bravais 0.1.3 → 0.2.0
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/CHANGELOG.md +20 -0
- package/README.md +21 -18
- package/THIRD_PARTY_NOTICES.md +11 -3
- package/dist/bravais.js +498 -435
- package/dist/bravais.js.map +1 -1
- package/dist/types/cif/symmetry-operators.d.ts +2 -2
- package/dist/types/index.d.ts +7 -7
- package/dist/types/render/gizmo.d.ts +4 -1
- package/dist/types/render/materials.d.ts +1 -2
- package/dist/types/render/model.d.ts +9 -0
- package/dist/types/render/palette.d.ts +5 -6
- package/dist/types/render/thumbnails.d.ts +4 -3
- package/dist/types/render/view-state.d.ts +2 -2
- package/dist/types/render/viewer.d.ts +13 -13
- package/dist/types/scene/build.d.ts +7 -9
- package/dist/types/structure/expand.d.ts +3 -2
- package/dist/types/structure/lattice.d.ts +3 -3
- package/dist/types/symmetry/dataset.d.ts +2 -4
- package/dist/types/symmetry/moyo.d.ts +6 -8
- package/dist/types/symmetry/symbol.d.ts +5 -7
- package/examples/CoO.cif +254 -0
- package/package.json +3 -3
package/dist/bravais.js
CHANGED
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@@ -1,15 +1,15 @@
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1
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-
import { ACESFilmicToneMapping as e, AlwaysStencilFunc as t, AmbientLight as n, Box3 as r, BoxGeometry as i, BufferGeometry as a, CanvasTexture as o, Color as s, ConeGeometry as c, Controls as l, CylinderGeometry as u, DataTexture as d, DirectionalLight as f, DoubleSide as p, EqualStencilFunc as m, Float32BufferAttribute as h, FloatType as g, Fog as
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1
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import { ACESFilmicToneMapping as e, AlwaysStencilFunc as t, AmbientLight as n, Box3 as r, BoxGeometry as i, BufferGeometry as a, CanvasTexture as o, Color as s, ConeGeometry as c, Controls as l, CylinderGeometry as u, DataTexture as d, DirectionalLight as f, DoubleSide as p, EqualStencilFunc as m, Float32BufferAttribute as h, FloatType as g, Fog as ee, Group as _, InstancedMesh as v, LineBasicMaterial as y, LineSegments as b, LinearFilter as x, LinearMipmapLinearFilter as te, MOUSE as S, MathUtils as ne, Matrix4 as C, Mesh as w, MeshStandardMaterial as T, NearestFilter as E, NotEqualStencilFunc as D, Object3D as O, OrthographicCamera as k, PlaneGeometry as re, Quaternion as A, RGBAFormat as ie, ReplaceStencilOp as ae, SRGBColorSpace as oe, Scene as se, SphereGeometry as ce, Sprite as le, SpriteMaterial as ue, Vector2 as j, Vector3 as M, WebGLRenderer as N } from "three";
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//#region src/cif/tokenizer.ts
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var
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var P = class extends Error {
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line;
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constructor(e, t) {
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super(`CIF line ${t}: ${e}`), this.name = "CifSyntaxError", this.line = t;
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}
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};
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function
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function F(e) {
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return e === " " || e === " " || e === "\r" || e === "\n";
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}
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function
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function de(e, t) {
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let n = e.toLowerCase();
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return e.startsWith("_") ? {
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kind: "tag",
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line: t
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};
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}
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function
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function fe(e) {
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let t = [], n = e.split(/\r\n|\r|\n/), r = 0;
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for (; r < n.length;) {
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let e = n[r] ?? "", i = r + 1;
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}
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a.push(e), r += 1;
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}
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if (!o) throw new
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if (!o) throw new P("unterminated text field", i);
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t.push({
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kind: "value",
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text: a.join("\n"),
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let a = 0;
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let n = e.charAt(a);
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if (
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if (F(n)) {
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a += 1;
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continue;
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}
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let r = a + 1;
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let t = e.indexOf(n, r);
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if (t === -1) throw new P("unterminated quoted string", i);
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let a = e.charAt(t + 1);
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if (t + 1 >= e.length ||
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if (t + 1 >= e.length || F(a)) {
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}
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if (r >= e.length) throw new P("unterminated quoted string", i);
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t.push({
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kind: "value",
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text: e.slice(a + 1, r),
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continue;
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}
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let r = a;
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for (; r < e.length && !
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t.push(
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for (; r < e.length && !F(e.charAt(r));) r += 1;
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t.push(de(e.slice(a, r), i)), a = r;
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}
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}
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//#endregion
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//#region src/cif/parser.ts
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function
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function pe(e) {
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}
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var
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var me = class {
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name;
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items = /* @__PURE__ */ new Map();
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loops = [];
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}
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get(e) {
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for (let t of
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for (let t of pe(e)) {
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}
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findLoop(e) {
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for (let t of
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for (let t of pe(e)) {
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let e = t.toLowerCase(), n = this.loops.find((t) => t.tags.includes(e));
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function I(e, t) {
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for (let n of pe(t)) {
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let t = e.tags.indexOf(n.toLowerCase());
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}
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function
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function L(e) {
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function he(e) {
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function ge(e) {
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let t = fe(e), n = [], r = null, i = 0, a = 0, o = (e) => {
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if (r || (r = new me(""), n.push(r)), a > 0) throw new P(`unexpected ${e.kind} inside a save frame`, e.line);
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var _e = /* @__PURE__ */ "H.He.Li.Be.B.C.N.O.F.Ne.Na.Mg.Al.Si.P.S.Cl.Ar.K.Ca.Sc.Ti.V.Cr.Mn.Fe.Co.Ni.Cu.Zn.Ga.Ge.As.Se.Br.Kr.Rb.Sr.Y.Zr.Nb.Mo.Tc.Ru.Rh.Pd.Ag.Cd.In.Sn.Sb.Te.I.Xe.Cs.Ba.La.Ce.Pr.Nd.Pm.Sm.Eu.Gd.Tb.Dy.Ho.Er.Tm.Yb.Lu.Hf.Ta.W.Re.Os.Ir.Pt.Au.Hg.Tl.Pb.Bi.Po.At.Rn.Fr.Ra.Ac.Th.Pa.U.Np.Pu.Am.Cm.Bk.Cf.Es.Fm.Md.No.Lr.Rf.Db.Sg.Bh.Hs.Mt.Ds.Rg.Cn.Nh.Fl.Mc.Lv.Ts.Og".split("."), ve = new Set(_e);
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function ye(e) {
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return ve.has(e) || e === "D";
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function be(e) {
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//#endregion
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for (let e of this.buckets.get(Oe(o, n, r)) ?? []) Ee(this.positions[e], t, this.tolerance) && a.push(e);
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}
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}
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}
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return a.sort((e, t) => e - t);
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}
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};
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-
function
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+
function Ae(e, t) {
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return [
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(n[0] ?? 0) * r + (n[1] ?? 0) * i + (n[2] ?? 0) * a + o[0],
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@@ -278,12 +278,12 @@ function je(e, t) {
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}
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//#endregion
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//#region src/structure/lattice.ts
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-
var
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-
function
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+
var V = Math.PI / 180;
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+
function je(e, t, n) {
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return Math.min(n, Math.max(t, e));
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}
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-
function
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-
let { a: t, b: n, c: r } = e, i = e.alpha *
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+
function Me(e) {
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+
let { a: t, b: n, c: r } = e, i = e.alpha * V, a = e.beta * V, o = e.gamma * V, s = Math.cos(i), c = Math.cos(a), l = Math.cos(o), u = Math.sin(i), d = Math.sin(a), f = Math.acos(je((s * c - l) / (u * d), -1, 1)), p = [
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t * d,
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0,
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t * c
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@@ -305,8 +305,8 @@ function Ne(e) {
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]
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};
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}
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-
function
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-
let [t, n, r] = e, i = (e) => Math.hypot(e[0], e[1], e[2]), a = (e, t) => Math.acos(
|
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+
function Ne(e) {
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+
let [t, n, r] = e, i = (e) => Math.hypot(e[0], e[1], e[2]), a = (e, t) => Math.acos(je((e[0] * t[0] + e[1] * t[1] + e[2] * t[2]) / (i(e) * i(t)), -1, 1)) / V;
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return {
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a: i(t),
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b: i(n),
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@@ -317,7 +317,7 @@ function Pe(e) {
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vectors: e
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};
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}
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function
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+
function Pe(e, t) {
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let [n, r, i] = e.vectors, [a, o, s] = t;
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return [
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a * n[0] + o * r[0] + s * i[0],
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@@ -325,49 +325,49 @@ function Fe(e, t) {
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a * n[2] + o * r[2] + s * i[2]
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];
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}
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-
function
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+
function Fe(e, t) {
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|
let n = e[0] - t[0], r = e[1] - t[1], i = e[2] - t[2];
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return Math.sqrt(n * n + r * r + i * i);
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}
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//#endregion
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//#region src/cif/errors.ts
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var
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+
var H = class extends Error {
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|
constructor(e) {
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|
super(e), this.name = "CifStructureError";
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}
|
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-
},
|
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+
}, Ie = [
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|
"x",
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340
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"y",
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341
|
"z"
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342
|
];
|
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|
-
function
|
|
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|
+
function Le(e) {
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344
|
if (e === "" || e === "+") return 1;
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345
|
if (e === "-") return -1;
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346
|
let t = e.match(/^([+-]?\d+)\/(\d+)$/), n = t ? Number(t[1]) / Number(t[2]) : Number(e);
|
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347
|
-
if (!Number.isFinite(n)) throw new
|
|
347
|
+
if (!Number.isFinite(n)) throw new H(`Cannot read the number ${JSON.stringify(e)} in a symmetry operator.`);
|
|
348
348
|
return n;
|
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349
|
}
|
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|
-
function
|
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|
+
function Re(e) {
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351
|
let t = e.split(",").map((e) => e.toLowerCase().replace(/[^xyz0-9./+-]/g, ""));
|
|
352
|
-
if (t.length !== 3) throw new
|
|
352
|
+
if (t.length !== 3) throw new H(`A symmetry operator needs three components: ${JSON.stringify(e)}.`);
|
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353
|
let n = [], r = [];
|
|
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354
|
for (let i of t) {
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355
355
|
let t = i.match(/[+-]?[^+-]+/g);
|
|
356
|
-
if (!t || t.join("") !== i) throw new
|
|
356
|
+
if (!t || t.join("") !== i) throw new H(`Cannot read the symmetry operator ${JSON.stringify(e)}.`);
|
|
357
357
|
let a = [
|
|
358
358
|
0,
|
|
359
359
|
0,
|
|
360
360
|
0
|
|
361
361
|
], o = 0;
|
|
362
362
|
for (let e of t) {
|
|
363
|
-
let t =
|
|
364
|
-
if (t === -1) o +=
|
|
363
|
+
let t = Ie.findIndex((t) => e.includes(t));
|
|
364
|
+
if (t === -1) o += Le(e);
|
|
365
365
|
else {
|
|
366
|
-
let n =
|
|
366
|
+
let n = Le(e.replace(Ie[t], "").replace(/\*$/, ""));
|
|
367
367
|
a[t] = (a[t] ?? 0) + n;
|
|
368
368
|
}
|
|
369
369
|
}
|
|
370
|
-
n.push(...a), r.push(
|
|
370
|
+
n.push(...a), r.push(z(o));
|
|
371
371
|
}
|
|
372
372
|
return {
|
|
373
373
|
rotation: n,
|
|
@@ -376,99 +376,99 @@ function ze(e) {
|
|
|
376
376
|
}
|
|
377
377
|
//#endregion
|
|
378
378
|
//#region src/cif/structure.ts
|
|
379
|
-
var
|
|
379
|
+
var ze = 1e-4, Be = ["_space_group_symop_operation_xyz", "_symmetry_equiv_pos_as_xyz"], Ve = ["_space_group_it_number", "_symmetry_int_tables_number"], He = [
|
|
380
380
|
"_space_group_name_h-m_alt",
|
|
381
381
|
"_symmetry_space_group_name_h-m",
|
|
382
382
|
"_space_group_name_h-m_full"
|
|
383
|
-
],
|
|
384
|
-
function
|
|
385
|
-
let n =
|
|
386
|
-
if (n === null) throw new
|
|
383
|
+
], Ue = ["_space_group_name_hall", "_symmetry_space_group_name_hall"];
|
|
384
|
+
function U(e, t) {
|
|
385
|
+
let n = R(e.get(t));
|
|
386
|
+
if (n === null) throw new H(`${e.name || "The CIF"} has no usable ${t}.`);
|
|
387
387
|
return n;
|
|
388
388
|
}
|
|
389
|
-
function
|
|
389
|
+
function We(e, t, n) {
|
|
390
390
|
let r = e.find((e) => e.element === t);
|
|
391
391
|
r ? r.occupancy += n : e.push({
|
|
392
392
|
element: t,
|
|
393
393
|
occupancy: n
|
|
394
394
|
}), e.sort((e, t) => t.occupancy - e.occupancy);
|
|
395
395
|
}
|
|
396
|
-
function
|
|
396
|
+
function Ge(e) {
|
|
397
397
|
for (let t of e) {
|
|
398
398
|
let e = t.species.reduce((e, t) => e + t.occupancy, 0);
|
|
399
399
|
if (e > 1.000001) for (let n of t.species) n.occupancy /= e;
|
|
400
400
|
}
|
|
401
401
|
}
|
|
402
|
-
function
|
|
402
|
+
function Ke(e) {
|
|
403
403
|
let t = e.findLoop("_atom_site_fract_x");
|
|
404
|
-
if (!t) throw new
|
|
405
|
-
let n =
|
|
404
|
+
if (!t) throw new H(`${e.name || "The CIF"} has no atom sites.`);
|
|
405
|
+
let n = I(t, "_atom_site_fract_x") ?? [], r = I(t, "_atom_site_fract_y") ?? [], i = I(t, "_atom_site_fract_z") ?? [], a = I(t, "_atom_site_label"), o = I(t, "_atom_site_type_symbol"), s = I(t, "_atom_site_occupancy"), c = [], l = new ke(ze);
|
|
406
406
|
for (let e = 0; e < t.rows.length; e += 1) {
|
|
407
|
-
let t =
|
|
407
|
+
let t = R(n[e]), u = R(r[e]), d = R(i[e]);
|
|
408
408
|
if (t === null || u === null || d === null) continue;
|
|
409
|
-
let f = a?.[e] ?? o?.[e] ?? `site${e + 1}`, p = o?.[e], m = (p && !
