dev.advance(11e-3, { dtMax: 0.02e-3, probes: [{ interface: 0, species: 'Na+' }, { interface: 0, species: 'K+' }] });
|
|
615
|
+
const [na, k] = run.trace.probes.map((N) => N.map((x) => -FARADAY * x)); // outward currents, A/m²
|
|
616
|
+
const peak = na.indexOf(Math.min(...na)), EK = VT * Math.log(out['K+'] / inside['K+']);
|
|
617
|
+
console.log(`I_Na peaks ${((run.trace.t[peak] - 1e-3) * 1e3).toFixed(2)} ms into the step, ${(na[peak] * 0.1).toFixed(2)} mA/cm²`); // 0.73 ms, −1.48
|
|
618
|
+
console.log(`g_K after 10 ms: ${((k.at(-1) / (step - EK)) * 0.1).toFixed(2)} mS/cm²`); // 21.12: HH's 36 n∞⁴ is 21.5, which n nearly reaches by 10 ms
|
|
619
|
+
```
|
|
620
|
+
|
|
621
|
+
## Template: an action potential
|
|
622
|
+
|
|
623
|
+
Without `linear: true` (given `inside` and `outside`), `hodgkinHuxley` writes GHK permeabilities
|
|
624
|
+
matched to HH's conductances at −65 mV, which rectify as real channels do. A pump-less cell has no
|
|
625
|
+
steady rest (`solve()` finds Donnan), so start the transient from the concentrations given.
|
|
626
|
+
|
|
627
|
+
```js
|
|
628
|
+
import { Device } from 'driftlet';
|
|
629
|
+
import { build, layer, bath, aqueous, injector, pulse, hodgkinHuxley } from 'driftlet/kit';
|
|
630
|
+
|
|
631
|
+
const T = 279.45; // HH's 6.3 °C
|
|
632
|
+
const out = { 'Na+': 440, 'K+': 20, 'Cl-': 450, 'A-': 10 }, inside = { 'Na+': 50, 'K+': 400, 'Cl-': 52, 'A-': 398 }; // squid, mM
|
|
633
|
+
const water = aqueous(['Na+', 'K+', 'Cl-'], { epsr: 0 });
|
|
634
|
+
water.species.push({ name: 'A-', z: -1, cRef: 1000 });
|
|
635
|
+
water.materials.water.species['A-'] = { D: 0.5e-9, mu0: 0 };
|
|
636
|
+
const hh = hodgkinHuxley({ inside, outside: out, T }); // GHK channels; outside on the left
|
|
637
|
+
const axon = new Device(
|
|
638
|
+
build({
|
|
639
|
+
T,
|
|
640
|
+
library: [water],
|
|
641
|
+
stack: [
|
|
642
|
+
bath(out, 'Cl-'),
|
|
643
|
+
layer('water', 5e-6, { name: 'outside', c0: out }),
|
|
644
|
+
{ phi: { type: 'capacitive', C: 0.01 }, gates: hh.gates, species: { ...hh.species, 'A-': 'blocked' } },
|
|
645
|
+
layer('water', 20e-6, { name: 'cytoplasm', c0: inside }),
|
|
646
|
+
{ species: { 'Na+': 'blocked', 'K+': 'blocked', 'Cl-': 'blocked', 'A-': 'blocked' }, phi: 'neutral' },
|
|
647
|
+
],
|
|
648
|
+
// the stimulus: 10 µA/cm² of K⁺ for 1 ms at 20 ms, from a pipette in the cytoplasm
|
|
649
|
+
ports: [injector({ region: 'cytoplasm', from: 15e-6, to: 20e-6, species: 'K+', I: pulse({ start: 20e-3, width: 1e-3, amplitude: 0.1 }) })],
|
|
650
|
+
grid: { hmin: 50e-9, hmax: 1e-6 },
|
|
651
|
+
}),
|
|
652
|
+
);
|
|
653
|
+
let peak = -1;
|
|
654
|
+
for (let k = 1; k <= 300; k++) {
|
|
655
|
+
const sol = axon.advance(k * 1e-4); // 0.1 ms at a time
|
|
656
|
+
peak = Math.max(peak, sol.interfaces[0].V); // V_m, and sol.interfaces[0].gates = { m, h, n }
|
|
388
657
|
}
|
|
658
|
+
console.log(`peak ${(peak * 1e3).toFixed(1)} mV`); // +12.6: GHK's Na⁺ current is limited by the 50 mM inside (linear: true gives +37.9, HH's own)
|
|
659
|
+
```
|
|
660
|
+
|
|
661
|
+
## Template: an action potential travelling along an axon
|
|
662
|
+
|
|
663
|
+
Here x runs along the axon: the axoplasm is one region, and the membrane a port spanning it, a
|
|
664
|
+
capacitance and gated channels to an outside given as a `bath` (the port's V is then the
|
|
665
|
+
outside's φ). `hodgkinHuxley({ T, area })` writes HH's channels for it, `area` being the membrane
|
|
666
|
+
per volume, 2/a. Cable theory isn't put in; it comes out of the ions' drift. `ports[k].Vm[j]` and
|
|
667
|
+
`ports[k].gates[name][j]` give the membrane at each node. A myelinated axon is regions, each with
|
|
668
|
+
its own port (an internode's just a small capacitance).
