driftlet 0.13.0 → 0.14.0

package/README.md

@@ -56,7 +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@0.13.0/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).
 

package/docs/device.md

@@ -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
@@ -950,17 +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

@@ -432,7 +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
@@ -508,6 +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

package/docs/logo-dark.svg

@@ -1,7 +1,8 @@
-<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 300 74" width="300" height="74" role="img" aria-label="driftlet">
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 269 74" width="269" height="74" role="img" aria-label="driftlet">
   <path d="M4 18 C 34 18, 46 20, 58 34 S 72 54, 80 54" fill="none" stroke="#e8584f" stroke-width="5" stroke-linecap="round"/>
   <path d="M4 34 C 34 34, 46 36, 58 50 S 72 70, 80 70" fill="none" stroke="#e8584f" stroke-width="1.8" stroke-linecap="round" opacity="0.75"/>
   <path d="M44.9 9.7 L38.9 6.1 M41.0 13.4 L32.8 8.5" stroke="#ffb3ab" stroke-width="1.8" stroke-linecap="round" opacity="0.6"/>
   <circle cx="52.2" cy="17.1" r="6.2" fill="#ffb3ab"/>
-  <text x="96" y="52" fill="#ffffff" font-family="system-ui, -apple-system, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif" font-size="46" font-weight="600" letter-spacing="-0.5">driftlet</text>
+  <!-- "driftlet" in Recursive (Sans Casual, weight 700), as outlines -->
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package/docs/logo.svg

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package/docs/reliability.md

@@ -64,7 +64,7 @@ recipes.
 | 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; HH's voltage clamp with their linear channels between baths, the K⁺ current g_K n∞⁴ (V − E_K); 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; 2e-3; 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 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 for the mixtures tested | 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 |