matterviz 0.4.0 → 0.4.2

package/dist/structure/polyhedra.js

@@ -0,0 +1,587 @@
+// Coordination polyhedra detection and mesh generation.
+// Self-contained: vertices come from the rendered bond graph, hulls from a custom
+// quickhull tailored to small point sets (CN 4-12), output as merged typed arrays
+// so the whole scene renders in 1-2 draw calls regardless of supercell size.
+// Hot paths use scalar math and per-element caches to scale to large structures.
+import { rgb as parse_rgb } from 'd3-color';
+import { DEFAULTS } from '../settings';
+import { get_orig_site_idx } from './atom-properties';
+import { element_lookup, get_majority_element, has_framework_potential, is_spectator_center, } from './bonding';
+const face_of = (points, vert_a, vert_b, vert_c) => {
+    const [ax, ay, az] = points[vert_a];
+    const abx = points[vert_b][0] - ax;
+    const aby = points[vert_b][1] - ay;
+    const abz = points[vert_b][2] - az;
+    const acx = points[vert_c][0] - ax;
+    const acy = points[vert_c][1] - ay;
+    const acz = points[vert_c][2] - az;
+    let nx = aby * acz - abz * acy;
+    let ny = abz * acx - abx * acz;
+    let nz = abx * acy - aby * acx;
+    const len = Math.hypot(nx, ny, nz);
+    if (len > 0) {
+        nx /= len;
+        ny /= len;
+        nz /= len;
+    }
+    else
+        [nx, ny, nz] = [0, 0, 1];
+    return {
+        vert_a,
+        vert_b,
+        vert_c,
+        nx,
+        ny,
+        nz,
+        offset: nx * ax + ny * ay + nz * az,
+        outside: [],
+        deleted: false,
+    };
+};
+// Signed distance of point from face plane (positive = outside).
+const dist_to_face = (face, point) => face.nx * point[0] + face.ny * point[1] + face.nz * point[2] - face.offset;
+// Compute the 3D convex hull of a small point set via quickhull.
+// Returns a degenerate result (faces=[], volume=0) for <4 unique points or
+// collinear/coplanar sets (e.g. square-planar CN=4 coordination draws nothing,
+// matching VESTA behavior). Supports up to 65535 input points (edge keys are
+// packed into 32-bit integers) - far beyond any coordination shell.
+export function convex_hull_3d(points, eps_scale = 1e-7) {
+    // Dedup points (coordination shells are tiny, O(n^2) is fine)
+    const unique = [];
+    const unique_input_idx = [];
+    for (let p_idx = 0; p_idx < points.length; p_idx++) {
+        const [px, py, pz] = points[p_idx];
+        let is_dup = false;
+        for (const other of unique) {
+            const dx = px - other[0];
+            const dy = py - other[1];
+            const dz = pz - other[2];
+            if (dx * dx + dy * dy + dz * dz < 1e-12) {
+                is_dup = true;
+                break;
+            }
+        }
+        if (!is_dup) {
+            unique.push(points[p_idx]);
+            unique_input_idx.push(p_idx);
+        }
+    }
+    const degenerate = {
+        vertices: unique,
+        input_idxs: unique_input_idx,
+        faces: [],
+        volume: 0,
+    };
+    if (unique.length < 4)
+        return degenerate;
+    // Bounding-box diagonal sets the numerical tolerance scale
+    let [min_x, min_y, min_z] = unique[0];
+    let [max_x, max_y, max_z] = unique[0];
+    for (const [px, py, pz] of unique) {
+        if (px < min_x)
+            min_x = px;
+        if (px > max_x)
+            max_x = px;
+        if (py < min_y)
+            min_y = py;
+        if (py > max_y)
+            max_y = py;
+        if (pz < min_z)
+            min_z = pz;
+        if (pz > max_z)
+            max_z = pz;
+    }
+    const diag = Math.hypot(max_x - min_x, max_y - min_y, max_z - min_z);
+    const eps = eps_scale * Math.max(1, diag);