|
|
669
|
+
|
|
670
|
+
```js
|
|
671
|
+
import { Device, FARADAY, GAS_CONSTANT } from 'driftlet';
|
|
672
|
+
import { hodgkinHuxley, injector, pulse } from 'driftlet/kit';
|
|
673
|
+
|
|
674
|
+
const T = 291.65, VT = (GAS_CONSTANT * T) / FARADAY, a = 238e-6; // 18.5 °C, a squid giant axon
|
|
675
|
+
const inside = { 'Na+': 50, 'K+': 400, 'Cl-': 52.5, 'A-': 397.5 }; // mM
|
|
676
|
+
// Outside levels that put the Nernst potentials at HH's +50, −77 and −54.4 mV (leak as Cl⁻).
|
|
677
|
+
const outside = { 'Na+': 50 * Math.exp(0.05 / VT), 'K+': 400 * Math.exp(-0.077 / VT), 'Cl-': 52.5 * Math.exp(0.054387 / VT) };
|
|
678
|
+
// One D for the small ions, giving HH's 35.4 Ω·cm.
|
|
679
|
+
const D = 1 / 0.354 / ((FARADAY * FARADAY) / (GAS_CONSTANT * T)) / (50 + 400 + 52.5);
|
|
680
|
+
const sp = (d) => ({ D: d, mu0: 0, cRef: 1000 });
|
|
681
|
+
const sealed = { species: { 'Na+': 'blocked', 'K+': 'blocked', 'Cl-': 'blocked', 'A-': 'blocked' }, phi: 'neutral' };
|
|
682
|
+
const hh = hodgkinHuxley({ T, area: 2 / a });
|
|
683
|
+
const axon = new Device({
|
|
684
|
+
T,
|
|
685
|
+
species: [{ name: 'Na+', z: 1 }, { name: 'K+', z: 1 }, { name: 'Cl-', z: -1 }, { name: 'A-', z: -1 }],
|
|
686
|
+
materials: { axoplasm: { epsr: 0, species: { 'Na+': sp(D), 'K+': sp(D), 'Cl-': sp(D), 'A-': sp(1e-12) } } },
|
|
687
|
+
regions: [{ name: 'axon', material: 'axoplasm', length: 0.06, c0: inside }],
|
|
688
|
+
contacts: { left: sealed, right: sealed },
|
|
689
|
+
ports: [
|
|
690
|
+
{ name: 'membrane', region: 'axon', V: 0, area: 2 / a, capacitance: { C: 0.01, zeroCharge: 0 }, bath: { c: outside }, gates: hh.gates, species: hh.species },
|
|
691
|
+
injector({ name: 'stim', region: 'axon', from: 0, to: 1e-3, species: 'K+', I: pulse({ start: 30e-3, width: 0.2e-3, amplitude: 30 }) }),
|
|
692
|
+
],
|
|
693
|
+
grid: { hmin: 2e-4, hmax: 2e-4 },
|
|
694
|
+
});
|
|
695
|
+
axon.advance(30e-3); // settle to rest (no pump: start from the concentrations, not solve())
|
|
696
|
+
const sol = axon.advance(34e-3, { dtMax: 5e-6, probes: [{ x: 0.02, quantity: 'phi' }, { x: 0.04, quantity: 'phi' }] });
|
|
697
|
+
const { t, probes } = sol.trace, at = (v) => t[v.findIndex((x) => x > 0)]; // (φ inside, the outside's held at 0)
|
|
698
|
+
console.log(`${(0.02 / (at(probes[1]) - at(probes[0]))).toFixed(1)} m/s`); // 18.8 here (finely resolved, 18.73; HH computed 18.8)
|
|
389
699
|
```
|
|
390
700
|
|
|
391
|
-
|
|
392
|
-
(a drive only, so it's cheap and keeps the state as a warm start). An organic electrochemical
|
|
393
|
-
transistor is the same with a volumetric capacitance C*: `area: 1 / t, capacitance: { C: Cstar * t }`
|
|
394
|
-
(docs/device.md, "A capacitance through a window").