|
|
410
|
-
if (!m) throw new
|
|
411
|
-
let h =
|
|
412
|
-
|
|
413
|
-
|
|
414
|
-
|
|
415
|
-
], [
|
|
416
|
-
|
|
409
|
+
let f = a?.[e] ?? o?.[e] ?? `site${e + 1}`, p = o?.[e], m = (p && !L(p) ? xe(p) : null) ?? xe(f);
|
|
410
|
+
if (!m) throw new H(`Atom site ${JSON.stringify(f)} names no element (type symbol ${JSON.stringify(p ?? "")}).`);
|
|
411
|
+
let h = R(s?.[e]) ?? 1, g = [
|
|
412
|
+
z(t),
|
|
413
|
+
z(u),
|
|
414
|
+
z(d)
|
|
415
|
+
], [ee] = l.near(g);
|
|
416
|
+
ee === void 0 ? (l.add(g), c.push({
|
|
417
417
|
label: f,
|
|
418
418
|
species: [{
|
|
419
419
|
element: m,
|
|
420
420
|
occupancy: h
|
|
421
421
|
}],
|
|
422
422
|
fractional: g
|
|
423
|
-
})) :
|
|
423
|
+
})) : We(c[ee].species, m, h);
|
|
424
424
|
}
|
|
425
|
-
if (c.length === 0) throw new
|
|
426
|
-
return
|
|
425
|
+
if (c.length === 0) throw new H(`${e.name || "The CIF"} has no atom sites with coordinates.`);
|
|
426
|
+
return Ge(c), c;
|
|
427
427
|
}
|
|
428
|
-
function
|
|
429
|
-
let t = e.findLoop(
|
|
428
|
+
function qe(e) {
|
|
429
|
+
let t = e.findLoop(Be);
|
|
430
430
|
if (!t) {
|
|
431
|
-
let t = e.get(
|
|
432
|
-
return t === null ? null : [
|
|
431
|
+
let t = e.get(Be);
|
|
432
|
+
return t === null ? null : [Re(t)];
|
|
433
433
|
}
|
|
434
|
-
let n = (
|
|
434
|
+
let n = (I(t, Be) ?? []).filter((e) => !L(e)).map(Re);
|
|
435
435
|
return n.length > 0 ? n : null;
|
|
436
436
|
}
|
|
437
|
-
function
|
|
438
|
-
let t = e.get(
|
|
437
|
+
function Je(e) {
|
|
438
|
+
let t = e.get(Ve), n = t === null ? null : R(t), r = e.get(He), i = e.get(Ue);
|
|
439
439
|
return {
|
|
440
440
|
number: n !== null && Number.isInteger(n) && n >= 1 && n <= 230 ? n : null,
|
|
441
|
-
symbol: r !== null && !
|
|
442
|
-
hallSymbol: i !== null && !
|
|
441
|
+
symbol: r !== null && !L(r) ? r.trim() : null,
|
|
442
|
+
hallSymbol: i !== null && !L(i) ? i.trim() : null
|
|
443
443
|
};
|
|
444
444
|
}
|
|
445
|
-
function
|
|
445
|
+
function Ye(e) {
|
|
446
446
|
return e.findLoop("_atom_site_fract_x") !== null;
|
|
447
447
|
}
|
|
448
|
-
function
|
|
448
|
+
function Xe(e) {
|
|
449
449
|
return {
|
|
450
|
-
lattice:
|
|
451
|
-
a:
|
|
452
|
-
b:
|
|
453
|
-
c:
|
|
454
|
-
alpha:
|
|
455
|
-
beta:
|
|
456
|
-
gamma:
|
|
450
|
+
lattice: Me({
|
|
451
|
+
a: U(e, "_cell_length_a"),
|
|
452
|
+
b: U(e, "_cell_length_b"),
|
|
453
|
+
c: U(e, "_cell_length_c"),
|
|
454
|
+
alpha: U(e, "_cell_angle_alpha"),
|
|
455
|
+
beta: U(e, "_cell_angle_beta"),
|
|
456
|
+
gamma: U(e, "_cell_angle_gamma")
|
|
457
457
|
}),
|
|
458
|
-
sites:
|
|
459
|
-
operations:
|
|
460
|
-
spaceGroup:
|
|
458
|
+
sites: Ke(e),
|
|
459
|
+
operations: qe(e),
|
|
460
|
+
spaceGroup: Je(e)
|
|
461
461
|
};
|
|
462
462
|
}
|
|
463
463
|
//#endregion
|
|
464
464
|
//#region src/structure/closure.ts
|
|
465
|
-
function
|
|
466
|
-
let n = new
|
|
465
|
+
function Ze(e, t) {
|
|
466
|
+
let n = new ke(Ce);
|
|
467
467
|
for (let t of e) n.add(t.fractional);
|
|
468
468
|
let r = !1, i = !0;
|
|
469
469
|
return e.forEach((e, a) => {
|
|
470
470
|
for (let o of t) {
|
|
471
|
-
let t = n.near(
|
|
471
|
+
let t = n.near(Ae(o, e.fractional));
|
|
472
472
|
t.some((e) => e !== a) && (r = !0), t.length === 0 && (i = !1);
|
|
473
473
|
}
|
|
474
474
|
}), {
|
|
@@ -478,7 +478,7 @@ function Qe(e, t) {
|
|
|
478
478
|
}
|
|
479
479
|
//#endregion
|
|
480
480
|
//#region src/structure/types.ts
|
|
481
|
-
var
|
|
481
|
+
var Qe = {
|
|
482
482
|
rotation: [
|
|
483
483
|
1,
|
|
484
484
|
0,
|
|
@@ -495,29 +495,29 @@ var $e = {
|
|
|
495
495
|
0,
|
|
496
496
|
0
|
|
497
497
|
]
|
|
498
|
-
},
|
|
499
|
-
function
|
|
500
|
-
return
|
|
501
|
-
await e.instantiate(),
|
|
498
|
+
}, $e = null, et = null;
|
|
499
|
+
function tt() {
|
|
500
|
+
return et ||= import("./moyo-wasm.js").then(async (e) => {
|
|
501
|
+
await e.instantiate(), $e = e;
|
|
502
502
|
}).catch((e) => {
|
|
503
|
-
throw
|
|
504
|
-
}),
|
|
503
|
+
throw et = null, e;
|
|
504
|
+
}), et;
|
|
505
505
|
}
|
|
506
|
-
function
|
|
507
|
-
if (
|
|
508
|
-
return
|
|
506
|
+
function W() {
|
|
507
|
+
if (!$e) throw Error("moyo is not loaded yet; await ensureMoyo() first.");
|
|
508
|
+
return $e;
|
|
509
509
|
}
|
|
510
510
|
//#endregion
|
|
511
511
|
//#region src/symmetry/moyo.ts
|
|
512
|
-
var
|
|
512
|
+
var nt = class extends Error {
|
|
513
513
|
constructor(e) {
|
|
514
514
|
super(e), this.name = "SpaceGroupLookupError";
|
|
515
515
|
}
|
|
516
|
-
},
|
|
517
|
-
function
|
|
518
|
-
return
|
|
516
|
+
}, G = null;
|
|
517
|
+
function rt() {
|
|
518
|
+
return tt();
|
|
519
519
|
}
|
|
520
|
-
function
|
|
520
|
+
function it(e) {
|
|
521
521
|
let t = e.rotation;
|
|
522
522
|
return {
|
|
523
523
|
rotation: [
|
|
@@ -538,119 +538,119 @@ function at(e) {
|
|
|
538
538
|
]
|
|
539
539
|
};
|
|
540
540
|
}
|
|
541
|
-
function
|
|
542
|
-
if (!
|
|
543
|
-
|
|
544
|
-
for (let e = 1; e <= 230; e += 1)
|
|
541
|
+
function at() {
|
|
542
|
+
if (!G) {
|
|
543
|
+
G = [];
|
|
544
|
+
for (let e = 1; e <= 230; e += 1) G.push(...W().hall_symbol_entries_from_number(e));
|
|
545
545
|
}
|
|
546
|
-
return
|
|
546
|
+
return G;
|
|
547
547
|
}
|
|
548
|
-
function
|
|
548
|
+
function K(e) {
|
|
549
549
|
return e.replace(/[\s_]/g, "").toLowerCase();
|
|
550
550
|
}
|
|
551
|
-
function
|
|
551
|
+
function ot(e) {
|
|
552
552
|
let t = e.trim(), n = t.match(/^(.*?)\s*:\s*(\S+)$/);
|
|
553
553
|
if (n && n[1] && n[2]) return {
|
|
554
|
-
base:
|
|
554
|
+
base: K(n[1]),
|
|
555
555
|
setting: n[2].toLowerCase()
|
|
556
556
|
};
|
|
557
557
|
let r = t.match(/^(.*\S)\s+([HRhr])$/);
|
|
558
558
|
return r && r[1] && r[2] ? {
|
|
559
|
-
base:
|
|
559
|
+
base: K(r[1]),
|
|
560
560
|
setting: r[2].toLowerCase()
|
|
561
561
|
} : {
|
|
562
|
-
base:
|
|
562
|
+
base: K(t),
|
|
563
563
|
setting: null
|
|
564
564
|
};
|
|
565
565
|
}
|
|
566
|
-
function
|
|
566
|
+
function st(e) {
|
|
567
567
|
let t = e[0];
|
|
568
568
|
if (!t) return e;
|
|
569
|
-
let n =
|
|
569
|
+
let n = W().space_group_type(t.number).hall_number;
|
|
570
570
|
return [...e].sort((e, t) => Number(t.hall_number === n) - Number(e.hall_number === n));
|
|
571
571
|
}
|
|
572
|
-
function
|
|
573
|
-
let t =
|
|
572
|
+
function ct(e) {
|
|
573
|
+
let t = at().filter((t) => e.number === null || t.number === e.number);
|
|
574
574
|
if (e.hallSymbol) {
|
|
575
|
-
let n =
|
|
575
|
+
let n = K(e.hallSymbol), r = t.filter((e) => K(e.hall_symbol) === n);
|
|
576
576
|
if (r.length > 0) return r;
|
|
577
577
|
}
|
|
578
578
|
if (e.symbol) {
|
|
579
|
-
let { base: n, setting: r } =
|
|
579
|
+
let { base: n, setting: r } = ot(e.symbol), i = t.filter((e) => K(e.hm_short) === n || K(e.hm_full) === n);
|
|
580
580
|
if (r) {
|
|
581
581
|
let e = i.filter((e) => e.setting.toLowerCase() === r);
|
|
582
582
|
if (e.length > 0) return e;
|
|
583
583
|
}
|
|
584
|
-
return
|
|
584
|
+
return st(i);
|
|
585
585
|
}
|
|
586
586
|
return [];
|
|
587
587
|
}
|
|
588
|
-
function
|
|
588
|
+
function lt(e) {
|
|
589
589
|
return [
|
|
590
590
|
e.hallSymbol,
|
|
591
591
|
e.symbol,
|
|
592
592
|
e.number
|
|
593
593
|
].filter((e) => e !== null).join(" / ");
|
|
594
594
|
}
|
|
595
|
-
async function
|
|
596
|
-
await
|
|
597
|
-
let { operations_from_number: t } =
|
|
595
|
+
async function ut(e) {
|
|
596
|
+
await rt();
|
|
597
|
+
let { operations_from_number: t } = W();
|
|
598
598
|
if (e.hallSymbol || e.symbol) {
|
|
599
|
-
let n =
|
|
600
|
-
if (n.length === 0) throw new
|
|
599
|
+
let n = ct(e);
|
|
600
|
+
if (n.length === 0) throw new nt(`Space group ${lt(e)} is not in the symmetry table.`);
|
|
601
601
|
return n.map((e) => ({
|
|
602
602
|
setting: e.setting,
|
|
603
603
|
operations: t(e.number, {
|
|
604
604
|
type: "HallNumber",
|
|
605
605
|
value: e.hall_number
|
|
606
|
-
}, !1).map(
|
|
606
|
+
}, !1).map(it)
|
|
607
607
|
}));
|
|
608
608
|
}
|
|
609
|
-
if (e.number === null) throw new
|
|
609
|
+
if (e.number === null) throw new nt("The CIF names no space group.");
|
|
610
610
|
return [{
|
|
611
611
|
setting: "",
|
|
612
|
-
operations: t(e.number, { type: "Spglib" }, !1).map(
|
|
612
|
+
operations: t(e.number, { type: "Spglib" }, !1).map(it)
|
|
613
613
|
}];
|
|
614
614
|
}
|
|
615
|
-
async function
|
|
616
|
-
let [t] = await
|
|
615
|
+
async function dt(e) {
|
|
616
|
+
let [t] = await ut(e);
|
|
617
617
|
return t.operations;
|
|
618
618
|
}
|
|
619
619
|
//#endregion
|
|
620
620
|
//#region src/symmetry/resolve.ts
|
|
621
|
-
var
|
|
622
|
-
function
|
|
623
|
-
return new
|
|
621
|
+
var ft = .001, pt = .01;
|
|
622
|
+
function mt() {
|
|
623
|
+
return new H("The symmetry does not fit the listed atoms: they are already expanded, yet the operations generate positions the file does not list.");
|
|
624
624
|
}
|
|
625
|
-
function
|
|
626
|
-
let n =
|
|
627
|
-
if (n.preExpanded && !n.closed) throw
|
|
625
|
+
function ht(e, t) {
|
|
626
|
+
let n = Ze(e, t);
|
|
627
|
+
if (n.preExpanded && !n.closed) throw mt();
|
|
628
628
|
}
|
|
629
|
-
function
|
|
630
|
-
let o = (e, t) => Math.abs(e - t) <=
|
|
629
|
+
function gt({ a: e, b: t, c: n, alpha: r, beta: i, gamma: a }) {
|
|
630
|
+
let o = (e, t) => Math.abs(e - t) <= ft * Math.max(e, t), s = (e, t) => Math.abs(e - t) <= pt;
|
|
631
631
|
return o(e, t) && o(t, n) && s(r, i) && s(i, a) && !s(r, 90) ? "R" : o(e, t) && s(r, 90) && s(i, 90) && s(a, 120) ? "H" : null;
|
|
632
632
|
}
|
|
633
|
-
async function
|
|
634
|
-
if (e.operations) return
|
|
633
|
+
async function _t(e) {
|
|
634
|
+
if (e.operations) return ht(e.sites, e.operations), e.operations;
|
|
635
635
|
let { spaceGroup: t } = e;
|
|
636
|
-
if (t.hallSymbol === null && t.symbol === null && t.number === null) return [
|
|
637
|
-
let n = await
|
|
636
|
+
if (t.hallSymbol === null && t.symbol === null && t.number === null) return [Qe];
|
|
637
|
+
let n = await ut(t);
|
|
638
638
|
if (n.length === 1) {
|
|
639
639
|
let [t] = n;
|
|
640
|
-
return
|
|
640
|
+
return ht(e.sites, t.operations), t.operations;
|
|
641
641
|
}
|
|
642
|
-
let r = n.map((t) =>
|
|
642
|
+
let r = n.map((t) => Ze(e.sites, t.operations)), i = n.find((e, t) => r[t].preExpanded && r[t].closed);
|
|
643
643
|
if (i) return i.operations;
|
|
644
|
-
if (r.some((e) => e.preExpanded)) throw
|
|
645
|
-
let a =
|
|
644
|
+
if (r.some((e) => e.preExpanded)) throw mt();
|
|
645
|
+
let a = gt(e.lattice);
|
|
646
646
|
return ((a === null ? void 0 : n.find((e) => e.setting.toUpperCase() === a)) ?? n[0]).operations;
|
|
647
647
|
}
|
|
648
648
|
//#endregion
|
|
649
649
|
//#region src/structure/expand.ts
|
|
650
|
-
function
|
|
651
|
-
let t = [], n = new
|
|
650
|
+
function vt(e) {
|
|
651
|
+
let t = [], n = new ke(Ce);
|
|
652
652
|
for (let r of e.sites) for (let i of e.operations) {
|
|
653
|
-
let e =
|
|
653
|
+
let e = Te(Ae(i, r.fractional));
|
|
654
654
|
n.near(e).length === 0 && (n.add(e), t.push({
|
|
655
655
|
label: r.label,
|
|
656
656
|
species: r.species,
|
|
@@ -660,17 +660,17 @@ function yt(e) {
|
|
|
660
660
|
return {
|
|
661
661
|
...e,
|
|
662
662
|
sites: t,
|
|
663
|
-
operations: [
|
|
663
|
+
operations: [Qe]
|
|
664
664
|
};
|
|
665
665
|
}
|
|
666
666
|
//#endregion
|
|
667
667
|
//#region src/symmetry/dataset.ts
|
|
668
|
-
var
|
|
668
|
+
var yt = .01, bt = class extends Error {
|
|
669
669
|
constructor(e) {
|
|
670
670
|
super(e), this.name = "SymmetryAnalysisError";
|
|
671
671
|
}
|
|
672
672
|
};
|
|
673
|
-
function
|
|
673
|
+
function xt(e) {
|
|
674
674
|
let t = /* @__PURE__ */ new Map(), n = /* @__PURE__ */ new Map();
|
|
675
675
|
return {
|
|
676
676
|
numbers: e.map((e) => {
|
|
@@ -680,7 +680,7 @@ function St(e) {
|
|
|
680
680
|
speciesByLabel: n
|
|
681
681
|
};
|
|
682
682
|
}
|
|
683
|
-
function
|
|
683
|
+
function St(e, t, n) {
|
|
684
684
|
let r = e.std_cell.lattice.basis, i = [
|
|
685
685
|
[
|
|
686
686
|
r[0],
|
|
@@ -702,13 +702,13 @@ function Ct(e, t, n) {
|
|
|
702
702
|
return a.set(s, c), {
|
|
703
703
|
label: `${s}${c}`,
|
|
704
704
|
species: o,
|
|
705
|
-
fractional:
|
|
705
|
+
fractional: Te(n)
|
|
706
706
|
};
|
|
707
707
|
});
|
|
708
708
|
return {
|
|
709
|
-
lattice:
|
|
709
|
+
lattice: Ne(i),
|
|
710
710
|
sites: o,
|
|
711
|
-
operations: [
|
|
711
|
+
operations: [Qe],
|
|
712
712
|
spaceGroup: {
|
|
713
713
|
number: e.number,
|
|
714
714
|
symbol: e.hm_symbol,
|
|
@@ -716,9 +716,9 @@ function Ct(e, t, n) {
|
|
|
716
716
|
}
|
|
717
717
|
};
|
|
718
718
|
}
|
|
719
|
-
async function
|
|
720
|
-
await
|
|
721
|
-
let { analyze_cell: n, hall_symbol_entry: r, space_group_type: i } =
|
|
719
|
+
async function Ct(e, t = {}) {
|
|
720
|
+
await rt();
|
|
721
|
+
let { analyze_cell: n, hall_symbol_entry: r, space_group_type: i } = W(), a = vt(e), { numbers: o, speciesByLabel: s } = xt(a.sites), [c, l, u] = a.lattice.vectors, d = {
|
|
722
722
|
lattice: { basis: [
|
|
723
723
|
...c,
|
|
724
724
|
...l,
|
|
@@ -728,11 +728,11 @@ async function wt(e, t = {}) {
|
|
|
728
728
|
numbers: o
|
|
729
729
|
}, f;
|
|
730
730
|
try {
|
|
731
|
-
f = n(JSON.stringify(d), t.symprec ??
