driftlet 0.12.0 → 0.13.0

package/src/types.js

@@ -114,7 +114,8 @@
  * @typedef {'blocked' | 'equilibrium'
  *   | { type: 'equilibrium', offset?: number, mu?: number }
  *   | { type: 'conductance', G: number, offset?: number }
- *   | { type: 'exchange', k: number, mu: number }} ContactSpeciesLink
+ *   | { type: 'exchange', k: number, mu: number }
+ *   | { type: 'velocity', v: number, offset?: number, mu?: number }} ContactSpeciesLink
  */
 /**
  * 'bulk': the end node is plain bulk (locally neutral, no double layer); 'neutral': no charge at

package/types/channels.d.ts

@@ -1,6 +1,6 @@
 export function ghkCurrent(z: any, inside: any, outside: any, V: any, T: any): number;
 /**
- * Hodgkin and Huxley's squid-axon channels, for a membrane face with the outside on its left
+ * Hodgkin and Huxley's squid-axon channels: for a membrane face with the outside on its left
  * (so the gates' voltage, φ_right − φ_left, is the membrane potential): the face's `gates`, and
  * `species` links for Na⁺ (P·m³h), K⁺ (P·n⁴) and the leak (ungated), to spread into the face
  * beside its φ law, `{ phi: { type: 'capacitive', C: 0.01 }, ...hh }`, adding links (or blocks)
@@ -12,12 +12,21 @@ export function ghkCurrent(z: any, inside: any, outside: any, V: any, T: any): n
  * (`leak`, of charge `leakZ`: Cl⁻ by default, whose Nernst level in squid is near their leak
  * reversal, −54 mV). The
  * rates are theirs at 6.3 °C, scaled to `T` by Q₁₀ = 3.
+ *
+ * Or with `linear: true`, Hodgkin and Huxley's own linear channels on the face: conductance links,
+ * G = g, gated the same, whose currents are g(V − E) with E each ion's Nernst level at the
+ * concentrations on either side (so `inside`, `outside` and `at` aren't needed).
+ *
+ * Or, given `area` (membrane per volume of the region, 2/a for an axon of radius a), for a membrane
+ * port along a region: links that are their linear conductances, G = g × area per volume, gated the
+ * same, each ion's reversal potential following from the port's bath and the concentrations inside
+ * (so `inside`, `outside` and `at` aren't needed).
  * @param {{ inside: object, outside: object, T?: number, g?: { Na?: number, K?: number, leak?: number },
- *   leak?: string, leakZ?: number, at?: number, names?: { Na?: string, K?: string } }} opts concentrations in
+ *   leak?: string, leakZ?: number, at?: number, names?: { Na?: string, K?: string }, linear?: boolean, area?: number }} opts concentrations in
  *   mol/m³ by species name, K, S/m², V
  * @returns {{ gates: object, species: object }}
  */
-export function hodgkinHuxley({ inside, outside, T, g, leak, leakZ, at, names }?: {
+export function hodgkinHuxley({ inside, outside, T, g, leak, leakZ, at, names, linear, area }?: {
     inside: object;
     outside: object;
     T?: number;
@@ -33,6 +42,8 @@ export function hodgkinHuxley({ inside, outside, T, g, leak, leakZ, at, names }?
         Na?: string;
         K?: string;
     };
+    linear?: boolean;
+    area?: number;
 }): {
     gates: object;
     species: object;

package/types/solver.d.ts

@@ -294,6 +294,7 @@ export class Solver {
      * animation can call it once per frame; the step size carries over between calls.
      */
     integrate(tEnd: any, opts?: {}): {
+        stopped?: string;
         converged: boolean;
         done: boolean;
         steps: number;
@@ -307,7 +308,7 @@ export class Solver {
         };
     };
     landing: any;
-    _extrapolate(out: any, t: any): any;
+    _extrapolate(out: any, h: any): any;
     _predict(pred: any, bdf: any): {
         scale: number;
         order: number;
@@ -381,6 +382,7 @@ export class Solver {
     _regionShift(yr: any, yi: any): Float64Array<any>[];
     _regionEdgeRows(): Uint8Array<any>;
     _currentCuts(): {
+        s: any;
         idx: any[];
         g: any[];
         d: any[];
@@ -424,7 +426,7 @@ export class Solver {
         iterations: any;
         history: any;
     };
-    _continuation(opts: any, level: any, target: any, r: any, warm: any): any;
+    _continuation(opts: any, k: any, level: any, target: any, r: any, warm: any, hold: any): any;
     _solveSteady(opts?: {}): {
         converged: boolean;
         steps: number;

package/types/stack.d.ts

@@ -31,16 +31,17 @@ export function drive(d: any, path: any): any;
  */
 export function ohmic(d?: number, carriers?: string[]): any;
 /**
- * A bath: a neutral composition `c` (mol/m³) held at the contact, its levels referred to the
- * charged `reference` species (the ion a reference electrode would sense, e.g. Cl⁻ for
- * Ag/AgCl), which is the terminal.
+ * A bath: a neutral composition `c` (mol/m³) held at the contact. With a `reference`, the charged
+ * species a reference electrode would sense (Cl⁻ for Ag/AgCl), its levels are referred to that
+ * species, which is the terminal. Without one, `bath(c, drive)`, the terminal voltage is the
+ * bath's φ: an ideal salt bridge, the convention of membrane potentials.
  * @param {Record<string, number>} c
- * @param {string} reference
+ * @param {string | number | object} [reference] the reference species, or the drive
  * @param {number | object} [drive]
  * @param {{ offset?: number }} [opts] where the reference species sits relative to the terminal
  *   voltage, V_ref = V + offset (V)
  */
-export function bath(c: Record<string, number>, reference: string, d?: number, { offset }?: {
+export function bath(c: Record<string, number>, reference?: string | number | object, d?: number, { offset }?: {
     offset?: number;
 }): any;
 /**

package/types/types.d.ts

@@ -264,6 +264,11 @@ export type ContactSpeciesLink = "blocked" | "equilibrium" | {
     type: "exchange";
     k: number;
     mu: number;
+} | {
+    type: "velocity";
+    v: number;
+    offset?: number;
+    mu?: number;
 };
 /**
  * 'bulk': the end node is plain bulk (locally neutral, no double layer); 'neutral': no charge at