|
|
701
|
+
## Transients
|
|
395
702
|
|
|
396
|
-
|
|
703
|
+
`advance(t, opts)` steps adaptively from the device's present state (its `c0`, or the steady
|
|
704
|
+
state if you called `solve()`) to time t. It returns the solution there, with `done` and a `trace`
|
|
705
|
+
of this call's accepted steps (`t`, `current`, `voltage`: V_right − V_left). It stops short at
|
|
706
|
+
`budgetMs` (an animation frame: call again) or, with a warning saying why, at `maxSteps` (100000)
|
|
707
|
+
or a step that won't converge. `probes`, read at accepted steps (give `dtMax` to resolve them):
|
|
708
|
+
`{ x, species }` (c, or `quantity: 'V'`), `{ x, quantity: 'phi' }`, and at a face `{ interface: f,
|
|
709
|
+
species }` (its flux) or `{ interface: f, gate }`.
|
|
397
710
|
|
|
398
|
-
|
|
399
|
-
|
|
400
|
-
|
|
401
|
-
steady state
|
|
711
|
+
- **Events.** To stop at one (a cut-off voltage, a diode's storage time), advance in short calls
|
|
712
|
+
and test after each: a driven current held past what the device can pass fails to converge.
|
|
713
|
+
- **Storage.** A device that only stores what comes in (a battery host filling at a current) has
|
|
714
|
+
no steady state: `advance()` it from its `c0`, don't `solve()` it (docs/statistics.md).
|
|
715
|
+
- **Other steps.** `dev.step(dt)` is one backward-Euler step, and `dev.impedance(frequencies,
|
|
716
|
+
{ terminal })` the small-signal Z(f) about the steady state, in Ω·m².
|
|
402
717
|
|
|
403
718
|
```js
|
|
404
719
|
import { Device, units, FARADAY } from 'driftlet';
|
|
@@ -418,191 +733,107 @@ const def = build({
|
|
|
418
733
|
});
|
|
419
734
|
const dev = new Device(def);
|
|
420
735
|
const rest = dev.solve(); // the steady state at t = 0 (solve() doesn't advance time)
|
|
421
|
-
// In a page, call advance(tNext, { budgetMs: 12, probes }) once per animation frame, carrying on
|
|
422
|
-
// next frame while sol.done is false (or let recorder() join the traces and keep frames to scrub
|
|
423
|
-
// back through). Probes read at accepted steps; dtMax keeps them close.
|
|
424
736
|
const run = dev.advance(10e-6, { dtMax: 20e-9, probes: [{ x: 1.525e-3, species: 'h+' }] });
|
|
425
737
|
const seen = run.trace.probes[0], k = seen.indexOf(Math.max(...seen));
|
|
426
738
|
const tArrive = run.trace.t[k] - width / 2; // from the pulse's middle
|
|
427
739
|
console.log(`peak at ${(run.trace.t[k] * 1e6).toFixed(2)} µs, Δp ${units.toPerCm3(seen[k] - rest.c['h+'][0]).toExponential(1)} cm⁻³: μ_p ≈ ${(1e-3 / (E * tArrive) * 1e4).toFixed(0)} cm²/(V·s)`); // ≈ 1950 for the 1900 put in: a spreading, decaying pulse peaks a little early
|
|
428
740
|
```
|
|
429
741
|
|
|
430
|
-
To start from a state
|
|
431
|
-
|
|
432
|
-
|
|
433
|
-
even for a species a contact feeds;
|
|
434
|
-
|
|
435
|
-
|
|
436
|
-
|
|
742
|
+
To start from a state rather than simulate how it got there (a packet already injected, a salt
|
|
743
|
+
gradient laid down), give a region's `c0` a profile, `{ 'h+': { x: [...], values: [...] } }` against
|
|
744
|
+
the device's x, and `advance()` the new `Device` without `solve()`. A given `c0` is the starting
|
|
745
|
+
state even for a species a contact feeds; the rest start at their contact's level. The grid isn't
|
|
746
|
+
fitted to the profile: grade it fine where the profile is steep (a warning says where it isn't).