|
|
731
|
+
f = n(JSON.stringify(d), t.symprec ?? yt, "Standard");
|
|
732
732
|
} catch (e) {
|
|
733
|
-
throw new
|
|
733
|
+
throw new bt(`moyo could not analyse the structure: ${e instanceof Error ? e.message : String(e)}`);
|
|
734
734
|
}
|
|
735
|
-
let p = r(f.hall_number), m = i(f.number), h =
|
|
735
|
+
let p = r(f.hall_number), m = i(f.number), h = St(f, s, p);
|
|
736
736
|
return {
|
|
737
737
|
number: f.number,
|
|
738
738
|
symbol: f.hm_symbol,
|
|
@@ -741,7 +741,7 @@ async function wt(e, t = {}) {
|
|
|
741
741
|
hallNumber: f.hall_number,
|
|
742
742
|
setting: p.setting,
|
|
743
743
|
crystalSystem: m.crystal_system,
|
|
744
|
-
operations: f.operations.map(
|
|
744
|
+
operations: f.operations.map(it),
|
|
745
745
|
wyckoffs: f.wyckoffs,
|
|
746
746
|
siteSymmetries: f.site_symmetry_symbols,
|
|
747
747
|
structure: a,
|
|
@@ -750,34 +750,34 @@ async function wt(e, t = {}) {
|
|
|
750
750
|
}
|
|
751
751
|
//#endregion
|
|
752
752
|
//#region src/symmetry/symbol.ts
|
|
753
|
-
var
|
|
754
|
-
function
|
|
755
|
-
return
|
|
753
|
+
var wt = "₀₁₂₃₄₅₆₇₈₉", Tt = "̅";
|
|
754
|
+
function Et(e) {
|
|
755
|
+
return wt[Number(e)] ?? e;
|
|
756
756
|
}
|
|
757
|
-
function
|
|
757
|
+
function Dt(e) {
|
|
758
758
|
let t = e.trim(), n = t.indexOf(":"), r = n === -1 ? t : t.slice(0, n).trim(), i = n === -1 ? "" : ` ${t.slice(n)}`, a = r.split(/\s+/);
|
|
759
|
-
return a.map((e) => a.length > 1 ? e.replace(/^([2346])([1-5])(?=$|\/)/, (e, t, n) => Number(n) < Number(t) ? t +
|
|
759
|
+
return a.map((e) => a.length > 1 ? e.replace(/^([2346])([1-5])(?=$|\/)/, (e, t, n) => Number(n) < Number(t) ? t + Et(n) : e) : e).join("").replace(/(\d)_(\d)/g, (e, t, n) => t + Et(n)).replace(/-(\d)/g, (e, t) => t + Tt) + i;
|
|
760
760
|
}
|
|
761
761
|
//#endregion
|
|
762
762
|
//#region src/structure/bonds.ts
|
|
763
|
-
var
|
|
763
|
+
var Ot = {
|
|
764
764
|
source: "VESTA bond-search cutoffs (K. Momma and F. Izumi), as distributed in pymatgen's vesta_cutoffs.yaml (MIT). Where VESTA lists a pair twice (H-O, D-O), the shorter cutoff is kept.",
|
|
765
765
|
pairs: /* @__PURE__ */ 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":3.42093,\"Hg-Se\":2.82642,\"Hg-Te\":2.76642,\"Ho-I\":3.44159,\"Ho-N\":2.41898,\"Ho-O\":2.67047,\"Ho-P\":2.79898,\"Ho-S\":3.13547,\"Ho-Se\":2.84898,\"Ho-Te\":3.03898,\"I-I\":2.4,\"I-In\":3.19291,\"I-Ir\":2.70998,\"I-K\":4.11717,\"I-La\":3.64293,\"I-Li\":3.37676,\"I-Lu\":3.36945,\"I-Mg\":3.17293,\"I-Mn\":3.23293,\"I-Mo\":2.74701,\"I-Na\":3.88251,\"I-Nb\":3.1439,\"I-Nd\":3.59452,\"I-Ni\":3.00649,\"I-Np\":3.44233,\"I-O\":2.47646,\"I-P\":2.44998,\"I-Pb\":3.69562,\"I-Pd\":2.96649,\"I-Pr\":3.49649,\"I-Pt\":2.41998,\"I-Pu\":3.43233,\"I-Rb\":4.33462,\"I-Re\":2.65998,\"I-Rh\":2.52998,\"I-Ru\":2.52998,\"I-S\":2.40998,\"I-Sb\":3.21646,\"I-Sc\":3.15291,\"I-Se\":2.58998,\"I-Si\":2.76002,\"I-Sm\":3.44649,\"I-Sn\":3.52293,\"I-Sr\":3.74295,\"I-Ta\":2.81642,\"I-Tb\":3.40945,\"I-Te\":3.13702,\"I-Th\":3.56649,\"I-Ti\":3.08291,\"I-Tl\":3.94142,\"I-Tm\":3.37945,\"I-U\":3.62452,\"I-V\":2.66642,\"I-W\":2.70998,\"I-Y\":3.37649,\"I-Yb\":3.37945,\"I-Zn\":3.07293,\"I-Zr\":3.19004,\"In-Mn\":3.14729,\"In-N\":2.18642,\"In-O\":2.46491,\"In-P\":2.68642,\"In-S\":2.93291,\"In-Se\":2.62642,\"In-Te\":2.84642,\"Ir-N\":2.10998,\"Ir-O\":2.27746,\"Ir-P\":2.50998,\"Ir-S\":2.42998,\"Ir-Se\":2.55998,\"Ir-Te\":2.75998,\"K-N\":3.41942,\"K-O\":3.25142,\"K-P\":3.44942,\"K-S\":3.79285,\"K-Se\":4.00186,\"K-Te\":4.23284,\"La-N\":3.05293,\"La-O\":2.90983,\"La-P\":3.32293,\"La-S\":3.35593,\"La-Se\":3.45293,\"La-Te\":3.65293,\"Li-N\":2.66213,\"Li-O\":2.60087,\"Li-S\":3.02481,\"Li-Se\":3.2433,\"Li-Te\":3.42496,\"Lu-N\":2.71649,\"Lu-O\":2.57749,\"Lu-P\":3.11649,\"Lu-S\":3.03649,\"Lu-Se\":3.16649,\"Lu-Te\":3.35649,\"Mg-N\":2.56293,\"Mg-O\":2.41824,\"Mg-P\":3.00293,\"Mg-S\":2.89293,\"Mg-Se\":3.03293,\"Mg-Te\":3.24293,\"Mn-N\":2.56193,\"Mn-O\":2.51652,\"Mn-P\":2.39642,\"Mn-S\":2.93293,\"Mn-Se\":2.47642,\"Mn-Te\":2.70642,\"Mo-N\":2.4735,\"Mo-O\":2.3475,\"Mo-P\":2.54701,\"Mo-S\":2.80067,\"Mo-Se\":2.59701,\"Mo-Te\":2.79701,\"N-N\":1.8826,\"N-Na\":3.12942,\"N-Nb\":2.46046,\"N-Nd\":3.01293,\"N-Ni\":2.30649,\"N-O\":1.81746,\"N-P\":1.97146,\"N-Pb\":3.0967,\"N-Pd\":2.40451,\"N-Pr\":2.90649,\"N-Pt\":2.41649,\"N-Rb\":3.79645,\"N-Re\":2.10998,\"N-Rh\":2.2626,\"N-Ru\":2.2626,\"N-S\":2.28849,\"N-Sb\":2.56446,\"N-Sc\":2.54291,\"N-Se\":2.1,\"N-Si\":2.12002,\"N-Sm\":3.02351,\"N-Sn\":2.7152,\"N-Sr\":3.09295,\"N-Ta\":2.16642,\"N-Tb\":2.80649,\"N-Te\":2.16998,\"N-Th\":2.94649,\"N-Ti\":2.08642,\"N-Tl\":2.59644,\"N-Tm\":2.74649,\"N-U\":2.78649,\"N-V\":2.38329,\"N-W\":2.10998,\"N-Y\":2.77649,\"N-Yb\":2.84851,\"N-Zn\":2.43293,\"N-Zr\":2.65004,\"NH-O\":3.08895,\"Na-O\":2.95693,\"Na-P\":3.47942,\"Na-S\":3.57685,\"Na-Se\":3.71593,\"Na-Te\":3.95459,\"Nb-O\":2.45329,\"Nb-P\":2.61642,\"Nb-S\":2.74,\"Nb-Se\":2.66642,\"Nb-Te\":2.85642,\"Nd-O\":2.8587,\"Nd-S\":3.42712,\"Nd-Se\":3.42293,\"Nd-Te\":3.60293,\"Ni-O\":2.28149,\"Ni-P\":2.31998,\"Ni-S\":2.58649,\"Ni-Se\":2.18998,\"Ni-Te\":2.47998,\"Np-O\":2.63646,\"Np-S\":3.2,\"O-O\":1.7,\"O-Os\":2.23,\"O-P\":2.08646,\"O-Pa\":2.63383,\"O-Pb\":3.04096,\"O-Pd\":2.39849,\"O-Po\":2.64646,\"O-Pr\":2.74449,\"O-Pt\":2.40649,\"O-Pu\":2.68329,\"O-Rb\":3.43945,\"O-Re\":2.3426,\"O-Rh\":2.24946,\"O-Ru\":2.22646,\"O-S\":1.8,\"O-Sb\":2.45237,\"O-Sc\":2.42029,\"O-Se\":2.16102,\"O-Si\":1.99002,\"O-Sm\":2.88251,\"O-Sn\":2.82146,\"O-Sr\":2.98095,\"O-Ta\":2.74646,\"O-Tb\":2.65549,\"O-Tc\":2.22446,\"O-Te\":2.3334,\"O-Th\":2.77349,\"O-Ti\":2.35391,\"O-Tl\":3.36945,\"O-Tm\":2.60649,\"O-U\":2.94295,\"O-V\":2.84939,\"O-W\":2.20102,\"O-Xe\":2.63451,\"O-Y\":2.62549,\"O-Yb\":2.74551,\"O-Zn\":2.41693,\"O-Zr\":3.09651,\"Os-S\":2.56002,\"P-P\":2.48381,\"P-Pb\":2.94644,\"P-Pd\":2.46998,\"P-Pr\":3.28649,\"P-Pt\":2.23998,\"P-Rb\":3.50645,\"P-Re\":2.50998,\"P-Rh\":2.43998,\"P-Ru\":2.33998,\"P-S\":2.57646,\"P-Sb\":2.56998,\"P-Sc\":2.96291,\"P-Se\":2.69646,\"P-Si\":2.58002,\"P-Sm\":3.23649,\"P-Sn\":2.60642,\"P-Sr\":3.43295,\"P-Ta\":2.62642,\"P-Tb\":3.19649,\"P-Te\":2.56998,\"P-Th\":3.33649,\"P-Ti\":2.51642,\"P-Tl\":3.01644,\"P-Tm\":3.13649,\"P-U\":2.94644,\"P-V\":2.46642,\"P-W\":2.50998,\"P-Y\":3.17649,\"P-Yb\":3.13649,\"P-Zn\":2.86293,\"P-Zr\":3.02004,\"Pb-S\":3.40395,\"Pb-Se\":3.55295,\"Pb-Te\":3.14644,\"Pd-S\":2.69649,\"Pd-Se\":2.26998,\"Pd-Te\":2.52998,\"Pr-S\":3.20649,\"Pr-Se\":3.32649,\"Pr-Te\":3.50649,\"Pt-S\":2.76649,\"Pt-Se\":2.23998,\"Pt-Te\":2.49998,\"Pu-S\":3.3,\"Rb-S\":3.97645,\"Rb-Se\":4.13773,\"Rb-Te\":4.28802,\"Re-S\":2.61998,\"Re-Se\":2.54998,\"Re-Te\":2.74998,\"Rh-S\":2.19998,\"Rh-Se\":2.37998,\"Rh-Te\":2.59998,\"Ru-S\":2.6426,\"Ru-Se\":2.69451,\"Ru-Te\":2.58998,\"S-S\":2.2,\"S-Sb\":3.05,\"S-Sc\":2.88391,\"S-Se\":2.81649,\"S-Si\":2.47602,\"S-Sm\":3.15649,\"S-Sn\":3.15293,\"S-Sr\":3.51295,\"S-Ta\":2.8439,\"S-Tb\":3.11649,\"S-Te\":2.79002,\"S-Th\":3.24649,\"S-Ti\":2.74646,\"S-Tl\":3.66442,\"S-Tm\":3.05649,\"S-U\":3.25293,\"S-V\":2.82293,\"S-W\":2.43998,\"S-Y\":3.08649,\"S-Yb\":3.03649,\"S-Zn\":2.80293,\"S-Zr\":2.91004,\"Sb-Se\":3.05646,\"Sb-Te\":2.82998,\"Sc-Se\":3.00291,\"Sc-Te\":3.20291,\"Se-Se\":2.93649,\"Se-Si\":2.61002,\"Se-Sm\":3.27649,\"Se-Sn\":2.96646,\"Se-Sr\":3.58295,\"Se-Ta\":2.66642,\"Se-Tb\":3.23649,\"Se-Te\":2.57998,\"Se-Th\":3.36649,\"Se-Ti\":2.53642,\"Se-Tl\":3.00644,\"Se-Tm\":3.18649,\"Se-U\":3.00644,\"Se-V\":2.48642,\"Se-W\":2.55998,\"Se-Y\":3.21649,\"Se-Yb\":3.16649,\"Se-Zn\":2.93293,\"Se-Zr\":3.03004,\"Si-Si\":2.6,\"Si-Te\":2.84002,\"Sm-Te\":3.46649,\"Sn-Te\":2.91642,\"Sr-Te\":3.73295,\"Ta-Te\":2.85642,\"Tb-Te\":3.42649,\"Te-Te\":2.80998,\"Te-Th\":3.54649,\"Te-Ti\":2.95642,\"Te-Tl\":3.23644,\"Te-Tm\":3.37649,\"Te-U\":3.16644,\"Te-V\":2.72642,\"Te-W\":2.75998,\"Te-Y\":3.40649,\"Te-Yb\":3.36649,\"Te-Zn\":3.16293,\"Te-Zr\":3.17004}")
|
|
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|
-
}.pairs,
|
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|
-
function
|
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768
|
-
return
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}.pairs, kt = .4;
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function At(e, t) {
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return Ot[e < t ? `${e}-${t}` : `${t}-${e}`] ?? null;
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|
}
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function
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function jt(e) {
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|
let t = /* @__PURE__ */ new Map(), n = e.map((e) => {
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|
let n = t.get(e.element);
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return n === void 0 && (n = t.size, t.set(e.element, n)), n;
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}), r = [...t.keys()], i = new Float64Array(r.length * r.length), a = 0;
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if (r.forEach((e, t) => {
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r.forEach((n, o) => {
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let s =
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let s = At(e, n) ?? 0;
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i[t * r.length + o] = s, a = Math.max(a, s);
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});
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}), a <
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}), a < kt) return [];
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let o = e.map((e) => e.position.map((e) => Math.floor(e / a) | 0)), s = [
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Infinity,
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Infinity,
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@@ -799,9 +799,9 @@ function Mt(e) {
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m.length = 0;
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for (let r = -1; r <= 1; r += 1) for (let o = -1; o <= 1; o += 1) for (let p = -1; p <= 1; p += 1) for (let h of f.get(d(s + r, c + o, l + p)) ?? []) {
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let o =
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o >=
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if (h <= a || r < kt) continue;
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let o = Fe(t.position, e[h].position);
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o >= kt && o <= r && m.push({
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start: a,
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end: h,
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length: o
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}
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//#endregion
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//#region src/structure/images.ts
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function
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var Mt = 1e-4;
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function Nt(e, t) {
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let n = [];
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let i = e.fractional.map((e) => z(e, Mt));
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if (n.push({
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siteIndex: r,
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fractional: i,
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0,
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1,
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2
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].filter((e) => i[e] <
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].filter((e) => i[e] < Mt), o = 1 << a.length;
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|
for (let e = 1; e < o; e += 1) {
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let t = [
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i[0],
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}
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//#endregion
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//#region src/scene/build.ts
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function
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function Pt(e) {
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849
|
let t = [];
|
|
850
850
|
for (let n of e.sites) for (let e of n.species) {
|
|
851
|
-
let n =
|
|
851
|
+
let n = Se(e.element);
|
|
852
852
|
t.includes(n) || t.push(n);
|
|
853
853
|
}
|
|
854
854
|
return t;
|
|
855
855
|
}
|
|
856
|
-
function
|
|
857
|
-
let n =
|
|
856
|
+
function Ft(e, t = {}) {
|
|
857
|
+
let n = Nt(e.sites, t.imageAtoms ?? !0).map((t) => {
|
|
858
858
|
let n = e.sites[t.siteIndex];
|
|
859
859
|
if (!n) throw Error(`Site ${t.siteIndex} is missing.`);
|
|
860
860
|
let r = n.species[0];
|
|
@@ -863,7 +863,7 @@ function It(e, t = {}) {
|
|
|
863
863
|
siteIndex: t.siteIndex,
|
|
864
864
|
element: r.element,
|
|
865
865
|
species: n.species,
|
|
866
|
-
position:
|
|
866
|
+
position: Pe(e.lattice, t.fractional),
|
|
867
867
|
fractional: t.fractional,
|
|
868
868
|
isImage: t.isImage
|
|
869
869
|
};
|
|
@@ -871,20 +871,20 @@ function It(e, t = {}) {
|
|
|
871
871
|
return {
|
|
872
872
|
cell: e.lattice.vectors,