+    // Initial simplex: farthest pair along principal axes -> farthest from line -> from plane
+    let [pt_0, pt_1] = [0, 1];
+    let max_dist = -1;
+    for (let axis = 0; axis < 3; axis++) {
+        let [lo_idx, hi_idx] = [0, 0];
+        for (let idx = 1; idx < unique.length; idx++) {
+            if (unique[idx][axis] < unique[lo_idx][axis])
+                lo_idx = idx;
+            if (unique[idx][axis] > unique[hi_idx][axis])
+                hi_idx = idx;
+        }
+        const dx = unique[hi_idx][0] - unique[lo_idx][0];
+        const dy = unique[hi_idx][1] - unique[lo_idx][1];
+        const dz = unique[hi_idx][2] - unique[lo_idx][2];
+        const dist = Math.hypot(dx, dy, dz);
+        if (dist > max_dist)
+            [max_dist, pt_0, pt_1] = [dist, lo_idx, hi_idx];
+    }
+    if (max_dist < eps)
+        return degenerate; // all points coincide
+    const [ox, oy, oz] = unique[pt_0];
+    let dir_x = unique[pt_1][0] - ox;
+    let dir_y = unique[pt_1][1] - oy;
+    let dir_z = unique[pt_1][2] - oz;
+    const dir_len = Math.hypot(dir_x, dir_y, dir_z);
+    dir_x /= dir_len;
+    dir_y /= dir_len;
+    dir_z /= dir_len;
+    let pt_2 = -1;
+    max_dist = eps;
+    for (let idx = 0; idx < unique.length; idx++) {
+        const rx = unique[idx][0] - ox;
+        const ry = unique[idx][1] - oy;
+        const rz = unique[idx][2] - oz;
+        const proj = rx * dir_x + ry * dir_y + rz * dir_z;
+        const perp_sq = rx * rx + ry * ry + rz * rz - proj * proj;
+        if (perp_sq > max_dist * max_dist) {
+            max_dist = Math.sqrt(perp_sq);
+            pt_2 = idx;
+        }
+    }
+    if (pt_2 === -1)
+        return degenerate; // collinear
+    const base = face_of(unique, pt_0, pt_1, pt_2);
+    let pt_3 = -1;
+    max_dist = eps;
+    for (let idx = 0; idx < unique.length; idx++) {
+        const dist = Math.abs(dist_to_face(base, unique[idx]));
+        if (dist > max_dist)
+            [max_dist, pt_3] = [dist, idx];
+    }
+    if (pt_3 === -1)
+        return degenerate; // coplanar
+    // Build initial tetrahedron with outward-facing windings
+    const centroid = [
+        (unique[pt_0][0] + unique[pt_1][0] + unique[pt_2][0] + unique[pt_3][0]) / 4,
+        (unique[pt_0][1] + unique[pt_1][1] + unique[pt_2][1] + unique[pt_3][1]) / 4,
+        (unique[pt_0][2] + unique[pt_1][2] + unique[pt_2][2] + unique[pt_3][2]) / 4,
+    ];
+    const faces = [];
+    for (const [idx_a, idx_b, idx_c] of [
+        [pt_0, pt_1, pt_2],
+        [pt_0, pt_1, pt_3],
+        [pt_0, pt_2, pt_3],
+        [pt_1, pt_2, pt_3],
+    ]) {
+        let face = face_of(unique, idx_a, idx_b, idx_c);
+        if (dist_to_face(face, centroid) > 0)
+            face = face_of(unique, idx_a, idx_c, idx_b);
+        faces.push(face);
+    }
+    // Assign each remaining point to the face it lies farthest outside of
+    const assign_point = (point_idx, candidates) => {
+        let [best_face, best_dist] = [null, eps];
+        for (const face of candidates) {
+            if (face.deleted)
+                continue;
+            const dist = dist_to_face(face, unique[point_idx]);
+            if (dist > best_dist)
+                [best_face, best_dist] = [face, dist];
+        }
+        best_face?.outside.push(point_idx);
+    };
+    for (let idx = 0; idx < unique.length; idx++) {
+        if (idx !== pt_0 && idx !== pt_1 && idx !== pt_2 && idx !== pt_3) {
+            assign_point(idx, faces);
+        }
+    }
+    // Expand hull: repeatedly absorb the farthest outside point. Horizon edges are
+    // tracked as packed 32-bit integers (from * 2^16 + to) instead of strings.
