matterviz 0.3.4 → 0.3.6

package/dist/brillouin/compute.js

@@ -1,422 +0,0 @@
-// Brillouin zone generation via convex hull
-import * as math from '../math';
-import { Vector3 } from 'three';
-import { ConvexGeometry } from 'three/examples/jsm/geometries/ConvexGeometry.js';
-const TOL = 1e-8;
-const normalize = (vec) => {
-    const mag = Math.hypot(...vec);
-    return mag < 1e-10 ? [0, 0, 0] : [vec[0] / mag, vec[1] / mag, vec[2] / mag];
-};
-// Check if rotation matrix is identity
-function is_identity_rotation(rot) {
-    return rot.every((row, idx) => row.every((val, jdx) => Math.abs(val - (idx === jdx ? 1 : 0)) < TOL));
-}
-// Extract unique point group rotation matrices from space group operations.
-// Returns fractional-coordinate rotations (W matrices from spglib convention).
-// These must be converted to Cartesian k-space before use in clipping.
-export function extract_point_group_from_operations(operations) {
-    const seen = new Set();
-    const unique_rotations = [];
-    for (const { rotation } of operations) {
-        const key = rotation.map((val) => val.toFixed(6)).join(`,`);
-        if (seen.has(key))
-            continue;
-        seen.add(key);
-        const rot = math.vec9_to_mat3x3(Array.from(rotation));
-        unique_rotations.push(rot);
-    }
-    return unique_rotations;
-}
-// Multiply two 3x3 matrices: C = A · B
-function mat3x3_multiply(A, B) {
-    const result = [
-        [0, 0, 0],
-        [0, 0, 0],
-        [0, 0, 0],
-    ];
-    for (let row = 0; row < 3; row++) {
-        for (let col = 0; col < 3; col++) {
-            result[row][col] = A[row][0] * B[0][col] + A[row][1] * B[1][col] + A[row][2] * B[2][col];
-        }
-    }
-    return result;
-}
-// Convert fractional-coordinate rotation W to Cartesian k-space rotation.
-// In reciprocal space: R_cart = B · W^{-T} · B^{-1}, where B is the k_lattice
-// and W^{-T} is the inverse transpose of the direct-space rotation matrix.
-// This follows the dual-basis relation: if direct fractional rotation is x' = W·x,
-// then reciprocal fractional rotation is q' = W^{-T}·q. For non-orthogonal lattices
-// (monoclinic, triclinic, hexagonal), W^{-1} ≠ W^T since integer rotation matrices
-// are not orthogonal in these systems.
-export function fractional_to_cartesian_rotation(W, k_lattice) {
-    try {
-        const k_lattice_inv = math.matrix_inverse_3x3(k_lattice);
-        const W_inv = math.matrix_inverse_3x3(W);
-        const W_inv_T = math.transpose_3x3_matrix(W_inv);
-        // R_cart = B · W^{-T} · B^{-1}
-        return mat3x3_multiply(mat3x3_multiply(k_lattice, W_inv_T), k_lattice_inv);
-    }
-    catch {
-        // Fallback to identity if inversion fails (shouldn't happen for valid rotations)
-        return [
-            [1, 0, 0],
-            [0, 1, 0],
-            [0, 0, 1],
-        ];
-    }
-}
-// Compute reciprocal lattice: k = inv(real).T * 2π
-export function reciprocal_lattice(real_lattice) {
-    const inv = math.matrix_inverse_3x3(real_lattice);
-    const transposed = math.transpose_3x3_matrix(inv);
-    return transposed.map((row) => math.scale(row, 2 * Math.PI));
-}
-// Generate k-space grid with size based on BZ order
-function generate_k_space_grid(k_lattice, order) {
-    const points = [];
-    // For order n, we need to include points up to ±n to capture all nearest neighbors
-    const range = Math.max(1, order);
-    for (let idx_i = -range; idx_i <= range; idx_i++) {
-        for (let idx_j = -range; idx_j <= range; idx_j++) {
-            for (let idx_k = -range; idx_k <= range; idx_k++) {
-                const point = math.add(math.scale(k_lattice[0], idx_i), math.scale(k_lattice[1], idx_j), math.scale(k_lattice[2], idx_k));
-                points.push(point);
-            }
-        }
-    }
-    return points;