|
|
873
873
|
atoms: n,
|
|
874
|
-
bonds:
|
|
875
|
-
elements:
|
|
874
|
+
bonds: jt(n),
|
|
875
|
+
elements: Pt(e)
|
|
876
876
|
};
|
|
877
877
|
}
|
|
878
878
|
//#endregion
|
|
879
879
|
//#region node_modules/three/examples/jsm/controls/TrackballControls.js
|
|
880
|
-
var
|
|
880
|
+
var It = { type: "change" }, Lt = { type: "start" }, Rt = { type: "end" }, zt = 1e-6, q = {
|
|
881
881
|
NONE: -1,
|
|
882
882
|
ROTATE: 0,
|
|
883
883
|
ZOOM: 1,
|
|
884
884
|
PAN: 2,
|
|
885
885
|
TOUCH_ROTATE: 3,
|
|
886
886
|
TOUCH_ZOOM_PAN: 4
|
|
887
|
-
}, Bt = new
|
|
887
|
+
}, Bt = new j(), J = new j(), Vt = new M(), Ht = new M(), Ut = new M(), Y = new A(), Wt = new M(), Gt = new M(), Kt = new M(), qt = new M(), Jt = class extends l {
|
|
888
888
|
constructor(e, t = null) {
|
|
889
889
|
super(e, t), this.screen = {
|
|
890
890
|
left: 0,
|
|
@@ -896,10 +896,10 @@ var Lt = { type: "change" }, Rt = { type: "start" }, zt = { type: "end" }, K = 1
|
|
|
896
896
|
"KeyS",
|
|
897
897
|
"KeyD"
|
|
898
898
|
], this.mouseButtons = {
|
|
899
|
-
LEFT:
|
|
900
|
-
MIDDLE:
|
|
901
|
-
RIGHT:
|
|
902
|
-
}, this.target = new
|
|
899
|
+
LEFT: S.ROTATE,
|
|
900
|
+
MIDDLE: S.DOLLY,
|
|
901
|
+
RIGHT: S.PAN
|
|
902
|
+
}, this.target = new M(), this.state = q.NONE, this.keyState = q.NONE, this._lastPosition = new M(), this._lastUp = new M(), this._lastZoom = 1, this._touchZoomDistanceStart = 0, this._touchZoomDistanceEnd = 0, this._touchRollAngle = 0, this._touchRollPointerIds = "", this._lastAngle = 0, this._lastRollAngle = 0, this._eye = new M(), this._movePrev = new j(), this._moveCurr = new j(), this._lastAxis = new M(), this._zoomStart = new j(), this._zoomEnd = new j(), this._panStart = new j(), this._panEnd = new j(), this._pointers = [], this._pointerPositions = {}, this._onPointerMove = Xt.bind(this), this._onPointerDown = Yt.bind(this), this._onPointerUp = Zt.bind(this), this._onPointerCancel = Qt.bind(this), this._onContextMenu = on.bind(this), this._onMouseWheel = an.bind(this), this._onKeyDown = en.bind(this), this._onKeyUp = $t.bind(this), this._onTouchStart = sn.bind(this), this._onTouchMove = cn.bind(this), this._onTouchEnd = ln.bind(this), this._onMouseDown = tn.bind(this), this._onMouseMove = nn.bind(this), this._onMouseUp = rn.bind(this), this._target0 = this.target.clone(), this._position0 = this.object.position.clone(), this._up0 = this.object.up.clone(), this._zoom0 = this.object.zoom, t !== null && (this.connect(t), this.handleResize()), this.update();
|
|
903
903
|
}
|
|
904
904
|
connect(e) {
|
|
905
905
|
super.connect(e), window.addEventListener("keydown", this._onKeyDown), window.addEventListener("keyup", this._onKeyUp), this.domElement.addEventListener("pointerdown", this._onPointerDown), this.domElement.addEventListener("pointercancel", this._onPointerCancel), this.domElement.addEventListener("wheel", this._onMouseWheel, { passive: !1 }), this.domElement.addEventListener("contextmenu", this._onContextMenu), this.domElement.style.touchAction = "none";
|
|
@@ -917,16 +917,16 @@ var Lt = { type: "change" }, Rt = { type: "start" }, zt = { type: "end" }, K = 1
|
|
|
917
917
|
update() {
|
|
918
918
|
if (this._eye.subVectors(this.object.position, this.target), this.noRotate || (this._rotateCamera(), this.multiTouchRoll === !0 && this._rollCamera()), this.noZoom || this._zoomCamera(), this.noPan || this._panCamera(), this.object.position.addVectors(this.target, this._eye), this.object.isPerspectiveCamera) {
|
|
919
919
|
this._checkDistances(), this.object.lookAt(this.target);
|
|
920
|
-
let e = this._lastPosition.distanceToSquared(this.object.position) >
|
|
921
|
-
(e || t) && (this.dispatchEvent(
|
|
920
|
+
let e = this._lastPosition.distanceToSquared(this.object.position) > zt, t = this._lastUp.distanceToSquared(this.object.up) > zt;
|
|
921
|
+
(e || t) && (this.dispatchEvent(It), this._lastPosition.copy(this.object.position), this._lastUp.copy(this.object.up));
|
|
922
922
|
} else if (this.object.isOrthographicCamera) {
|
|
923
923
|
this.object.lookAt(this.target);
|
|
924
|
-
let e = this._lastPosition.distanceToSquared(this.object.position) >
|
|
925
|
-
(e || t || n) && (this.dispatchEvent(
|
|
924
|
+
let e = this._lastPosition.distanceToSquared(this.object.position) > zt, t = this._lastUp.distanceToSquared(this.object.up) > zt, n = this._lastZoom !== this.object.zoom;
|
|
925
|
+
(e || t || n) && (this.dispatchEvent(It), this._lastPosition.copy(this.object.position), this._lastUp.copy(this.object.up), this._lastZoom = this.object.zoom);
|
|
926
926
|
} else console.warn("THREE.TrackballControls: Unsupported camera type.");
|
|
927
927
|
}
|
|
928
928
|
reset() {
|
|
929
|
-
this.state = q.NONE, this.keyState = q.NONE, this.target.copy(this._target0), this.object.position.copy(this._position0), this.object.up.copy(this._up0), this.object.zoom = this._zoom0, this.object.updateProjectionMatrix(), this._eye.subVectors(this.object.position, this.target), this.object.lookAt(this.target), this.dispatchEvent(
|
|
929
|
+
this.state = q.NONE, this.keyState = q.NONE, this.target.copy(this._target0), this.object.position.copy(this._position0), this.object.up.copy(this._up0), this.object.zoom = this._zoom0, this.object.updateProjectionMatrix(), this._eye.subVectors(this.object.position, this.target), this.object.lookAt(this.target), this.dispatchEvent(It), this._lastPosition.copy(this.object.position), this._lastUp.copy(this.object.up), this._lastZoom = this.object.zoom;
|
|
930
930
|
}
|
|
931
931
|
_panCamera() {
|
|
932
932
|
if (J.copy(this._panEnd).sub(this._panStart), J.lengthSq()) {
|
|
@@ -959,7 +959,7 @@ var Lt = { type: "change" }, Rt = { type: "start" }, zt = { type: "end" }, K = 1
|
|
|
959
959
|
}
|
|
960
960
|
_zoomCamera() {
|
|
961
961
|
let e;
|
|
962
|
-
this.state === q.TOUCH_ZOOM_PAN ? (e = this._touchZoomDistanceStart / this._touchZoomDistanceEnd, this._touchZoomDistanceStart = this._touchZoomDistanceEnd, this.object.isPerspectiveCamera ? this._eye.multiplyScalar(e) : this.object.isOrthographicCamera ? (this.object.zoom =
|
|
962
|
+
this.state === q.TOUCH_ZOOM_PAN ? (e = this._touchZoomDistanceStart / this._touchZoomDistanceEnd, this._touchZoomDistanceStart = this._touchZoomDistanceEnd, this.object.isPerspectiveCamera ? this._eye.multiplyScalar(e) : this.object.isOrthographicCamera ? (this.object.zoom = ne.clamp(this.object.zoom / e, this.minZoom, this.maxZoom), this._lastZoom !== this.object.zoom && this.object.updateProjectionMatrix()) : console.warn("THREE.TrackballControls: Unsupported camera type")) : (e = 1 + (this._zoomEnd.y - this._zoomStart.y) * this.zoomSpeed, e !== 1 && e > 0 && (this.object.isPerspectiveCamera ? this._eye.multiplyScalar(e) : this.object.isOrthographicCamera ? (this.object.zoom = ne.clamp(this.object.zoom / e, this.minZoom, this.maxZoom), this._lastZoom !== this.object.zoom && this.object.updateProjectionMatrix()) : console.warn("THREE.TrackballControls: Unsupported camera type")), this.staticMoving ? this._zoomStart.copy(this._zoomEnd) : this._zoomStart.y += (this._zoomEnd.y - this._zoomStart.y) * this.dynamicDampingFactor);
|
|
963
963
|
}
|
|
964
964
|
_getMouseOnScreen(e, t) {
|
|
965
965
|
return Bt.set((e - this.screen.left) / this.screen.width, (t - this.screen.top) / this.screen.height), Bt;
|
|
@@ -979,7 +979,7 @@ var Lt = { type: "change" }, Rt = { type: "start" }, zt = { type: "end" }, K = 1
|
|
|
979
979
|
}
|
|
980
980
|
_trackPointer(e) {
|
|
981
981
|
let t = this._pointerPositions[e.pointerId];
|
|
982
|
-
t === void 0 && (t = new
|
|
982
|
+
t === void 0 && (t = new j(), this._pointerPositions[e.pointerId] = t), t.set(e.pageX, e.pageY);
|
|
983
983
|
}
|
|
984
984
|
_getSecondPointerPosition(e) {
|
|
985
985
|
let t = e.pointerId === this._pointers[0].pointerId ? this._pointers[1] : this._pointers[0];
|
|
@@ -1022,26 +1022,26 @@ function tn(e) {
|
|
|
1022
1022
|
default: t = -1;
|
|
1023
1023
|
}
|
|
1024
1024
|
switch (t) {
|
|
1025
|
-
case
|
|
1025
|
+
case S.DOLLY:
|
|
1026
1026
|
this.state = q.ZOOM;
|
|
1027
1027
|
break;
|
|
1028
|
-
case
|
|
1028
|
+
case S.ROTATE:
|
|
1029
1029
|
this.state = q.ROTATE;
|
|
1030
1030
|
break;
|
|
1031
|
-
case
|
|
1031
|
+
case S.PAN:
|
|
1032
1032
|
this.state = q.PAN;
|
|
1033
1033
|
break;
|
|
1034
1034
|
default: this.state = q.NONE;
|
|
1035
1035
|
}
|
|
1036
1036
|
let n = this.keyState === q.NONE ? this.state : this.keyState;
|
|
1037
|
-
n === q.ROTATE && !this.noRotate ? (this._moveCurr.copy(this._getMouseOnCircle(e.pageX, e.pageY)), this._movePrev.copy(this._moveCurr)) : n === q.ZOOM && !this.noZoom ? (this._zoomStart.copy(this._getMouseOnScreen(e.pageX, e.pageY)), this._zoomEnd.copy(this._zoomStart)) : n === q.PAN && !this.noPan && (this._panStart.copy(this._getMouseOnScreen(e.pageX, e.pageY)), this._panEnd.copy(this._panStart)), this.dispatchEvent(
|
|
1037
|
+
n === q.ROTATE && !this.noRotate ? (this._moveCurr.copy(this._getMouseOnCircle(e.pageX, e.pageY)), this._movePrev.copy(this._moveCurr)) : n === q.ZOOM && !this.noZoom ? (this._zoomStart.copy(this._getMouseOnScreen(e.pageX, e.pageY)), this._zoomEnd.copy(this._zoomStart)) : n === q.PAN && !this.noPan && (this._panStart.copy(this._getMouseOnScreen(e.pageX, e.pageY)), this._panEnd.copy(this._panStart)), this.dispatchEvent(Lt);
|
|
1038
1038
|
}
|
|
1039
1039
|
function nn(e) {
|
|
1040
1040
|
let t = this.keyState === q.NONE ? this.state : this.keyState;
|
|
1041
1041
|
t === q.ROTATE && !this.noRotate ? this._moveCurr.copy(this._getMouseOnCircle(e.pageX, e.pageY)) : t === q.ZOOM && !this.noZoom ? this._zoomEnd.copy(this._getMouseOnScreen(e.pageX, e.pageY)) : t === q.PAN && !this.noPan && this._panEnd.copy(this._getMouseOnScreen(e.pageX, e.pageY));
|
|
1042
1042
|
}
|
|
1043
1043
|
function rn() {
|
|
1044
|
-
this.state = q.NONE, this.dispatchEvent(
|
|
1044
|
+
this.state = q.NONE, this.dispatchEvent(Rt);
|
|
1045
1045
|
}
|
|
1046
1046
|
function an(e) {
|
|
1047
1047
|
if (this.enabled !== !1 && this.noZoom !== !0) {
|
|
@@ -1054,7 +1054,7 @@ function an(e) {
|
|
|
1054
1054
|
break;
|
|
1055
1055
|
default: this._zoomStart.y -= e.deltaY * 25e-5;
|
|
1056
1056
|
}
|
|
1057
|
-
this.dispatchEvent(
|
|
1057
|
+
this.dispatchEvent(Lt), this.dispatchEvent(Rt);
|
|
1058
1058
|
}
|
|
1059
1059
|
}
|
|
1060
1060
|
function on(e) {
|
|
@@ -1072,7 +1072,7 @@ function sn(e) {
|
|
|
1072
1072
|
let n = (this._pointers[0].pageX + this._pointers[1].pageX) / 2, r = (this._pointers[0].pageY + this._pointers[1].pageY) / 2;
|
|
1073
1073
|
this._panStart.copy(this._getMouseOnScreen(n, r)), this._panEnd.copy(this._panStart);
|
|
1074
1074
|
}
|
|
1075
|
-
this.dispatchEvent(
|
|
1075
|
+
this.dispatchEvent(Lt);
|
|
1076
1076
|
}
|
|
1077
1077
|
function cn(e) {
|
|
1078
1078
|
switch (this._trackPointer(e), this._pointers.length) {
|
|
@@ -1102,28 +1102,28 @@ function ln(e) {
|
|
|
1102
1102
|
break;
|
|
1103
1103
|
}
|
|
1104
1104
|
}
|
|
1105
|
-
this.dispatchEvent(
|
|
1105
|
+
this.dispatchEvent(Rt);
|
|
1106
1106
|
}
|
|
1107
1107
|
//#endregion
|
|
1108
1108
|
//#region src/render/camera.ts
|
|
1109
|
-
var un = 1 / 3, dn = 1 / 6, fn = 2, pn = 1e-12, mn = new
|
|
1109
|
+
var un = 1 / 3, dn = 1 / 6, fn = 2, pn = 1e-12, mn = new M(0, 0, -1), hn = new M(0, 1, 0);
|
|
1110
1110
|
function gn(e, t) {
|
|
1111
1111
|
let n = e.clone().sub(t.clone().multiplyScalar(e.dot(t)));
|
|
1112
1112
|
return n.lengthSq() < pn ? null : n.normalize();
|
|
1113
1113
|
}
|
|
1114
1114
|
function _n(e) {
|
|
1115
1115
|
for (let t of [
|
|
1116
|
-
new
|
|
1117
|
-
new
|
|
1118
|
-
new
|
|
1116
|
+
new M(0, 0, 1),
|
|
1117
|
+
new M(0, 1, 0),
|
|
1118
|
+
new M(1, 0, 0)
|
|
1119
1119
|
]) {
|
|
1120
1120
|
let n = gn(t, e);
|
|
1121
1121
|
if (n) return n;
|
|
1122
1122
|
}
|
|
1123
|
-
return new
|
|
1123
|
+
return new M(0, 1, 0);
|
|
1124
1124
|
}
|
|
1125
1125
|
function vn(e) {
|
|
1126
|
-
let t = new
|
|
1126
|
+
let t = new M(...e[0]), n = new M(...e[1]), r = new M(...e[2]).normalize(), i = gn(t, r) ?? gn(n, r) ?? _n(r), a = r.clone().cross(i).normalize(), o = i.clone().add(a.multiplyScalar(un)).add(r.clone().multiplyScalar(dn)).normalize();
|
|
1127
1127
|
return {
|
|
1128
1128
|
outward: o,
|
|
1129
1129
|
up: gn(r, o) ?? _n(o)
|
|
@@ -1134,7 +1134,7 @@ function yn(e) {
|
|
|
1134
1134
|
}
|
|
1135
1135
|
function bn(e) {
|
|
1136
1136
|
let { outward: t, up: n } = vn(e), r = n.clone().cross(t).normalize(), i = t.clone().cross(r).normalize(), a = new C().makeBasis(r, i, t);
|
|
1137
|
-
return new
|
|
1137
|
+
return new A().setFromRotationMatrix(a).normalize();
|
|
1138
1138
|
}
|
|
1139
1139
|
function xn(e) {
|
|
1140
1140
|
return {
|
|
@@ -1148,7 +1148,7 @@ function xn(e) {
|
|
|
1148
1148
|
};
|
|
1149
1149
|
}
|
|
1150
1150
|
function Sn(e, t, n, r) {
|
|
1151
|
-
let i = new
|
|
1151
|
+
let i = new A(...t.quaternion).normalize(), a = new M(...t.target), o = mn.clone().applyQuaternion(i);
|
|
1152
1152
|
e.position.copy(a).sub(o.multiplyScalar(n)), e.up.copy(hn.clone().applyQuaternion(i)), e.quaternion.copy(i), e.near = .01, e.far = Math.max(1e3, n + r * 8), e.updateProjectionMatrix();
|
|
1153
1153
|
}
|
|
1154
1154
|
function Cn(e) {
|
|
@@ -1160,9 +1160,9 @@ function Cn(e) {
|
|
|
1160
1160
|
];
|
|
1161
1161
|
}
|
|
1162
1162
|