+    const edge_set = new Set(); // packed directed edges
+    for (let guard = 0; guard < unique.length * 4; guard++) {
+        const active = faces.find((face) => !face.deleted && face.outside.length > 0);
+        if (!active)
+            break;
+        let [eye, eye_dist] = [-1, -Infinity];
+        for (const point_idx of active.outside) {
+            const dist = dist_to_face(active, unique[point_idx]);
+            if (dist > eye_dist)
+                [eye, eye_dist] = [point_idx, dist];
+        }
+        // Find all faces visible from the eye point and collect orphaned points
+        const orphans = [];
+        edge_set.clear();
+        for (const face of faces) {
+            if (face.deleted || dist_to_face(face, unique[eye]) <= eps)
+                continue;
+            face.deleted = true;
+            for (const point_idx of face.outside)
+                if (point_idx !== eye)
+                    orphans.push(point_idx);
+            for (const [from, to] of [
+                [face.vert_a, face.vert_b],
+                [face.vert_b, face.vert_c],
+                [face.vert_c, face.vert_a],
+            ]) {
+                const reverse_key = to * 65536 + from;
+                if (edge_set.has(reverse_key))
+                    edge_set.delete(reverse_key); // internal edge
+                else
+                    edge_set.add(from * 65536 + to);
+            }
+        }
+        // Horizon edges (directed, so new faces inherit outward winding)
+        const new_faces = [];
+        for (const packed of edge_set) {
+            const from = Math.floor(packed / 65536);
+            const to = packed % 65536;
+            const face = face_of(unique, from, to, eye);
+            faces.push(face);
+            new_faces.push(face);
+        }
+        for (const point_idx of orphans)
+            assign_point(point_idx, new_faces);
+    }
+    // Compact vertices used by surviving faces and remap indices
+    const vert_remap = new Map();
+    const vertices = [];
+    const input_idxs = [];
+    const remap = (old_idx) => {
+        let new_idx = vert_remap.get(old_idx);
+        if (new_idx === undefined) {
+            new_idx = vertices.length;
+            vert_remap.set(old_idx, new_idx);
+            vertices.push(unique[old_idx]);
+            input_idxs.push(unique_input_idx[old_idx]);
+        }
+        return new_idx;
+    };
+    const remapped = [];
+    for (const face of faces) {
+        if (!face.deleted) {
+            remapped.push([remap(face.vert_a), remap(face.vert_b), remap(face.vert_c)]);
+        }
+    }
+    // Volume via signed tetrahedra from the hull centroid (positive with outward winding)
+    let [cx, cy, cz] = [0, 0, 0];
+    for (const [vx, vy, vz] of vertices) {
+        cx += vx;
+        cy += vy;
+        cz += vz;
+    }
+    cx /= vertices.length;
+    cy /= vertices.length;
+    cz /= vertices.length;
+    let volume = 0;
+    for (const [idx_a, idx_b, idx_c] of remapped) {
+        const ax = vertices[idx_a][0] - cx;
+        const ay = vertices[idx_a][1] - cy;
+        const az = vertices[idx_a][2] - cz;
+        const bx = vertices[idx_b][0] - cx;
+        const by = vertices[idx_b][1] - cy;
+        const bz = vertices[idx_b][2] - cz;
+        const dx = vertices[idx_c][0] - cx;
+        const dy = vertices[idx_c][1] - cy;
+        const dz = vertices[idx_c][2] - cz;
+        volume +=
+            (ax * (by * dz - bz * dy) + ay * (bz * dx - bx * dz) + az * (bx * dy - by * dx)) / 6;
+    }
+    return { vertices, input_idxs, faces: remapped, volume: Math.abs(volume) };
+}
+// --- Bond graph adjacency ---
+// Symmetric site_idx -> neighbor site_idx set from rendered bond pairs.