|
|
747
|
+
`advance()`'s `tol` (1e-3) is each step's error, in thermal units: tighten it, or cap `dtMax`, for
|
|
748
|
+
numbers to compare with theory.
|
|
437
749
|
|
|
438
|
-
Transients cost more where a carrier's density spans many decades (minority holes in silicon
|
|
439
|
-
|
|
440
|
-
|
|
441
|
-
|
|
442
|
-
opts)` takes the same options, `rec.trace` is the whole run's trace from the start, and
|
|
443
|
-
`rec.frames` are whole solutions (at the start, then at `times`, every `every` s, or the end of
|
|
444
|
-
each call), with `rec.frame(t)` the one at or before t, for a time slider.
|
|
445
|
-
|
|
446
|
-
**Prefer a curated device to inventing numbers** where one fits: `perovskiteCell({ V, light,
|
|
447
|
-
bulkSRH })` is IonMonger's default perovskite solar cell (mobile iodide vacancies, SRH in the bulk
|
|
448
|
-
and at both faces), and `PEROVSKITE_SCANS` holds IonMonger's J–V scans of it at seven rates;
|
|
449
|
-
`hysteresis(rec.trace, turn)` reads the same figures from yours, so a demo can show its agreement.
|
|
450
|
-
The definition is plain data: print it, edit what your demo varies.
|
|
451
|
-
|
|
452
|
-
## Template: a live page with a slider
|
|
453
|
-
|
|
454
|
-
`live()` merges slider moves made during a solve, warm-starts each solve and keeps the last
|
|
455
|
-
good solution. `bandDiagram()` returns an SVG string. Pass `worker: true` to `live()` to solve in
|
|
456
|
-
a Web Worker (it works with the library loaded from a CDN: a same-origin stub imports it). Calling
|
|
457
|
-
`set()` from `onsolution` is fine, for a quantity the page solves for itself (it queues the next
|
|
458
|
-
solve), as long as it settles rather than ping-pongs.
|
|
459
|
-
|
|
460
|
-
```html
|
|
461
|
-
<!doctype html>
|
|
462
|
-
<meta charset="utf-8">
|
|
463
|
-
<title>pn junction</title>
|
|
464
|
-
<label>bias <input id="V" type="range" min="-0.5" max="0.7" step="0.01" value="0"></label>
|
|
465
|
-
<span id="readout"></span>
|
|
466
|
-
<div id="figure"></div>
|
|
467
|
-
<script type="module">
|
|
468
|
-
import { units } from 'https://cdn.jsdelivr.net/npm/driftlet@0.12.0/src/index.js';
|
|
469
|
-
import { build, layer, ohmic, semiconductor, live } from 'https://cdn.jsdelivr.net/npm/driftlet@0.12.0/src/kit.js';
|
|
470
|
-
import { bandDiagram } from 'https://cdn.jsdelivr.net/npm/driftlet@0.12.0/src/plot.js';
|
|
471
|
-
|
|
472
|
-
const def = build({
|
|
473
|
-
T: 300,
|
|
474
|
-
library: [semiconductor('Si')],
|
|
475
|
-
stack: [ohmic(0), layer('Si', 1e-6, { donors: units.perCm3(1e17) }), layer('Si', 1e-6, { acceptors: units.perCm3(1e16) }), ohmic(0)],
|
|
476
|
-
bulkReactions: [{ equation: 'e- + h+ = 0', kf: { Si: 1e8 } }],
|
|
477
|
-
grid: { hmin: 1e-9, hmax: 20e-9 },
|
|
478
|
-
});
|
|
479
|
-
const slider = document.getElementById('V');
|
|
480
|
-
const dev = live(def, {
|
|
481
|
-
onsolution(sol, info) {
|
|
482
|
-
document.getElementById('figure').innerHTML = bandDiagram(sol, { energy: true, title: `V = ${sol.terminals.right.V.toFixed(2)} V` });
|
|
483
|
-
document.getElementById('readout').textContent = info.failed ? 'no solution here' : `I = ${sol.current.toExponential(2)} A/m²`;
|
|
484
|
-
},
|
|
485
|
-
});
|
|
486
|
-
slider.addEventListener('input', () => dev.set({ contacts: { right: { V: +slider.value } } }));
|
|
487
|
-
</script>
|
|
488
|
-
```
|
|
750
|
+
Transients cost more where a carrier's density spans many decades (minority holes in silicon)
|
|
751
|
+
and at strong injection; budget for that, or coarsen the grid. `recorder(dev, { every, times,
|
|
752
|
+
probes })` (kit) runs one in pieces: `rec.trace` is the whole run's, and `rec.frame(t)` the
|
|
753
|
+
whole solution at or before t, for a time slider.