function wn(e, t) {
|
|
1163
|
-
let n = new
|
|
1163
|
+
let n = new M(1, 0, 0).applyQuaternion(t), r = new M(0, 1, 0).applyQuaternion(t), i = Infinity, a = -Infinity, o = Infinity, s = -Infinity;
|
|
1164
1164
|
for (let t of [e.min.x, e.max.x]) for (let c of [e.min.y, e.max.y]) for (let l of [e.min.z, e.max.z]) {
|
|
1165
|
-
let e = new
|
|
1165
|
+
let e = new M(t, c, l), u = e.dot(n), d = e.dot(r);
|
|
1166
1166
|
i = Math.min(i, u), a = Math.max(a, u), o = Math.min(o, d), s = Math.max(s, d);
|
|
1167
1167
|
}
|
|
1168
1168
|
return {
|
|
@@ -1184,17 +1184,17 @@ var Dn = .1, On = .6, kn = .8, An = 2.2, jn = [
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.2,
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], Mn = "#fafafa", Nn = "#444444", Pn = "#f2f2f2", Fn = .3, In = "6.28318530718";
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function
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function Ln(e, t) {
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return t.reduce((e, [t, n]) => {
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if (!e.includes(t)) throw Error(`bravais cannot draw with this three.js: its shader has no ${t}.`);
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return e.replace(t, n);
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}, e);
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}
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function Ln(e) {
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return X(e, [["#include <common>", "#include <common>\nflat varying int vSectorSite;\nflat varying vec3 vSphereCenter;\nflat varying float vSphereRadius;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vSpherePoint;"], ["#include <project_vertex>", "mat4 sphereMatrix = modelViewMatrix * instanceMatrix;\nvSphereCenter = sphereMatrix[3].xyz;\nvSphereRadius = length(sphereMatrix[0].xyz);\nvSpherePoint = vSphereCenter + vec3(position.xy * vSphereRadius, 0.0);\nvDepthCoefficients = vec2(projectionMatrix[2][2], projectionMatrix[3][2]);\nvSectorSite = gl_InstanceID;\nvec4 mvPosition = vec4(vSpherePoint, 1.0);\ngl_Position = projectionMatrix * mvPosition;"]]);
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}
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function Rn(e) {
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return
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return Ln(e, [["#include <common>", "#include <common>\nflat varying int vSectorSite;\nflat varying vec3 vSphereCenter;\nflat varying float vSphereRadius;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vSpherePoint;"], ["#include <project_vertex>", "mat4 sphereMatrix = modelViewMatrix * instanceMatrix;\nvSphereCenter = sphereMatrix[3].xyz;\nvSphereRadius = length(sphereMatrix[0].xyz);\nvSpherePoint = vSphereCenter + vec3(position.xy * vSphereRadius, 0.0);\nvDepthCoefficients = vec2(projectionMatrix[2][2], projectionMatrix[3][2]);\nvSectorSite = gl_InstanceID;\nvec4 mvPosition = vec4(vSpherePoint, 1.0);\ngl_Position = projectionMatrix * mvPosition;"]]);
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}
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function zn(e) {
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return Ln(e, [
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["#include <common>", "#include <common>\nuniform sampler2D sectorTexture;\nuniform float vacancyOpacity;\nflat varying int vSectorSite;\nflat varying vec3 vSphereCenter;\nflat varying float vSphereRadius;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vSpherePoint;"],
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["#include <clipping_planes_fragment>", "// Where the view ray meets the sphere. The outline is smoothed over one\n// pixel through the alpha: sample coverage, or blending in a see-through layer.\nvec2 sphereOffset = vSpherePoint.xy - vSphereCenter.xy;\nfloat sphereDistance = length(sphereOffset);\nfloat sphereCoverage = clamp(\n (vSphereRadius - sphereDistance) / max(fwidth(sphereDistance), 1e-6) + 0.5,\n 0.0,\n 1.0\n);\nif (sphereCoverage <= 0.0) {\n discard;\n}\nfloat sphereHeight = sqrt(\n max(0.0, vSphereRadius * vSphereRadius - dot(sphereOffset, sphereOffset))\n);\nvec3 sphereNormal = vec3(sphereOffset, sphereHeight) / vSphereRadius;\nfloat sphereZ = vSphereCenter.z + sphereHeight;\ngl_FragDepth = (vDepthCoefficients.x * sphereZ + vDepthCoefficients.y) * 0.5 + 0.5;\n#include <clipping_planes_fragment>"],
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["#include <color_fragment>", `#include <color_fragment>
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@@ -1222,7 +1222,7 @@ function Rn(e) {
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["#include <normal_fragment_begin>", "#include <normal_fragment_begin>\nnormal = sphereNormal;\nnonPerturbedNormal = normal;"]
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]);
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}
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function
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function Bn(e, t, n) {
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let r = e < 1 || n, i = new T({
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color: "#ffffff",
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metalness: Dn,
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@@ -1232,21 +1232,21 @@ function zn(e, t, n) {
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alphaToCoverage: !r
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});
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return i.onBeforeCompile = (e) => {
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e.uniforms.sectorTexture = { value: t }, e.uniforms.vacancyOpacity = { value: Fn }, e.vertexShader =
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e.uniforms.sectorTexture = { value: t }, e.uniforms.vacancyOpacity = { value: Fn }, e.vertexShader = Rn(e.vertexShader), e.fragmentShader = zn(e.fragmentShader);
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}, i.customProgramCacheKey = () => "bravais-atom-spheres", i;
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}
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function Bn(e) {
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return X(e, [["#include <common>", "#include <common>\nuniform float capRadius;\nflat varying vec3 vTubeCenter;\nflat varying vec3 vTubeAxis;\nflat varying vec3 vAtomCenter;\nflat varying float vTubeRadius;\nflat varying float vTubeHalfLength;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vBoxPoint;"], ["#include <project_vertex>", "mat4 tubeMatrix = modelViewMatrix * instanceMatrix;\nfloat tubeLength = max(length(tubeMatrix[1].xyz), 1e-6);\nvTubeRadius = length(tubeMatrix[0].xyz);\nvTubeHalfLength = tubeLength * 0.5;\nvTubeCenter = tubeMatrix[3].xyz;\nvTubeAxis = tubeMatrix[1].xyz / tubeLength;\nfloat rim = sqrt(max(0.0, capRadius * capRadius - vTubeRadius * vTubeRadius));\nvAtomCenter = vTubeCenter - vTubeAxis * (rim + vTubeHalfLength);\nvDepthCoefficients = vec2(projectionMatrix[2][2], projectionMatrix[3][2]);\nvec4 mvPosition = tubeMatrix * vec4(position, 1.0);\nvBoxPoint = mvPosition.xyz;\ngl_Position = projectionMatrix * mvPosition;"]]);
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}
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function Vn(e) {
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return
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return Ln(e, [["#include <common>", "#include <common>\nuniform float capRadius;\nflat varying vec3 vTubeCenter;\nflat varying vec3 vTubeAxis;\nflat varying vec3 vAtomCenter;\nflat varying float vTubeRadius;\nflat varying float vTubeHalfLength;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vBoxPoint;"], ["#include <project_vertex>", "mat4 tubeMatrix = modelViewMatrix * instanceMatrix;\nfloat tubeLength = max(length(tubeMatrix[1].xyz), 1e-6);\nvTubeRadius = length(tubeMatrix[0].xyz);\nvTubeHalfLength = tubeLength * 0.5;\nvTubeCenter = tubeMatrix[3].xyz;\nvTubeAxis = tubeMatrix[1].xyz / tubeLength;\nfloat rim = sqrt(max(0.0, capRadius * capRadius - vTubeRadius * vTubeRadius));\nvAtomCenter = vTubeCenter - vTubeAxis * (rim + vTubeHalfLength);\nvDepthCoefficients = vec2(projectionMatrix[2][2], projectionMatrix[3][2]);\nvec4 mvPosition = tubeMatrix * vec4(position, 1.0);\nvBoxPoint = mvPosition.xyz;\ngl_Position = projectionMatrix * mvPosition;"]]);
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}
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function Hn(e) {
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return Ln(e, [
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["#include <common>", "#include <common>\nuniform float capRadius;\nflat varying vec3 vTubeCenter;\nflat varying vec3 vTubeAxis;\nflat varying vec3 vAtomCenter;\nflat varying float vTubeRadius;\nflat varying float vTubeHalfLength;\nflat varying vec2 vDepthCoefficients;\nvarying vec3 vBoxPoint;"],
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["#include <clipping_planes_fragment>", "// The view ray through this pixel runs down view z. The tube's surface is\n// the nearest of: the wall outside the atom's sphere, the sphere's far side\n// inside the tube (the cut face) and the midpoint disc. Along the ray,\n// q(z) = p(z) - centre has q.a = k + (z - cz) a.z and |q|^2 = u + (z - cz)^2.\nvec2 tubePixel = vBoxPoint.xy;\nvec2 tubeOffset = tubePixel - vTubeCenter.xy;\nfloat tubeK = dot(tubeOffset, vTubeAxis.xy);\nfloat tubeU = dot(tubeOffset, tubeOffset);\nfloat axisZ = vTubeAxis.z;\nfloat quadA = 1.0 - axisZ * axisZ;\nfloat quadB = -2.0 * tubeK * axisZ;\nfloat quadC = tubeU - tubeK * tubeK - vTubeRadius * vTubeRadius;\nfloat tubeRadius2 = vTubeRadius * vTubeRadius;\n// The ray's closest approach to the axis, for the outline's coverage.\nfloat axisDistance2 = tubeU - tubeK * tubeK;\nif (quadA > 1e-6) {\n axisDistance2 -= quadB * quadB / (4.0 * quadA);\n}\nfloat axisDistance = sqrt(max(0.0, axisDistance2));\nfloat tubeCoverage = clamp(\n (vTubeRadius - axisDistance) / max(fwidth(axisDistance), 1e-6) + 0.5,\n 0.0,\n 1.0\n);\nif (tubeCoverage <= 0.0) {\n discard;\n}\nfloat tubeHitZ = -1e30;\nvec3 tubeNormal = vec3(0.0, 0.0, 1.0);\nif (quadA > 1e-6) {\n float discriminant = quadB * quadB - 4.0 * quadA * quadC;\n if (discriminant >= 0.0) {\n float z = vTubeCenter.z + (-quadB + sqrt(discriminant)) / (2.0 * quadA);\n vec3 d = vec3(tubePixel, z) - vTubeCenter;\n float s = dot(d, vTubeAxis);\n if (abs(s) <= vTubeHalfLength && distance(vec3(tubePixel, z), vAtomCenter) >= capRadius) {\n tubeHitZ = z;\n tubeNormal = (d - s * vTubeAxis) / vTubeRadius;\n }\n }\n}\nif (axisZ > 1e-6) {\n float z = vTubeCenter.z + (vTubeHalfLength - tubeK) / axisZ;\n vec3 d = vec3(tubePixel, z) - vTubeCenter;\n if (dot(d, d) - vTubeHalfLength * vTubeHalfLength <= tubeRadius2 && z > tubeHitZ &&\n distance(vec3(tubePixel, z), vAtomCenter) >= capRadius) {\n tubeHitZ = z;\n tubeNormal = vTubeAxis;\n }\n}\n{\n vec2 m = tubePixel - vAtomCenter.xy;\n float inside = capRadius * capRadius - dot(m, m);\n if (inside >= 0.0) {\n float z = vAtomCenter.z - sqrt(inside);\n vec3 d = vec3(tubePixel, z) - vTubeCenter;\n float s = dot(d, vTubeAxis);\n if (abs(s) <= vTubeHalfLength && dot(d, d) - s * s <= tubeRadius2 && z > tubeHitZ) {\n tubeHitZ = z;\n tubeNormal = (vAtomCenter - vec3(tubePixel, z)) / capRadius;\n }\n }\n}\nif (tubeHitZ < -1e29) {\n discard;\n}\ngl_FragDepth = (vDepthCoefficients.x * tubeHitZ + vDepthCoefficients.y) * 0.5 + 0.5;\n#include <clipping_planes_fragment>"],
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["#include <color_fragment>", "#include <color_fragment>\ndiffuseColor.a *= tubeCoverage;"],
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["#include <normal_fragment_begin>", "#include <normal_fragment_begin>\nnormal = tubeNormal;\nnonPerturbedNormal = normal;"]
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]);
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}
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function
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function Un(e, t) {
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let n = e < 1, r = new T({
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color: "#ffffff",
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metalness: Dn,
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alphaToCoverage: !n
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});
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return r.onBeforeCompile = (e) => {
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e.uniforms.capRadius = { value: t }, e.vertexShader =
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e.uniforms.capRadius = { value: t }, e.vertexShader = Vn(e.vertexShader), e.fragmentShader = Hn(e.fragmentShader);
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}, r.customProgramCacheKey = () => "bravais-bond-tubes", r;
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}
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function
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return new
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function Wn(e) {