+export function build_adjacency(bonds) {
+    const adjacency = new Map();
+    const link = (from, to) => {
+        const neighbors = adjacency.get(from);
+        if (neighbors)
+            neighbors.add(to);
+        else
+            adjacency.set(from, new Set([to]));
+    };
+    for (const { site_idx_1, site_idx_2 } of bonds) {
+        if (site_idx_1 === site_idx_2)
+            continue;
+        link(site_idx_1, site_idx_2);
+        link(site_idx_2, site_idx_1);
+    }
+    return adjacency;
+}
+// --- Center selection ---
+// A bonded neighbor counts as a polyhedron vertex only if it's an anion-former:
+// a nonmetal or metalloid that is more electronegative than the center. This keeps
+// spurious cation-cation bonds (e.g. Ti-Ba in perovskites, Li-P in thiophosphates)
+// from contaminating coordination environments.
+function is_anion_vertex(center_en, center_is_metal, neighbor_element, electronegativity_margin) {
+    if (!neighbor_element)
+        return false;
+    const n_data = element_lookup.get(neighbor_element);
+    if (n_data?.metal)
+        return false;
+    const n_en = n_data?.electronegativity ?? null;
+    if (center_en !== null && n_en !== null) {
+        return n_en > center_en + electronegativity_margin;
+    }
+    // EN data missing: only metal centers with nonmetal neighbors qualify
+    return center_is_metal && n_data?.nonmetal === true;
+}
+// --- Top-level polyhedra computation ---
+// Detect coordination polyhedra from the rendered bond graph, VESTA-style:
+// vertices are anion-former neighbors (nonmetals/metalloids more electronegative
+// than the center) within `1 + distance_factor` of the shortest such bond, so
+// over-long bond-graph noise doesn't inflate e.g. PO4 tetrahedra. Spectator A-site
+// cations (alkali, heavy alkaline-earth) are skipped when framework cations exist,
+// CN > max_neighbors hulls (e.g. CN-12 cuboctahedra) are skipped, and
+// boundary-truncated copies only render when their vertex count matches the max
+// among all copies of the same original site. Every polyhedron corner is a
+// displayed atom (boundary shells are completed upstream by bond-completing image
+// atoms - see find_image_atoms in pbc.ts).
+export function compute_polyhedra(structure, bonds, options = {}) {
+    const { 
+    // Neighbor-count fallbacks derive from DEFAULTS.structure so they can't drift
+    // from the polyhedra_min/max_neighbors settings defaults
+    min_neighbors = DEFAULTS.structure.polyhedra_min_neighbors, max_neighbors = DEFAULTS.structure.polyhedra_max_neighbors, excluded_center_elements = [], included_center_elements = [], electronegativity_margin = 0, distance_factor = 0.3, weak_bond_norm = 1.15, volume_eps = 1e-3, } = options;
+    const sites = structure?.sites;
+    if (!sites?.length || bonds.length === 0)
+        return [];
+    const adjacency = build_adjacency(bonds);
+    const excluded = new Set(excluded_center_elements);
+    const included = new Set(included_center_elements);
+    const site_elements = sites.map((site) => get_majority_element(site));
+    const unique_elements = [
+        ...new Set(site_elements.filter((el) => el !== null)),
+    ];
+    const center_info_cache = new Map();
+    const center_info = (element) => {
+        let info = center_info_cache.get(element);
+        if (!info) {
+            const data = element_lookup.get(element);
+            const center_en = data?.electronegativity ?? null;
+            const r_center = data?.covalent_radius ?? null;
+            const accepts = new Set(unique_elements.filter((n_elem) => is_anion_vertex(center_en, data?.metal === true, n_elem, electronegativity_margin)));
+            const radii_sums = new Map(unique_elements.map((n_elem) => {
+                const r_n = element_lookup.get(n_elem)?.covalent_radius ?? null;
+                return [n_elem, r_center !== null && r_n !== null ? r_center + r_n : null];
+            }));
+            info = { accepts, radii_sums };
+            center_info_cache.set(element, info);