|
|
489
754
|
|
|
490
755
|
## Reading level diagrams
|
|
491
756
|
|
|
492
|
-
What `bandDiagram()` and `traces()` draw, and how to explain it
|
|
493
|
-
|
|
494
|
-
|
|
495
|
-
|
|
496
|
-
|
|
497
|
-
|
|
498
|
-
|
|
499
|
-
|
|
500
|
-
|
|
501
|
-
|
|
502
|
-
|
|
503
|
-
|
|
504
|
-
|
|
505
|
-
- **Which picture.** For a device of electrons and holes only, draw the familiar band diagram,
|
|
506
|
-
energy up: `bandDiagram(sol, { energy: true })` (E_c, E_v, E_Fn, E_Fp in eV). The species
|
|
507
|
-
voltages below are the same lines in volts, turned over; use them where ions share the diagram,
|
|
508
|
-
or for equilibrium between species, and don't present them in place of the band diagram.
|
|
509
|
-
|
|
510
|
-
- **Fermi level** V_e⁻ = −μ̄_e⁻/F: the circuit voltage, what a voltmeter reads. A cell's voltage is
|
|
511
|
-
the difference between its terminals' V_e⁻.
|
|
512
|
-
- **Redox level** of Ox + z e⁻ ⇌ Red, `level(sol, half)`: V_e⁻(Ox/Red) = (μ̄_Ox − μ̄_Red)/(zF), where
|
|
513
|
-
an electrode exchanging electrons by that couple would sit in equilibrium with the local
|
|
514
|
-
composition. Drawn thick and dashed. At an electrode face, the step from the metal's Fermi level
|
|
515
|
-
to it is the surface overpotential; through the solution it slopes with ohmic drop and
|
|
516
|
-
concentration polarisation. Each couple has its own; they agree only in redox equilibrium.
|
|
517
|
-
- **Standard redox level** (`{ standard: true }`), thin and dashed: every participant at reference
|
|
518
|
-
concentration. The redox level sits RT/(zF) ln(a_Ox/a_Red) from it (Nernst, locally).
|
|
519
|
-
- **Electrode potentials** are gaps to the SHE's standard level V°_e⁻(SHE): E = V_e⁻(electrode) −
|
|
520
|
-
V°_e⁻(SHE), E° = V°_e⁻(Ox/Red) − V°_e⁻(SHE), η = E − E_eq. With the data library's μ°,
|
|
521
|
-
V°_e⁻(SHE) in water is φ, so `phi: true` draws it. It slopes under current: "vs SHE" needs a
|
|
522
|
-
place (say, the stirred bulk).
|
|
523
|
-
- **Species voltage** V_i = μ̄_i/(z_iF) (thick, solid) for every charged species: the Fermi level
|
|
524
|
-
for e⁻, a quasi-Fermi level for e⁻ and h⁺ in a semiconductor, what a reversible electrode reads
|
|
525
|
-
for an ion. It's a display of μ̄_i (the physics, which also covers neutral species): each
|
|
526
|
-
species moves down its own μ̄_i, drift and diffusion together, so its current flows down slopes
|
|
527
|
-
in V_i (cations and holes move downhill, electrons and anions uphill), and it's in equilibrium
|
|
528
|
-
where V_i is flat. A step at a face means resistance there.