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return new y({
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color: Nn,
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opacity: e,
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transparent: !0,
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fog: !1
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});
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}
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function Gn(e, n) {
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return new T({
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color: e,
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metalness: 0,
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stencilWrite: !0,
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stencilRef: n,
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stencilFunc: t,
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stencilZPass:
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stencilZPass: ae
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});
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}
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function Gn(e) {
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for (let t of Array.isArray(e) ? e : [e]) t.dispose();
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}
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//#endregion
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//#region src/render/gizmo.ts
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var Kn = {
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a: "#d27686",
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b: "#80c393",
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c: "#75a4dd"
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}, qn = .82, Jn = .055, Yn = .24, Xn = .13, Zn = .13, Qn = 1.3, $n = .5, er = 128, tr = "#2a2a2a", nr = "#ffffff", rr = 3.2, ir = new
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}, qn = .82, Jn = .055, Yn = .24, Xn = .13, Zn = .13, Qn = 1.3, $n = .5, er = 128, tr = "#2a2a2a", nr = "#ffffff", rr = 3.2, ir = new M(0, 1, 0);
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function ar(e, t) {
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let n = document.createElement("canvas");
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n.width = er, n.height = er;
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r.clearRect(0, 0, n.width, n.height), r.font = `italic 600 ${i}px ${t}`, r.textAlign = "center", r.textBaseline = "middle", r.fillStyle = "#ffffff", r.fillText(e, n.width / 2, n.height / 2);
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}
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let i = new o(n);
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return i.colorSpace =
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}
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function or(e, t, n
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let i = new
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let
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o.position.y =
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let s =
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let n = new ue(new de({
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map: l,
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return i.colorSpace = oe, i.premultiplyAlpha = !0, i.magFilter = x, i.minFilter = te, i;
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}
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function or(e, t, n) {
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let r = new _(), i = Gn(e, 1), a = new w(new u(Jn, Jn, qn, 24), i);
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a.position.y = qn / 2;
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let o = new w(new c(Xn, Yn, 32), i);
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o.position.y = .94, r.add(a, o);
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let s = ar(t, n), l = [[tr, D], [nr, m]];
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for (let [e, t] of l) {
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let n = new le(new ue({
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map: s,
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color: e,
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depthTest: !1,
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depthWrite: !1,
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stencilRef: 1,
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stencilFunc: t
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}));
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n.scale.set($n, $n, 1), n.position.y = Qn, n.renderOrder = 10,
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n.scale.set($n, $n, 1), n.position.y = Qn, n.renderOrder = 10, r.add(n);
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}
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return
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return r;
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}
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var sr = class {
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scene = new se();
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camera = new k(-1, 1, 1, -1, .1, 20);
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axes = new _();
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arrows;
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headlight = new f("#ffffff", 1.78);
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inverse = new
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inverse = new A();
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direction = new M();
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constructor(e) {
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this.
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this.camera.position.set(0, 0, 5), this.camera.lookAt(0, 0, 0), this.scene.add(new n("#ffffff", .68)), this.headlight.position.set(1.6, 1.1, 5), this.scene.add(this.headlight), this.arrows = [
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"a",
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"b",
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"c"
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].map((t) => or(Kn[t], t, e));
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let t = new w(new ce(Zn, 32, 16), Gn("#f3f2ee", 0));
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this.axes.add(...this.arrows, t), this.scene.add(this.axes);
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}
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setCell(e) {
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this.
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["b", new j(...e[1])],
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["c", new j(...e[2])]
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];
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for (let [e, n] of t) this.axes.add(or(n, Kn[e], e, this.fontFamily));
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let n = new w(new le(Zn, 32, 16), Wn("#f3f2ee", 0));
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this.axes.add(n);
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this.arrows.forEach((t, n) => {
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t.quaternion.setFromUnitVectors(ir, this.direction.set(...e[n]).normalize());
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});
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}
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render(e, t, n) {
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this.axes.quaternion.copy(this.inverse.copy(t).invert());
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@@ -1353,7 +1349,7 @@ var sr = class {
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}
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dispose() {
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this.axes.traverse((e) => {
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if (e instanceof w || e instanceof
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if (e instanceof w || e instanceof le) {
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e.geometry.dispose();
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let t = e.material;
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"map" in t && t.map && t.map.dispose(), t.dispose();
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@@ -1532,7 +1528,7 @@ var vr = cr.elements, yr = {
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Cr: "#6d87c9",
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V: "#bf4b62",
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F: "#9bd7d0"
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-
}, br = /* @__PURE__ */ "O.Li.Na.K.Mg.Ca.Sr.Ba.Al.Si.Ti.Mn.Fe.Co.Ni.Cu.Zn.V.Cr.Ga.Ge.Y.Zr.Nb.Mo.Ru.Ag.Cd.In.Sn.Sb.La.Ce.Nd.Sm.Gd.Ta.W.Pt.Au.Pb.Bi.H.C.N.F.P.S.Cl.Se.Te.I.Br.B.Sc.Rb.Cs.Hf.Re.Ir.Pd.Rh.Os.Pr.Eu.Tb.Dy.Ho.Er.Tm.Yb.Lu.Th.U".split("."), xr = new Map(br.map((e, t) => [e, t])), Sr = .1, Cr = .7,
|
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}, br = /* @__PURE__ */ "O.Li.Na.K.Mg.Ca.Sr.Ba.Al.Si.Ti.Mn.Fe.Co.Ni.Cu.Zn.V.Cr.Ga.Ge.Y.Zr.Nb.Mo.Ru.Ag.Cd.In.Sn.Sb.La.Ce.Nd.Sm.Gd.Ta.W.Pt.Au.Pb.Bi.H.C.N.F.P.S.Cl.Se.Te.I.Br.B.Sc.Rb.Cs.Hf.Re.Ir.Pd.Rh.Os.Pr.Eu.Tb.Dy.Ho.Er.Tm.Yb.Lu.Th.U".split("."), xr = new Map(br.map((e, t) => [e, t])), Sr = .1, Cr = .7, X = {
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function zr(e) {
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let t = Rr(e);
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if (t) return hr(dr(t));
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let n =
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let n = _e.indexOf(e) + 1;
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return {
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L: .68,
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C: .12,
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function Br(e) {
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let t = xr.get(e);
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if (t !== void 0) return t;
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let n =
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return br.length + (n >= 0 ? n :
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let n = _e.indexOf(e);
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return br.length + (n >= 0 ? n : _e.length);
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function Vr(e) {
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L: Math.min(
|
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C: Math.min(
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L: Math.min(X.maxL, Math.max(X.minL, e.L)),
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C: Math.min(X.maxC, Math.max(0, e.C)),
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@@ -1655,7 +1651,7 @@ function Wr(e) {
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}
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let n = e.C / Math.max(1e-6, Hr(e.L, e.h));
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for (let r of Dr) for (let i of Or) for (let a of kr) {
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let o = Math.min(
|
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let o = Math.min(X.maxL, Math.max(X.minL, e.L + i)), s = e.h + r, c = Math.min(1, Math.max(.1, n + a)) * Hr(o, s), l = Math.abs(r) / jr + Math.abs(i) / Mr + Math.abs(a) / Nr;
|
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t.push(Ur({
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C: c,
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@@ -1664,9 +1660,9 @@ function Wr(e) {
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}
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return t.sort((e, t) => e.cost - t.cost);
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}
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var
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var Z = /* @__PURE__ */ new Map();
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function Gr(e, t) {
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let n = [...
|
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let n = [...Z.values()].map((e) => e.lab), r = (e) => n.reduce((t, n) => Math.min(t, Ir(e, n)), Infinity), i = gr(t);
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if (r(i) >= Sr) return {
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hex: e ?? mr(i),
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lab: i
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@@ -1689,18 +1685,18 @@ function Gr(e, t) {
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};
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}
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function Kr(e) {
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let t = [...new Set(e)].filter((e) => !