-}
-// O(1) duplicate vertex detection using spatial hashing
-class VertexDeduplicator {
-    grid = new Map();
-    cell_size;
-    constructor(cell_size) {
-        this.cell_size = cell_size;
-    }
-    has_duplicate(vertex) {
-        const [base_x, base_y, base_z] = vertex.map((val) => Math.floor(val / this.cell_size));
-        for (let dx = -1; dx <= 1; dx++) {
-            for (let dy = -1; dy <= 1; dy++) {
-                for (let dz = -1; dz <= 1; dz++) {
-                    const neighbors = this.grid.get(`${base_x + dx},${base_y + dy},${base_z + dz}`);
-                    if (neighbors?.some(([v1, v2, v3]) => Math.abs(v1 - vertex[0]) < TOL &&
-                        Math.abs(v2 - vertex[1]) < TOL &&
-                        Math.abs(v3 - vertex[2]) < TOL))
-                        return true;
-                }
-            }
-        }
-        return false;
-    }
-    add(vertex) {
-        const key = vertex.map((vert) => Math.floor(vert / this.cell_size)).join(`,`);
-        const cell = this.grid.get(key);
-        if (cell)
-            cell.push(vertex);
-        else
-            this.grid.set(key, [vertex]);
-    }
-}
-// Find intersection of three Bragg planes by solving N·v = d
-function intersect_planes(p1, p2, p3) {
-    try {
-        const matrix = [p1.normal, p2.normal, p3.normal];
-        const distances = [p1.dist, p2.dist, p3.dist];
-        return math.mat3x3_vec3_multiply(math.matrix_inverse_3x3(matrix), distances);
-    }
-    catch {
-        return null;
-    }
-}
-// Generate BZ vertices for nth-order zone via three-plane intersections
-export function generate_bz_vertices(k_lattice, order = 1, 
-// Maximum number of Bragg planes to consider for each BZ order.
-// Limits the number of three-plane intersections tested (O(n³) operation).
-// Higher values give more accurate zones but increase computation time significantly.
-// Default values: 26 (1st order), 80 (2nd order), 150 (3rd+ order)
-max_planes_by_order = { 1: 26, 2: 80, 3: 150 }) {
-    if (order > 3)
-        order = 3; // Performance limit
-    const k_points = generate_k_space_grid(k_lattice, order);
-    const center_idx = Math.floor(k_points.length / 2);
-    // Determine max planes for this order (default to highest value for orders > 3)
-    const max_planes = max_planes_by_order[order] ?? 150;
-    // Create Bragg planes (perpendicular bisectors of k-points)
-    const planes = k_points
-        .map((pt, idx) => {
-        if (idx === center_idx)
-            return null;
-        const dist_sq = pt[0] ** 2 + pt[1] ** 2 + pt[2] ** 2;
-        return { normal: normalize(pt), dist: Math.sqrt(dist_sq) / 2, dist_sq };
-    })
-        .filter((p) => p !== null)
-        .sort((a, b) => a.dist_sq - b.dist_sq)
-        .slice(0, max_planes);
-    // Pre-compute plane data for fast access
-    const normals = planes.map((p) => p.normal);
-    const distances = planes.map((p) => p.dist);
-    const dedup = new VertexDeduplicator(TOL * 10);
-    const vertices = [];
-    // Test all three-plane intersections
-    for (let idx_i = 0; idx_i < planes.length; idx_i++) {
-        for (let idx_j = idx_i + 1; idx_j < planes.length; idx_j++) {
-            for (let idx_k = idx_j + 1; idx_k < planes.length; idx_k++) {
-                const vertex = intersect_planes(planes[idx_i], planes[idx_j], planes[idx_k]);
-                if (!vertex)
-                    continue;
-                // Count how many planes this vertex is beyond (with early termination)
-                let beyond_count = 0;
-                for (let p_idx = 0; p_idx < normals.length; p_idx++) {
-                    const dot = vertex[0] * normals[p_idx][0] +
-                        vertex[1] * normals[p_idx][1] +
-                        vertex[2] * normals[p_idx][2];