|
|
757
|
+
What `bandDiagram()` and `traces()` draw, and how to explain it (docs/visualization.md has more):
|
|
758
|
+
|
|
759
|
+
- **Which picture.** For electrons and holes only, draw the familiar band diagram, energy up:
|
|
760
|
+
`bandDiagram(sol, { energy: true })` (E_c, E_v, E_Fn, E_Fp in eV, E = −V). The species voltages
|
|
761
|
+
below are the same lines in volts, turned over: use them where ions share the diagram, or for
|
|
762
|
+
equilibrium between species, never in place of the band diagram.
|
|
763
|
+
- **Species voltage** V_i = μ̄_i/(z_iF) (thick, solid): the Fermi level for e⁻ (what a voltmeter
|
|
764
|
+
reads), a quasi-Fermi level in a semiconductor, what a reversible electrode reads for an ion.
|
|
765
|
+
Each species moves down its own μ̄_i, drift and diffusion together, so its current flows down
|
|
766
|
+
slopes in V_i (cations and holes downhill, electrons and anions uphill); flat is equilibrium,
|
|
767
|
+
and a step at a face is resistance there. Call it the species voltage and say what it is, since
|
|
768
|
+
it's new to most readers; credit Jamnik and Maier (Phys. Chem. Chem. Phys. 3, 1668 (2001))
|
|
769
|
+
where V_i rails explain impedance or linear response.
|
|
529
770
|
- **Standard level** V°_i = φ + μ°_i/(z_iF) (thin, solid): a band edge for e⁻ and h⁺; V_i − V°_i =
|
|
530
|
-
(RT/z_iF) ln(c/c_ref) for ideal species.
|
|
531
|
-
|
|
532
|
-
|
|
533
|
-
|
|
534
|
-
|
|
535
|
-
|
|
536
|
-
|
|
537
|
-
|
|
538
|
-
|
|
539
|
-
|
|
540
|
-
|
|
541
|
-
|
|
542
|
-
|
|
543
|
-
|
|
544
|
-
|
|
545
|
-
|
|
771
|
+
(RT/z_iF) ln(c/c_ref) for ideal species. Its steps at faces are bookkeeping.
|
|
772
|
+
- **Redox level** of Ox + z e⁻ ⇌ Red (`level(sol, half)`, or `levels: [{ half }]` in the plot
|
|
773
|
+
options; thick, dashed): (μ̄_Ox − μ̄_Red)/(zF), where an electrode by that couple would sit in
|
|
774
|
+
equilibrium with the local solution. At an electrode its step from the metal's Fermi level is
|
|
775
|
+
the surface overpotential. `standard: true` gives its standard level (thin, dashed).
|
|
776
|
+
- **Electrode potentials** are gaps to the SHE's standard level, which with the library's μ° is φ
|
|
777
|
+
in water (`phi: true` draws it): E = V_e⁻(electrode) − V°_e⁻(SHE).
|
|
778
|
+
- **What's left out.** φ is a per-material convention, and −eφ isn't any electron's energy, so it
|
|
779
|
+
isn't drawn, except across an insulator with no mobile species (`phi: ['SiO2']`: its slope is
|
|
780
|
+
the field). No level is a fixed reference: shifting every line together changes nothing. A gap
|
|
781
|
+
between two species' levels carries the elements' conventional zeros, so read it through a
|
|
782
|
+
reaction; `shifts` (marked ⌇) moves one species' lines to fit a shared axis.
|
|
783
|
+
- **Your own style.** `traces(sol, opts)` gives `{ x, series: [{ id, label, kind, role, slot, y }],
|
|
784
|
+
regions, faces, range }`: `kind` says how a line reads (`'level'`, `'standard'`, `'redox'`,
|
|
785
|
+
`'redox-standard'`, `'phi'`), `themeColor(role, slot)` (plot) gives our colours,
|
|
786
|
+
`labelParts(label)` splits TeX-style subscripts, `NaN` breaks a line, and a face's doubled nodes
|
|
787
|
+
share an x (a vertical step).