+        }
+        return info;
+    };
+    const candidates = [];
+    for (const [site_idx, neighbors] of adjacency) {
+        if (neighbors.size < min_neighbors)
+            continue;
+        const element = site_elements[site_idx];
+        if (!element || excluded.has(element))
+            continue;
+        const { accepts, radii_sums } = center_info(element);
+        if (accepts.size === 0)
+            continue;
+        const [cx, cy, cz] = sites[site_idx].xyz;
+        // Bonded anion vertices (parallel arrays to avoid per-vertex object churn)
+        const vert_idxs = [];
+        const vert_dists = [];
+        let min_dist = Infinity;
+        for (const idx of neighbors) {
+            const n_elem = site_elements[idx];
+            if (!n_elem || !accepts.has(n_elem))
+                continue;
+            const [nx, ny, nz] = sites[idx].xyz;
+            const dist = Math.hypot(nx - cx, ny - cy, nz - cz);
+            vert_idxs.push(idx);
+            vert_dists.push(dist);
+            if (dist < min_dist)
+                min_dist = dist;
+        }
+        if (vert_idxs.length < min_neighbors)
+            continue;
+        // Trim over-long bonds relative to the shortest anion bond (VESTA-like local
+        // cutoff): keeps distorted/Jahn-Teller octahedra intact but rejects e.g. a 5th
+        // oxygen at 2.5 Å around P whose true tetrahedron has 1.5 Å bonds
+        const cutoff = min_dist * (1 + distance_factor);
+        const vertex_site_idxs = [];
+        let [norm_sum, norm_count] = [0, 0];
+        for (let pos = 0; pos < vert_idxs.length; pos++) {
+            if (vert_dists[pos] > cutoff)
+                continue;
+            const idx = vert_idxs[pos];
+            vertex_site_idxs.push(idx);
+            // Bond softness: how stretched the kept bonds are vs the covalent-radii sum
+            const n_elem = site_elements[idx];
+            const r_sum = n_elem ? (radii_sums.get(n_elem) ?? null) : null;
+            if (r_sum !== null) {
+                norm_sum += vert_dists[pos] / r_sum;
+                norm_count++;
+            }
+        }
+        if (vertex_site_idxs.length < min_neighbors)
+            continue;
+        candidates.push({
+            site_idx,
+            orig_idx: get_orig_site_idx(sites[site_idx], site_idx),
+            element,
+            vertex_site_idxs,
+            mean_norm_dist: norm_count > 0 ? norm_sum / norm_count : null,
+        });
+    }
+    // Pass 2: hide spectator A-site cations when the composition contains a
+    // potential framework cation (a non-spectator element less electronegative than
+    // the structure's most electronegative element, i.e. one that could coordinate
+    // the anions). Composition-based rather than candidate-based so boundary
+    // truncation of framework polyhedra doesn't promote Li/Na/Ba clutter; purely
+    // ionic binaries like NaCl or CaF2 still draw their spectator polyhedra.
+    const has_framework = has_framework_potential(unique_elements);
+    // Weakly-bound center species (mean bond length well beyond the covalent-radii
+    // sum, e.g. lone-pair Bi3+ with 8 long Bi-O bonds) are hidden when a
+    // strongly-bound framework species exists - mirrors how pyrochlore-type figures
+    // show only the B-site octahedra
+    const norm_by_species = new Map();
+    for (const { element, mean_norm_dist } of candidates) {
+        if (mean_norm_dist === null)
+            continue;
+        const entry = norm_by_species.get(element) ?? { sum: 0, count: 0 };
+        entry.sum += mean_norm_dist;
+        entry.count++;
+        norm_by_species.set(element, entry);
+    }
+    const species_norm = (el) => {
+        const entry = norm_by_species.get(el);
+        return entry ? entry.sum / entry.count : null;
+    };
+    const has_strong_species = [...norm_by_species.keys()].some((el) => (species_norm(el) ?? Infinity) <= weak_bond_norm && !is_spectator_center(el));