|
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for (let e of t)
|
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let t = [...new Set(e)].filter((e) => !Z.has(e)).sort((e, t) => Br(e) - Br(t));
|
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for (let e of t) Z.set(e, Gr(Rr(e), zr(e)));
|
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|
}
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|
function qr(e) {
|
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-
let t =
|
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return t ? t.hex : (Kr([e]),
|
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let t = Z.get(e);
|
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return t ? t.hex : (Kr([e]), Z.get(e).hex);
|
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|
}
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|
function Jr() {
|
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return [...
|
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|
+
return [...Z].map(([e, t]) => [e, t.hex]);
|
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|
}
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|
function Yr() {
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|
-
|
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+
Z.clear();
|
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}
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|
//#endregion
|
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|
//#region src/render/legend.ts
|
|
@@ -1730,11 +1726,11 @@ var ei = class {
|
|
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|
}
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|
this.element.hidden = e.length === 0;
|
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|
}
|
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|
-
},
|
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|
-
function
|
|
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|
-
let [t, n, r] = e.map((e) => new
|
|
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|
+
}, Q = .4, $ = .1, ti = .398, ni = Math.sqrt(ti * ti - $ * $), ri = new M(0, 1, 0);
|
|
1730
|
+
function ii(e) {
|
|
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|
+
let [t, n, r] = e.map((e) => new M(...e));
|
|
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|
return [
|
|
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|
-
new
|
|
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|
+
new M(),
|
|
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|
t.clone(),
|
|
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|
n.clone(),
|
|
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|
r.clone(),
|
|
@@ -1744,7 +1740,7 @@ function ai(e) {
|
|
|
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|
t.clone().add(n).add(r)
|
|
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|
];
|
|
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|
}
|
|
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|
-
function
|
|
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|
+
function ai(e) {
|
|
1748
1744
|
let [t, n, r] = e;
|
|
1749
1745
|
return [
|
|
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1746
|
(t[0] + n[0] + r[0]) / 2,
|
|
@@ -1752,7 +1748,7 @@ function oi(e) {
|
|
|
1752
1748
|
(t[2] + n[2] + r[2]) / 2
|
|
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1749
|
];
|
|
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1750
|
}
|
|
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|
-
var
|
|
1751
|
+
var oi = [
|
|
1756
1752
|
[0, 1],
|
|
1757
1753
|
[0, 2],
|
|
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|
[0, 3],
|
|
@@ -1766,85 +1762,85 @@ var si = [
|
|
|
1766
1762
|
[5, 7],
|
|
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1763
|
[6, 7]
|
|
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1764
|
];
|
|
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|
-
function
|
|
1770
|
-
let n =
|
|
1771
|
-
for (let [e, t] of
|
|
1765
|
+
function si(e, t) {
|
|
1766
|
+
let n = ii(e), r = [];
|
|
1767
|
+
for (let [e, t] of oi) {
|
|
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1768
|
let i = n[e], a = n[t];
|
|
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1769
|
r.push(i.x, i.y, i.z, a.x, a.y, a.z);
|
|
1774
1770
|
}
|
|
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1771
|
let i = new a();
|
|
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|
-
return i.setAttribute("position", new h(r, 3)), new b(i,
|
|
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|
+
return i.setAttribute("position", new h(r, 3)), new b(i, Wn(t));
|
|
1777
1773
|
}
|
|
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|
-
function
|
|
1774
|
+
function ci(e) {
|
|
1779
1775
|
let t = 2048, n = Math.max(1, Math.ceil(e.length / 256)), r = new Float32Array(t * n * 4).fill(1), i = new s(Pn), a = new s(), o = !1;
|
|
1780
1776
|
e.forEach((e, n) => {
|
|
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1777
|
let s = Math.floor(n / 256), c = n % 256 * 8, l = (s * t + c) * 4, u = 0, d = Math.min(1, e.species[0]?.occupancy ?? 1);
|
|
1782
1778
|
for (let t of e.species.slice(1)) u < 7 && (a.set(qr(t.element)).toArray(r, l), r[l + 3] = d, l += 4, u += 1), d = Math.min(1, d + t.occupancy);
|
|
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1779
|
d < 1 - 1e-6 && (i.toArray(r, l), r[l + 3] = d + 2, o = !0);
|
|
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1780
|
});
|
|
1785
|
-
let c = new d(r, t, n,
|
|
1781
|
+
let c = new d(r, t, n, ie, g);
|
|
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1782
|
return c.magFilter = E, c.minFilter = E, c.generateMipmaps = !1, c.needsUpdate = !0, {
|
|
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|
texture: c,
|
|
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1784
|
hasVacancies: o
|
|
1789
1785
|
};
|
|
1790
1786
|
}
|
|
1791
|
-
function
|
|
1787
|
+
function li() {
|
|
1792
1788
|
let e = /* @__PURE__ */ new Map();
|
|
1793
1789
|
return (t) => {
|
|
1794
1790
|
let n = e.get(t);
|
|
1795
1791
|
return n || (n = new s(qr(t)), e.set(t, n)), n;
|
|
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1792
|
};
|
|
1797
1793
|
}
|
|
1798
|
-
function
|
|
1799
|
-
let
|
|
1794
|
+
function ui(e, t, n = li()) {
|
|
1795
|
+
let r = new re(2, 2), i = ci(e), a = new v(r, Bn(t, i.texture, i.hasVacancies), e.length), o = new C();
|
|
1800
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|
return e.forEach((e, t) => {
|
|
1801
|
-
|
|
1802
|
-
}),
|
|
1797
|
+
o.makeScale(Q, Q, Q), o.setPosition(e.position[0], e.position[1], e.position[2]), a.setMatrixAt(t, o), a.setColorAt(t, n(e.element));
|
|
1798
|
+
}), a.instanceMatrix.needsUpdate = !0, a.instanceColor && (a.instanceColor.needsUpdate = !0), a.userData.sectorTexture = i.texture, a;
|
|
1803
1799
|
}
|
|
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|
-
function
|
|
1800
|
+
function di(e, t, n = li()) {
|
|
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1801
|
if (e.bonds.length === 0) return null;
|
|
1806
|
-
let
|
|
1807
|
-
return e.bonds.forEach((t,
|
|
1802
|
+
let r = new i(2, 1, 2), a = new v(r, Un(t, ti), e.bonds.length * 2), o = new O(), s = new M(), c = new M(), l = new M(), u = new A();
|
|
1803
|
+
return e.bonds.forEach((t, r) => {
|
|
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1804
|
let i = e.atoms[t.start], d = e.atoms[t.end];
|
|
1809
|
-
|
|
1810
|
-
let f =
|
|
1811
|
-
|
|
1805
|
+
s.set(...i.position), c.set(...d.position), l.subVectors(c, s);
|
|
1806
|
+
let f = l.length() / 2;
|
|
1807
|
+
l.normalize(), u.setFromUnitVectors(ri, l);
|
|
1812
1808
|
let p = [[
|
|
1813
1809
|
0,
|
|
1814
1810
|
i,
|
|
1815
|
-
|
|
1811
|
+
ni,
|
|
1816
1812
|
f
|
|
1817
1813
|
], [
|
|
1818
1814
|
1,
|
|
1819
1815
|
d,
|
|
1820
1816
|
f,
|
|
1821
|
-
2 * f -
|
|
1817
|
+
2 * f - ni
|
|
1822
1818
|
]];
|
|
1823
|
-
for (let [e, t, i,
|
|
1824
|
-
let d = Math.max(0,
|
|
1825
|
-
|
|
1819
|
+
for (let [e, t, i, c] of p) {
|
|
1820
|
+
let d = Math.max(0, c - i);
|
|
1821
|
+
o.position.copy(s).addScaledVector(l, i + d / 2), o.quaternion.copy(u), o.scale.set($, d, $), o.updateMatrix(), a.setMatrixAt(r * 2 + e, o.matrix), a.setColorAt(r * 2 + e, n(t.element));
|
|
1826
1822
|
}
|
|
1827
|
-
}),
|
|
1823
|
+
}), a.instanceMatrix.needsUpdate = !0, a.instanceColor && (a.instanceColor.needsUpdate = !0), a;
|
|
1828
1824
|
}
|
|
1829
|
-
function
|
|
1825
|
+
function fi(e) {
|
|
1830
1826
|
let t = e[0];
|
|
1831
1827
|
if (!t) throw Error("A scene model needs at least one layer.");
|
|
1832
1828
|
Kr(e.flatMap((e) => [...e.scene.elements, ...e.scene.atoms.map((e) => e.element)]));
|
|
1833
|
-
let n =
|
|
1829
|
+
let n = ai(t.scene.cell), i = new _();
|
|
1834
1830
|
i.position.set(-n[0], -n[1], -n[2]);
|
|
1835
|
-
let a = new r(), o = [], s = 1, c = [], l = new
|
|
1831
|
+
let a = new r(), o = [], s = 1, c = [], l = new M(...n), u = new M(), d = new M();
|
|
1836
1832
|
for (let t of e) {
|
|
1837
|
-
for (let e of
|
|
1838
|
-
for (let e of t.scene.atoms) u.set(...e.position).sub(l), a.expandByPoint(
|
|
1833
|
+
for (let e of ii(t.scene.cell)) a.expandByPoint(e.sub(l));
|
|
1834
|
+
for (let e of t.scene.atoms) u.set(...e.position).sub(l), a.expandByPoint(d.copy(u).addScalar(Q)), a.expandByPoint(d.copy(u).subScalar(Q));
|
|
1839
1835
|
for (let e of t.scene.cell) s = Math.max(s, Math.hypot(...e));
|
|
1840
1836
|
let e = t.opacity ?? 1;
|
|
1841
1837
|
if (e <= 0) continue;
|
|
1842
|
-
let n =
|
|
1838
|
+
let n = ui(t.scene.atoms, e);
|
|
1843
1839
|
i.add(n), c.push(n);
|
|
1844
|
-
let r =
|
|
1840
|
+
let r = di(t.scene, e);
|
|
1845
1841
|
r && (i.add(r), c.push(r));
|
|
1846
|
-
let
|
|
1847
|
-
i.add(
|
|
1842
|
+
let f = si(t.scene.cell, e);
|
|
1843
|
+
i.add(f), c.push(f);
|
|
1848
1844
|
for (let e of t.scene.elements) o.includes(e) || o.push(e);
|
|
1849
1845
|
}
|
|
1850
1846
|
return {
|
|
@@ -1855,27 +1851,83 @@ function pi(e) {
|
|
|
1855
1851
|
span: s,
|
|
1856
1852
|
elements: o,
|
|
1857
1853
|
dispose() {
|
|
1858
|
-
|
|
1859
|
-
e.geometry.dispose(), Gn(e.material);
|
|
1860
|
-
let t = e.userData.sectorTexture;
|
|
1861
|
-
t instanceof d && t.dispose();
|
|
1862
|
-
}
|
|
1863
|
-
i.clear();
|
|
1854
|
+
pi(c), i.clear();
|
|
1864
1855
|
}
|
|
1865
1856
|
};
|
|
1866
1857
|
}
|
|
1858
|
+
function pi(e) {
|
|
1859
|
+
for (let t of e) {
|
|
1860
|
+
t.geometry.dispose();
|
|
1861
|
+
let e = t.userData.sectorTexture;
|
|
1862
|
+
e instanceof d && e.dispose();
|
|
1863
|
+
}
|
|
1864
|
+
}
|
|
1865
|
+
var mi = {
|
|
1866
|
+
cell: [
|
|
1867
|
+
[
|
|
1868
|
+
1,
|
|
1869
|
+
0,
|
|
1870
|
+
0
|
|
1871
|
+
],
|
|
1872
|
+
[
|
|
1873
|
+
0,
|
|
1874
|
+
1,
|
|
1875
|
+
0
|
|
1876
|
+
],
|
|
1877
|
+
[
|
|
1878
|
+
0,
|
|
1879
|
+
0,
|
|
1880
|
+
1
|
|
1881
|
+
]
|
|
1882
|
+
],
|
|
1883
|
+
atoms: [0, 2].map((e, t) => ({
|
|
1884
|
+
siteIndex: t,
|
|
1885
|
+
element: "X",
|
|
1886
|
+
species: [{
|
|
1887
|
+
element: "X",
|
|
1888
|
+
occupancy: 1
|
|
1889
|
+
}],
|
|
1890
|
+
position: [
|
|
1891
|
+
0,
|
|
1892
|
+
0,
|
|
1893
|
+
e
|
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1894
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+
],
|
|
1895
|
+
fractional: [
|
|
1896
|
+
0,
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|
1897
|
+
0,
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1898
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+
e
|
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1899
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+