|
|
546
788
|
|
|
547
789
|
## Good habits
|
|
548
790
|
|
|
549
|
-
- **Draw the closed-form answer alongside the simulation
|
|
550
|
-
|
|
551
|
-
|
|
552
|
-
|
|
553
|
-
|
|
554
|
-
|
|
555
|
-
|
|
556
|
-
currents and fluxes are totals through it. Where the real device isn't one,
|
|
557
|
-
say so and pick the slice that still tells the true story: a MOSFET's gate stack, read as the
|
|
558
|
-
MOS capacitor its channel sits on (pinch-off along the channel is 2D); a BJT along its
|
|
559
|
-
emitter–base–collector axis; one particle of a porous battery electrode, or a thin dense film,
|
|
560
|
-
rather than the whole porous electrode with diffusion inside its particles (that's a P2D model).
|
|
561
|
-
A metal that reacts all along a film of electrolyte (corroding iron under a drop, a crevice's
|
|
562
|
-
walls, a well-conducting porous matrix) is a port with `reactions` and an `area` per volume:
|
|
563
|
-
an electrode spread through a window, not a face at each end.
|
|
564
|
-
- **Check `sol.converged` and `sol.warnings`** on every solve, and pin the CDN version you
|
|
565
|
-
tested against.
|
|
791
|
+
- **Draw the closed-form answer alongside the simulation** wherever a textbook limit exists, as
|
|
792
|
+
the templates do. A solver's output looks authoritative even when an input is wrong, and a
|
|
793
|
+
mismatch is the cheapest way to catch it. Where the two should differ, say why.
|
|
794
|
+
- **Stay honestly inside 1D.** Where the real device isn't one-dimensional, say so and pick the
|
|
795
|
+
slice that tells the true story: a MOSFET as its gate stack or its channel, never both (pinch-off
|
|
796
|
+
is 2D); a BJT along its emitter–base–collector axis; one particle of a porous battery electrode
|
|
797
|
+
rather than the whole electrode (that's a P2D model).
|
|
566
798
|
|
|
567
799
|
## Common mistakes
|
|
568
800
|
|
|
569
|
-
- **
|
|
570
|
-
|
|
571
|
-
|
|
572
|
-
|
|
573
|
-
of the
|
|
574
|
-
- **A
|
|
575
|
-
|
|
576
|
-
|
|
577
|
-
|
|
578
|
-
|
|
579
|
-
|
|
580
|
-
- **Ions on both sides of a reacting face.** Label them: `'Li+(left) = Li+(right)'`, and give
|
|
581
|
-
their link (`species: { 'Li+': 'blocked' }` if they cross only by the reaction).
|
|
582
|
-
- **Unit slips.** D in cm²/s, μ° in eV, capacitance in µF/cm², T in °C. `describe(def)` flags
|
|
583
|
-
numbers that look like these.
|
|
584
|
-
- **A closed system with no amount.** A species that doesn't reach a contact needs `c0`.
|
|
585
|
-
- **A strictly neutral `c0` that doesn't balance.** With `epsr: 0`, Σ z·c0 must be zero (traces
|
|
586
|
-
included): `… carries a net charge of … mol/m³`. Add the counter-ion's share.
|
|
587
|
-
- **A sharp junction between very different solutions** (3 M KCl against 1 µM traces) can't
|
|
588
|
-
start: grade it over a few thin layers mixing one solution into the other, as at a frit.
|
|
589
|
-
- **A steady solve of a closed cell where every ion can cross.** Its steady state is complete
|
|
590
|
-
mixing. To watch a junction or a salt bridge, step in time from the unmixed `c0` (`advance`).
|
|
591
|
-
- **Everything floating.** At least one terminal must be held at a voltage `V`.
|
|
801
|
+
- **Errors that say what to give.** A missing alignment at a heterointerface (`vacuumDipole`
|
|
802
|
+
estimates one from electron affinities, docs/alignment.md), a metal face with no φ law,
|
|
803
|
+
everything floating (hold one terminal at a `V`), a species that reaches no contact without a
|
|
804
|
+
`c0`, an unbalanced `c0` in a closed neutral region (add the counter-ion's share), `'2e-'` for
|
|
805
|
+
`'2 e-'`, a current drive of the wrong sign. `interfaces[f]` is the stack's f-th face.
|
|
806
|
+
- **A gate as a contact on an oxide.** It fails as `'e-' is blocked at this contact`: make the
|
|
807
|
+
gate a metal layer with a capacitive face, as in the MOS template.
|
|
808
|
+
- **`ohmic()` on a metal.** Its default holds e⁻ and h⁺; on a metal write `ohmic(V, ['e-'])`.