+    const is_weak_species = (el) => has_strong_species && (species_norm(el) ?? 0) > weak_bond_norm;
+    const visible = candidates.filter(({ element }) => {
+        if (included.has(element))
+            return true;
+        if (is_spectator_center(element) && has_framework)
+            return false;
+        return !is_weak_species(element);
+    });
+    // Pass 3: boundary completeness - copies of the same original site only render
+    // at the max observed vertex count, so any remaining truncated copies (bond
+    // completing image atoms handle most) are skipped
+    const max_cn_by_orig = new Map();
+    for (const { orig_idx, vertex_site_idxs } of visible) {
+        if (vertex_site_idxs.length > (max_cn_by_orig.get(orig_idx) ?? 0)) {
+            max_cn_by_orig.set(orig_idx, vertex_site_idxs.length);
+        }
+    }
+    // Pass 4: CN cap (after completeness so capped interior copies don't let
+    // truncated boundary copies of the same site slip through; force-included
+    // elements bypass the cap - an explicit user request beats the clutter
+    // heuristic), then build hulls, deduping identical center positions (base
+    // atom vs PBC image)
+    const polyhedra = [];
+    const seen_positions = new Set();
+    for (const { site_idx, orig_idx, element, vertex_site_idxs } of visible) {
+        if (vertex_site_idxs.length !== max_cn_by_orig.get(orig_idx))
+            continue;
+        if (vertex_site_idxs.length > max_neighbors && !included.has(element))
+            continue;
+        const [px, py, pz] = sites[site_idx].xyz;
+        const pos_key = `${Math.round(px * 1e3)},${Math.round(py * 1e3)},${Math.round(pz * 1e3)}`;
+        if (seen_positions.has(pos_key))
+            continue;
+        seen_positions.add(pos_key);
+        const hull = convex_hull_3d(vertex_site_idxs.map((idx) => sites[idx].xyz));
+        if (hull.faces.length === 0 || hull.volume < volume_eps)
+            continue;
+        polyhedra.push({
+            center_site_idx: site_idx,
+            center_orig_idx: orig_idx,
+            center_element: element,
+            vertices: hull.vertices,
+            vertex_site_idxs: hull.input_idxs.map((input_idx) => vertex_site_idxs[input_idx]),
+            faces: hull.faces,
+            volume: hull.volume,
+        });
+    }
+    return polyhedra;
+}
+// --- Merged render buffers ---
+// Merge all polyhedra into single non-indexed position/color arrays (one draw call)
+// plus crease-edge segments for outlines. Edges interior to coplanar face groups
+// (e.g. quad diagonals on a cube) are omitted. `get_vertex_color` resolves the
+// color of each hull vertex (e.g. the vertex atom's element color, the center
+// atom's color, or a uniform custom color) - parsed colors are cached by string.
+export function merge_polyhedra_buffers(polyhedra, get_vertex_color, coplanar_tol = 1e-3) {
+    let triangle_count = 0;
+    for (const poly of polyhedra)
+        triangle_count += poly.faces.length;
+    const positions = new Float32Array(triangle_count * 9);
+    const colors = new Float32Array(triangle_count * 9);
+    // A closed triangulated surface has at most 3F/2 unique edges
+    const edge_positions = new Float32Array(Math.ceil(triangle_count * 1.5) * 6);
+    const rgb_cache = new Map();
+    let offset = 0;
+    let edge_offset = 0;
+    // Per-polyhedron scratch: crease detection tracks the first face normal seen
+    // per undirected edge (packed vert_a * 2^16 + vert_b key)
+    const edge_normals = new Map();
+    for (const poly of polyhedra) {
+        const verts = poly.vertices;
+        // Resolve per-hull-vertex colors once
+        const vert_rgb = new Float32Array(verts.length * 3);
+        for (let v_idx = 0; v_idx < verts.length; v_idx++) {
+            const color = get_vertex_color(poly, v_idx);
+            let channels = rgb_cache.get(color);
+            if (!channels) {
+                // d3-color handles hex, rgb()/rgba() (d3 property-color scales) and named colors
+                const { r, g, b } = parse_rgb(color);