],
|
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1900
|
+
isImage: !1
|
|
1901
|
+
})),
|
|
1902
|
+
bonds: [{
|
|
1903
|
+
start: 0,
|
|
1904
|
+
end: 1,
|
|
1905
|
+
length: 2
|
|
1906
|
+
}],
|
|
1907
|
+
elements: []
|
|
1908
|
+
};
|
|
1909
|
+
function hi() {
|
|
1910
|
+
let e = new s("#ffffff"), t = [];
|
|
1911
|
+
for (let n of [1, .5]) t.push(ui(mi.atoms, n, () => e), di(mi, n, () => e));
|
|
1912
|
+
t.push(si(mi.cell, 1));
|
|
1913
|
+
let n = new _();
|
|
1914
|
+
return n.add(...t), {
|
|
1915
|
+
group: n,
|
|
1916
|
+
dispose: () => pi(t)
|
|
1917
|
+
};
|
|
1918
|
+
}
|
|
1867
1919
|
//#endregion
|
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1868
1920
|
//#region src/render/stage.ts
|
|
1869
|
-
function
|
|
1870
|
-
let r = new
|
|
1921
|
+
function gi(t = {}) {
|
|
1922
|
+
let r = new N({
|
|
1871
1923
|
antialias: !0,
|
|
1872
1924
|
alpha: !0,
|
|
1873
1925
|
stencil: t.stencil ?? !1
|
|
1874
1926
|
});
|
|
1875
1927
|
r.setClearColor(Mn, 1), r.toneMapping = e;
|
|
1876
|
-
let i = new
|
|
1928
|
+
let i = new se(), a = new k(-1, 1, 1, -1, .01, 1e3), o = new f("#ffffff", An);
|
|
1877
1929
|
i.add(new n("#ffffff", kn), o, o.target);
|
|
1878
|
-
let s = new
|
|
1930
|
+
let s = new M();
|
|
1879
1931
|
return {
|
|
1880
1932
|
renderer: r,
|
|
1881
1933
|
scene: i,
|
|
@@ -1888,76 +1940,86 @@ function mi(t = {}) {
|
|
|
1888
1940
|
}
|
|
1889
1941
|
//#endregion
|
|
1890
1942
|
//#region src/render/viewer.ts
|
|
1891
|
-
var
|
|
1892
|
-
function
|
|
1893
|
-
let r = new
|
|
1943
|
+
var _i = .4, vi = .4, yi = .4, bi = 2, xi = 1.2, Si = .2, Ci = 1500, wi = .2, Ti = 5, Ei = 3, Di = 1e-5, Oi = 4, ki = .35, Ai = 110, ji = 180;
|
|
1944
|
+
function Mi(e, t, n) {
|
|
1945
|
+
let r = new M(0, 0, 1).applyQuaternion(n), i = 0, a = 0, o = new M();
|
|
1894
1946
|
for (let t of [e.bounds.min.x, e.bounds.max.x]) for (let n of [e.bounds.min.y, e.bounds.max.y]) for (let s of [e.bounds.min.z, e.bounds.max.z]) {
|
|
1895
1947
|
let e = o.set(t, n, s).dot(r);
|
|
1896
1948
|
i = Math.max(i, e), a = Math.min(a, e);
|
|
1897
1949
|
}
|
|
1898
|
-
let s = Math.max(1, e.span), c = Math.max(.01 * s, -a), l = Math.min(c, -i), u = s *
|
|
1899
|
-
return new
|
|
1950
|
+
let s = Math.max(1, e.span), c = Math.max(.01 * s, -a), l = Math.min(c, -i), u = s * yi, d = l - u, f = t + (d + (Math.max(d, c - u) - d) * vi), p = f + (t + c - f) / _i;
|
|
1951
|
+
return new ee(Mn, f, p);
|
|
1900
1952
|
}
|
|
1901
|
-
function
|
|
1953
|
+
function Ni(e, t = {}) {
|
|
1902
1954
|
let n = e.ownerDocument;
|
|
1903
1955
|
Qr(n), e.classList.add("bravais-viewer");
|
|
1904
|
-
let { renderer: r, scene: i, camera: a, updateHeadlight: o } =
|
|
1956
|
+
let { renderer: r, scene: i, camera: a, updateHeadlight: o } = gi({ stencil: !0 });
|
|
1905
1957
|
r.setPixelRatio(n.defaultView?.devicePixelRatio ?? 1), r.domElement.className = "bravais-canvas", e.appendChild(r.domElement);
|
|
1906
1958
|
let s = t.legend === !1 ? null : new ei(n);
|
|
1907
1959
|
s && e.appendChild(s.element);
|
|
1908
1960
|
let c = n.defaultView?.getComputedStyle(e).fontFamily ?? "sans-serif", l = t.gizmo === !1 ? null : new sr(c), u = new Jt(a, r.domElement);
|
|
1909
|
-
u.rotateSpeed =
|
|
1910
|
-
let d = null, f =
|
|
1911
|
-
function
|
|
1912
|
-
|
|
1913
|
-
for (let e of
|
|
1914
|
-
}
|
|
1915
|
-
function
|
|
1916
|
-
if (o(), r.setViewport(0, 0,
|
|
1917
|
-
let e = Math.round(Math.min(
|
|
1961
|
+
u.rotateSpeed = bi, u.zoomSpeed = xi, u.dynamicDampingFactor = Si, u.staticMoving = !1, u.noPan = !0, u.mouseButtons.LEFT = S.ROTATE, u.mouseButtons.MIDDLE = S.DOLLY, u.mouseButtons.RIGHT = null;
|
|
1962
|
+
let d = null, f = null, p = 4, m = 1, h = 1, g = 1, _ = null, v = !1, y = 0, b = !1, x = 0, te = !1, ne = new j(), C = new A(), w = 0, T = new M(), E = /* @__PURE__ */ new Set();
|
|
1963
|
+
function D() {
|
|
1964
|
+
x = 0, te = !1;
|
|
1965
|
+
for (let e of E) e();
|
|
1966
|
+
}
|
|
1967
|
+
function O() {
|
|
1968
|
+
if (!f && (o(), r.setViewport(0, 0, h, g), r.render(i, a), l && d)) {
|
|
1969
|
+
let e = Math.round(Math.min(ji, Math.max(Ai, Math.min(h, g) * ki)));
|
|
1918
1970
|
l.render(r, a.quaternion, e);
|
|
1919
1971
|
}
|
|
1920
1972
|
}
|
|
1921
|
-
function
|
|
1973
|
+
function k() {
|
|
1922
1974
|
let t = e.getBoundingClientRect();
|
|
1923
|
-
|
|
1975
|
+
h = Math.max(1, Math.round(t.width)), g = Math.max(1, Math.round(t.height));
|
|
1976
|
+
let n = r.getSize(ne);
|
|
1977
|
+
(n.x !== h || n.y !== g) && r.setSize(h, g, !1), En(a, h, g), u.handleResize(), u.rotateSpeed = h / Ci * bi;
|
|
1924
1978
|
}
|
|
1925
1979
|
function re(e) {
|
|
1926
|
-
d && (
|
|
1980
|
+
d && (m = Tn(d.bounds, e, h, g), u.minZoom = m * wi, u.maxZoom = m * Ti);
|
|
1927
1981
|
}
|
|
1928
1982
|
function ie() {
|
|
1929
|
-
let e =
|
|
1930
|
-
return
|
|
1983
|
+
let e = C.angleTo(a.quaternion) > Di || Math.abs(w - a.zoom) > Di * m || T.distanceToSquared(u.target) > Di;
|
|
1984
|
+
return C.copy(a.quaternion), w = a.zoom, T.copy(u.target), e;
|
|
1931
1985
|
}
|
|
1932
1986
|
function ae() {
|
|
1933
|
-
|
|
1934
|
-
}
|
|
1935
|
-
function D() {
|
|
1936
|
-
v = 0, _ || (_ = !0, g = requestAnimationFrame(ae));
|
|
1987
|
+
_ = null, u.update(), ie() ? (y = 0, O(), x += 1, te = !0, x >= Oi && D()) : y += 1, b || y < Ei ? _ = requestAnimationFrame(ae) : (v = !1, te && D());
|
|
1937
1988
|
}
|
|
1938
1989
|
function oe() {
|
|
1939
|
-
|
|
1990
|
+
y = 0, v || (v = !0, _ = requestAnimationFrame(ae));
|
|
1940
1991
|
}
|
|
1941
|
-
u.addEventListener("start", () => {
|
|
1942
|
-
y = !0, D();
|
|
1943
|
-
}), u.addEventListener("end", () => {
|
|
1944
|
-
y = !1, D();
|
|
1945
|
-
}), u.addEventListener("change", D);
|
|
1946
1992
|
function se() {
|
|
1947
|
-
|
|
1948
|
-
E(), re(a.quaternion), a.zoom = p * e, a.updateProjectionMatrix(), T();
|
|
1993
|
+
_ !== null && (cancelAnimationFrame(_), _ = null), v = !1;
|
|
1949
1994
|
}
|
|
1950
|
-
|
|
1951
|
-
|
|
1952
|
-
|
|
1953
|
-
|
|
1995
|
+
u.addEventListener("start", () => {
|
|
1996
|
+
b = !0, oe();
|
|
1997
|
+
}), u.addEventListener("end", () => {
|
|
1998
|
+
b = !1, oe();
|
|
1999
|
+
}), u.addEventListener("change", oe);
|
|
2000
|
+
function ce() {
|
|
2001
|
+
let e = m > 0 ? a.zoom / m : 1;
|
|
2002
|
+
k(), re(a.quaternion), a.zoom = m * e, a.updateProjectionMatrix(), O();
|
|
2003
|
+
}
|
|
2004
|
+
let le = typeof ResizeObserver > "u" ? null : new ResizeObserver(ce);
|
|
2005
|
+
le?.observe(e), k();
|
|
2006
|
+
let ue = hi();
|
|
2007
|
+
i.add(ue.group), i.fog = new ee(Mn, 1, 2);
|
|
2008
|
+
let N = Promise.all([r.compileAsync(i, a), l && r.compileAsync(l.scene, l.camera)]);
|
|
2009
|
+
i.remove(ue.group), i.fog = null, ue.dispose(), f = N;
|
|
2010
|
+
let P = () => {
|
|
2011
|
+
f === N && (f = null, O());
|
|
2012
|
+
};
|
|
2013
|
+
N.then(P, P);
|
|
2014
|
+
function F(e) {
|
|
2015
|
+
d && (Sn(a, e, p, d.span), u.target.set(...e.target), re(a.quaternion), a.zoom = m * e.scale, a.updateProjectionMatrix(), u.update(), ie());
|
|
1954
2016
|
}
|
|
1955
|
-
let
|
|
2017
|
+
let de = {
|
|
1956
2018
|
setLayers(e, t = null) {
|
|
1957
|
-
|
|
2019
|
+
de.clear(), e.length !== 0 && (d = fi(e), i.add(d.group), p = yn(d.span), i.fog = Mi(d, p, bn(d.cell)), s?.setElements(d.elements), l?.setCell(d.cell), k(), F(t ?? xn(d.cell)), O());
|
|
1958
2020
|
},
|
|
1959
2021
|
clear() {
|
|
1960
|
-
|
|
2022
|
+
se(), d &&= (i.remove(d.group), d.dispose(), null), i.fog = null, s?.setElements([]), r.setViewport(0, 0, h, g), r.clear();
|
|
1961
2023
|
},
|
|
1962
2024
|
getView() {
|
|
1963
2025
|
return d ? {
|
|
@@ -1967,48 +2029,49 @@ function ji(e, t = {}) {
|
|
|
1967
2029
|
u.target.y,
|
|
1968
2030
|
u.target.z
|
|
1969
2031
|
],
|
|
1970
|
-
scale:
|
|
2032
|
+
scale: m > 0 ? a.zoom / m : 1
|
|
1971
2033
|
} : null;
|
|
1972
2034
|
},
|
|
1973
2035
|
setView(e) {
|
|
1974
|
-
|
|
2036
|
+
F(e), O();
|
|
1975
2037
|
},
|
|
1976
2038
|
resetView() {
|
|
1977
|
-
d &&
|
|
2039
|
+
d && F(xn(d.cell)), O(), D();
|
|
1978
2040
|
},
|
|
1979
|
-
resize:
|
|
1980
|
-
render:
|
|
2041
|
+
resize: ce,
|
|
2042
|
+
render: O,
|
|
1981
2043
|
onInteraction(e) {
|
|
1982
|
-
return
|
|
2044
|
+
return E.add(e), () => E.delete(e);
|
|
1983
2045
|
},
|
|
1984
2046
|
dispose() {
|
|
1985
|
-
|
|
2047
|
+
de.clear(), f = null, b = !1, le?.disconnect(), u.dispose(), l?.dispose(), r.dispose(), r.domElement.remove(), s?.element.remove(), e.classList.remove("bravais-viewer");
|
|
1986
2048
|
}
|
|
1987
2049
|
};
|
|
1988
|
-
return
|
|
2050
|
+
return de;
|
|
1989
2051
|
}
|
|
1990
2052
|
//#endregion
|
|
1991
2053
|
//#region src/render/thumbnails.ts
|
|
1992
|
-
function
|
|
1993
|
-
let { renderer: e, scene: t, camera: n, updateHeadlight: r } =
|
|
1994
|
-
|
|
2054
|
+
function Pi() {
|
|
2055
|
+
let { renderer: e, scene: t, camera: n, updateHeadlight: r } = gi(), i = /* @__PURE__ */ new Map(), a = hi();
|
|
2056
|
+
t.add(a.group), e.compile(t, n), t.remove(a.group), a.dispose();
|
|
2057
|
+
function o(e, t) {
|
|
1995
2058
|
let n = i.get(e);
|
|
1996
2059
|
if (n && n.layers === t) return n.model;
|
|
1997
2060
|
n?.model.dispose();
|
|
1998
|
-
let r =
|
|
2061
|
+
let r = fi(t);
|
|
1999
2062
|
return i.set(e, {
|
|
2000
2063
|
layers: t,
|
|
2001
2064
|
model: r
|
|
2002
2065
|
}), r;
|
|
2003
2066
|
}
|
|
2004
2067
|
return {
|
|
2005
|
-
render(i,
|
|
2068
|
+
render(i, a, s, c) {
|
|
2006
2069
|
let l = c.getContext("2d");
|
|
2007
|
-
if (!l ||
|
|
2008
|
-
let u =
|
|
2070
|
+
if (!l || a.length === 0) return;
|
|
2071
|
+
let u = o(i, a), d = Math.max(1, c.width), f = Math.max(1, c.height);
|
|
2009
2072
|
(e.domElement.width !== d || e.domElement.height !== f) && e.setSize(d, f, !1), En(n, d, f);
|
|
2010
2073
|
let p = yn(u.span), m = s ?? xn(u.cell);
|
|
2011
|
-
Sn(n, m, p, u.span), n.zoom = Tn(u.bounds, new
|
|
2074
|
+
Sn(n, m, p, u.span), n.zoom = Tn(u.bounds, new A(...m.quaternion), d, f) * m.scale, n.updateProjectionMatrix(), r(), t.add(u.group), e.render(t, n), t.remove(u.group), l.clearRect(0, 0, d, f), l.drawImage(e.domElement, 0, 0, d, f);
|
|
2012
2075
|
},
|
|
2013
2076
|
release(e) {
|
|
2014
2077
|
i.get(e)?.model.dispose(), i.delete(e);
|
|
@@ -2021,18 +2084,18 @@ function Mi() {
|
|
|
2021
2084
|
}
|
|
2022
2085
|
//#endregion
|
|
2023
2086
|
//#region src/index.ts
|
|
2024
|
-
async function
|
|
2025
|
-
let t =
|
|
2026
|
-
if (!n) throw new
|
|
2027
|
-
let r =
|
|
2087
|
+
async function Fi(e) {
|
|
2088
|
+
let t = ge(e), n = t.blocks.find(Ye) ?? t.blocks[0];
|
|
2089
|
+
if (!n) throw new H("The CIF has no data block.");
|
|
2090
|
+
let r = Xe(n);
|
|
2028
2091
|
return {
|
|
2029
2092
|
lattice: r.lattice,
|
|
2030
2093
|
sites: r.sites,
|
|
2031
|
-
operations: await
|
|
2094
|
+
operations: await _t(r),
|
|
2032
2095
|
spaceGroup: r.spaceGroup
|
|
2033
2096
|
};
|
|
2034
2097
|
}
|
|
2035
2098
|
//#endregion
|
|
2036
|
-
export {
|
|
2099
|
+
export { H as CifStructureError, P as CifSyntaxError, nt as SpaceGroupLookupError, bt as SymmetryAnalysisError, Ft as buildScene, Pi as createThumbnailRenderer, Ni as createViewer, qr as elementColor, Jr as elementColorAssignments, Kr as ensureElementColors, rt as ensureMoyo, vt as expandStructure, Me as latticeFromParameters, Ne as latticeFromVectors, dt as operationsForSpaceGroup, ge as parseCif, Xe as parseCifStructure, Re as parseSymmetryOperator, Fi as readCif, Yr as resetElementColors, Pt as structureElements, Ct as symmetryDataset, Dt as typesetSymbol };
|
|
2037
2100
|
|
|
2038
2101
|
//# sourceMappingURL=bravais.js.map
|