|
|
809
|
+
- **Ions on both sides of a reacting face.** Label them, `'Li+(left) = Li+(right)'`, and block
|
|
810
|
+
them (`species: { 'Li+': 'blocked' }`) if they cross only by the reaction.
|
|
811
|
+
- **Unit slips.** D in cm²/s, μ° in eV, µF/cm², mS/cm², T in °C. `describe(def)` flags them.
|
|
592
812
|
- **The library's data are for 25 °C** (its semiconductors for 300 K: give `T: 300`). At body
|
|
593
|
-
temperature
|
|
594
|
-
|
|
595
|
-
|
|
596
|
-
|
|
597
|
-
|
|
598
|
-
|
|
599
|
-
the right. `sol.terminalVoltage` (and a trace's `voltage`) is V_right − V_left of the contacts,
|
|
600
|
-
which at baths are their reference species' levels: it differs from Δφ by that ion's Nernst term.
|
|
601
|
-
- **A coefficient without its space.** `'2e- + …'` reads `2e-` as a species name; the error says
|
|
602
|
-
to write `2 e-`.
|
|
603
|
-
- **Changing c0 with `set()`.** A carried state keeps what it holds; `c0` is only the starting
|
|
604
|
-
composition. Make a new `Device` to start over from it.
|
|
605
|
-
- **`solve()` before advancing from a `c0` profile.** It replaces the profile with the steady
|
|
606
|
-
state. Advance from the new `Device` directly. A profile's x is the device's, in m.
|
|
813
|
+
temperature the same μ° and D are a fair start; D rises about 2% per kelvin in water.
|
|
814
|
+
- **A steady solve of a closed cell where every ion can cross**: its steady state is complete
|
|
815
|
+
mixing. To watch a junction or a salt bridge, `advance()` from the unmixed `c0`.
|
|
816
|
+
- **A sharp junction between very different solutions** (3 M KCl against 1 µM) can't start:
|
|
817
|
+
grade it over a few thin layers, as at a frit.
|
|
818
|
+
- **Changing `c0` with `set()`.** A carried state keeps what it holds: make a new `Device`.
|
|
607
819
|
- **An unresolved double layer.** If `sol.warnings` says so, refine the grid (`hmin` below the
|
|
608
820
|
Debye length) or use a neutral model (`epsr: 0`, `phi: 'neutral'`).
|
|
821
|
+
|
|
822
|
+
## Exports
|
|
823
|
+
|
|
824
|
+
- `driftlet`: `Device`, `units`, `DeviceError`, `SolverError`, and the constants `FARADAY`,
|
|
825
|
+
`GAS_CONSTANT`, `EPS0`, `BOLTZMANN`, `ELEMENTARY_CHARGE`, `AVOGADRO` (there's no thermal-voltage
|
|
826
|
+
constant: V_T = GAS_CONSTANT·T/FARADAY).
|
|
827
|
+
- `driftlet/kit`:
|
|
828
|
+
- building: `build`, `combine`, `layer`, `ohmic`, `bath`, `half`, `level`, `SHE`,
|
|
829
|
+
`vacuumLevel`, `vacuumDipole`, `vacuumZeroCharge`, and the data library (`aqueous`,
|
|
830
|
+
`semiconductor`, `metal`, `IONS`, `SEMICONDUCTORS`, `METALS`, `H2O`, `WATER_EPSR`);
|
|
831
|
+
- sources: `pulse`, `square`, `triangle`, `ramp`, `injector`, `recombination`,
|
|
832
|
+
`photogeneration`;
|
|
833
|
+
- channels: `hodgkinHuxley`, `ghkCurrent`;
|
|
834
|
+
- checking: `describe`, `check`, `polarization` (an electrode's reactions at hypothetical
|
|
835
|
+
metal levels, with the solution held: an Evans diagram), `henderson` and `planck`
|
|
836
|
+
(liquid-junction potentials);
|
|
837
|
+
- pages: `live`, `traces`, `recorder`, `particles`;
|
|
838
|
+
- curated devices: `perovskiteCell`, `PEROVSKITE_SCANS`, `hysteresis`.
|
|
839
|
+
- `driftlet/plot` (a quick look): `bandDiagram`, `levelChart`, `labelParts`, `themeColor`.
|