+                channels = Number.isFinite(r) ? [r / 255, g / 255, b / 255] : [0.5, 0.5, 0.5];
+                rgb_cache.set(color, channels);
+            }
+            vert_rgb[v_idx * 3] = channels[0];
+            vert_rgb[v_idx * 3 + 1] = channels[1];
+            vert_rgb[v_idx * 3 + 2] = channels[2];
+        }
+        edge_normals.clear();
+        for (const [idx_a, idx_b, idx_c] of poly.faces) {
+            const [ax, ay, az] = verts[idx_a];
+            const [bx, by, bz] = verts[idx_b];
+            const [px, py, pz] = verts[idx_c];
+            // Scalar face normal for crease detection
+            let nx = (by - ay) * (pz - az) - (bz - az) * (py - ay);
+            let ny = (bz - az) * (px - ax) - (bx - ax) * (pz - az);
+            let nz = (bx - ax) * (py - ay) - (by - ay) * (px - ax);
+            const len = Math.hypot(nx, ny, nz);
+            if (len > 0) {
+                nx /= len;
+                ny /= len;
+                nz /= len;
+            }
+            for (const v_idx of [idx_a, idx_b, idx_c]) {
+                const vert = verts[v_idx];
+                positions[offset] = vert[0];
+                positions[offset + 1] = vert[1];
+                positions[offset + 2] = vert[2];
+                colors[offset] = vert_rgb[v_idx * 3];
+                colors[offset + 1] = vert_rgb[v_idx * 3 + 1];
+                colors[offset + 2] = vert_rgb[v_idx * 3 + 2];
+                offset += 3;
+            }
+            for (const [from, to] of [
+                [idx_a, idx_b],
+                [idx_b, idx_c],
+                [idx_c, idx_a],
+            ]) {
+                const key = from < to ? from * 65536 + to : to * 65536 + from;
+                const entry = edge_normals.get(key);
+                if (entry) {
+                    entry.shared = true;
+                    entry.crease = nx * entry.nx + ny * entry.ny + nz * entry.nz < 1 - coplanar_tol;
+                }
+                else
+                    edge_normals.set(key, { nx, ny, nz, crease: false, shared: false });
+            }
+        }
+        // Draw an edge unless both adjacent faces are coplanar (quad diagonal)
+        for (const [key, entry] of edge_normals) {
+            if (entry.shared && !entry.crease)
+                continue;
+            const from = verts[Math.floor(key / 65536)];
+            const to = verts[key % 65536];
+            edge_positions[edge_offset] = from[0];
+            edge_positions[edge_offset + 1] = from[1];
+            edge_positions[edge_offset + 2] = from[2];
+            edge_positions[edge_offset + 3] = to[0];
+            edge_positions[edge_offset + 4] = to[1];
+            edge_positions[edge_offset + 5] = to[2];
+            edge_offset += 6;
+        }
+    }
+    return {
+        positions,
+        colors,
+        edge_positions: edge_positions.slice(0, edge_offset),
+        triangle_count,
+        edge_count: edge_offset / 6,
+    };
+}

package/dist/structure/site.d.ts

@@ -0,0 +1,4 @@
+import type { ElementSymbol } from '../element';
+import type { Vec3 } from '../math';
+import type { Site } from './';
+export declare const make_site: (element: ElementSymbol, abc: Vec3, xyz: Vec3, label: string, properties?: Record<string, unknown>, occu?: number) => Site;

package/dist/structure/site.js

@@ -0,0 +1 @@
+export const make_site = (element, abc, xyz, label, properties = {}, occu = 1) => ({ species: [{ element, occu, oxidation_state: 0 }], abc, xyz, label, properties });

package/dist/structure/supercell.d.ts

@@ -1,8 +1,7 @@
 import type { Vec3 } from '../math';
-import { scale_lattice_matrix } from '../math';
 import type { Crystal } from './index';
 export declare function parse_supercell_scaling(scaling: string | number | Vec3): Vec3;
 export declare function generate_lattice_points(scaling_factors: Vec3): Vec3[];
-export { scale_lattice_matrix };
+export { scale_lattice_matrix } from '../math';
 export declare function make_supercell(structure: Crystal, scaling: string | number | Vec3, to_unit_cell?: boolean): Crystal;
 export declare function is_valid_supercell_input(input: string): boolean;

package/dist/structure/supercell.js

@@ -1,5 +1,4 @@
 import * as math from '../math';
-import { scale_lattice_matrix } from '../math';
 import { wrap_frac_coord } from './pbc';
 import { normalize_structure_bond } from './bonding';
 const mod = (value, divisor) => ((value % divisor) + divisor) % divisor;
@@ -79,7 +78,7 @@ export function generate_lattice_points(scaling_factors) {
     return points;
 }
 // Re-export from $lib/math for backward compatibility
-export { scale_lattice_matrix };
+export { scale_lattice_matrix } from '../math';
 // Create a supercell from a Crystal
 // Takes original structure, scaling factors, and whether to fold coordinates back to unit cell (default: true)
 // Returns new supercell structure
@@ -96,26 +95,22 @@ export function make_supercell(structure, scaling, to_unit_cell = true) {
     }
     const orig_matrix = structure.lattice.matrix;
     // Create new scaled lattice
-    const new_lattice_matrix = scale_lattice_matrix(orig_matrix, supercell_scaling);
-    const lattice_params = math.calc_lattice_params(new_lattice_matrix);
-    const new_lattice = {
-        ...structure.lattice,
-        matrix: new_lattice_matrix,
-        ...lattice_params,
-    };
+    const new_matrix = math.scale_lattice_matrix(orig_matrix, supercell_scaling);
+    const lattice_params = math.calc_lattice_params(new_matrix);
+    const new_lattice = { ...structure.lattice, matrix: new_matrix, ...lattice_params };
     // Pre-allocate sites array
     const n_sites = structure.sites.length;
     const new_sites = Array(n_sites * total_cells);
     // Destructure lattice vectors for fast inline arithmetic (avoid function calls in hot loop)
     const [[ax, ay, az], [bx, by, bz], [cx, cy, cz]] = orig_matrix;
-    const [sx, sy, sz] = supercell_scaling;
     let write_idx = 0;
     const sites = structure.sites;
     // Loop order: k, j, i to match typical pymatgen/standard ordering
     for (let kk = 0; kk < scale_z; kk++) {
         for (let jj = 0; jj < scale_y; jj++) {
             for (let ii = 0; ii < scale_x; ii++) {
-                const label_suffix = total_cells > 1 ? `_${ii}${jj}${kk}` : ``;
+                // 1x1x1 short-circuits above, so every site gets a cell-index suffix
+                const label_suffix = `_${ii}${jj}${kk}`;
                 // Translation = ii * vec_a + jj * vec_b + kk * vec_c (inlined for performance)
                 const tx = ii * ax + jj * bx + kk * cx;
                 const ty = ii * ay + jj * by + kk * cy;
@@ -123,9 +118,9 @@ export function make_supercell(structure, scaling, to_unit_cell = true) {
                 for (let site_idx = 0; site_idx < n_sites; site_idx++) {
                     const site = sites[site_idx];
                     // new_abc = (old_abc + [ii, jj, kk]) / supercell_scaling
-                    let new_a = (site.abc[0] + ii) / sx;
-                    let new_b = (site.abc[1] + jj) / sy;
-                    let new_c = (site.abc[2] + kk) / sz;
+                    let new_a = (site.abc[0] + ii) / scale_x;
+                    let new_b = (site.abc[1] + jj) / scale_y;
+                    let new_c = (site.abc[2] + kk) / scale_z;
                     if (to_unit_cell) {
                         new_a = wrap_frac_coord(new_a);
                         new_b = wrap_frac_coord(new_b);
@@ -135,7 +130,7 @@ export function make_supercell(structure, scaling, to_unit_cell = true) {
                         species: site.species,
                         xyz: [site.xyz[0] + tx, site.xyz[1] + ty, site.xyz[2] + tz],
                         abc: [new_a, new_b, new_c],
-                        label: label_suffix ? `${site.label}${label_suffix}` : site.label,
+                        label: `${site.label}${label_suffix}`,
                         properties: { ...site.properties, orig_unit_cell_idx: site_idx },
                     };
                 }