-                    if (dot > distances[p_idx] + TOL) {
-                        beyond_count++;
-                        if (beyond_count >= order)
-                            break;
-                    }
-                }
-                // Vertex belongs to nth BZ if it's beyond fewer than n planes
-                if (beyond_count < order && !dedup.has_duplicate(vertex)) {
-                    vertices.push(vertex);
-                    dedup.add(vertex);
-                }
-            }
-        }
-    }
-    return vertices;
-}
-// Compute polyhedron volume via divergence theorem (sum of signed tetrahedral volumes)
-function compute_hull_volume(vertices, faces) {
-    if (faces.length === 0)
-        return 0;
-    return Math.abs(faces.reduce((sum, face) => {
-        if (face.length < 3)
-            return sum;
-        const [v0, v1, v2] = face.slice(0, 3).map((idx) => vertices[idx]);
-        const area_normal = math.scale(math.cross_3d(math.subtract(v1, v0), math.subtract(v2, v0)), 0.5);
-        return sum + math.dot(v0, area_normal) / 3;
-    }, 0));
-}
-// Build convex hull from vertices and extract topology
-export function compute_convex_hull(vertices, edge_sharp_angle_deg = 5) {
-    if (vertices.length < 4) {
-        throw new Error(`Need ≥4 vertices for convex hull, got ${vertices.length}`);
-    }
-    const geometry = new ConvexGeometry(vertices.map((cert) => new Vector3(...cert)));
-    const pos = geometry.getAttribute(`position`);
-    const idx = geometry.index;
-    // Deduplicate vertices from Three.js geometry
-    const unique_verts = [];
-    const vert_map = new Map();
-    for (let idx_vertex = 0; idx_vertex < pos.count; idx_vertex++) {
-        const vert = [pos.getX(idx_vertex), pos.getY(idx_vertex), pos.getZ(idx_vertex)];
-        const existing_idx = unique_verts.findIndex((u) => Math.abs(u[0] - vert[0]) < TOL &&
-            Math.abs(u[1] - vert[1]) < TOL &&
-            Math.abs(u[2] - vert[2]) < TOL);
-        vert_map.set(idx_vertex, existing_idx === -1 ? unique_verts.push(vert) - 1 : existing_idx);
-    }
-    // Build faces with deduplicated vertex indices
-    const faces = [];
-    const n_faces = idx ? idx.count / 3 : pos.count / 3;
-    for (let idx_face = 0; idx_face < n_faces; idx_face++) {
-        const tri = idx
-            ? [idx.getX(idx_face * 3), idx.getX(idx_face * 3 + 1), idx.getX(idx_face * 3 + 2)]
-            : [idx_face * 3, idx_face * 3 + 1, idx_face * 3 + 2];
-        faces.push(tri.map((j) => {
-            const mapped = vert_map.get(j);
-            if (mapped === undefined)
-                throw new Error(`Vertex ${j} not mapped`);
-            return mapped;
-        }));
-    }
-    // Compute face normals and build edge-to-face adjacency
-    const face_normals = faces.map((face) => {
-        const [v0, v1, v2] = face.slice(0, 3).map((vi) => unique_verts[vi]);
-        return normalize(math.cross_3d(math.subtract(v1, v0), math.subtract(v2, v0)));
-    });
-    const edge_to_faces = new Map();
-    faces.forEach((face, face_idx) => {
-        face.forEach((v1, idx) => {
-            const v2 = face[(idx + 1) % face.length];
-            const key = v1 < v2 ? `${v1},${v2}` : `${v2},${v1}`;
-            const adj = edge_to_faces.get(key);
-            if (adj)
-                adj.push(face_idx);
-            else
-                edge_to_faces.set(key, [face_idx]);
-        });
-    });
-    // Extract edges: keep boundary edges or sharp angles
-    const cos_threshold = Math.cos((edge_sharp_angle_deg * Math.PI) / 180);
-    const edges = [];
-    for (const [key, adj] of edge_to_faces) {
-        const is_sharp = adj.length === 1 ||
-            (adj.length === 2 &&
-                math.dot(face_normals[adj[0]], face_normals[adj[1]]) < cos_threshold);
-        if (is_sharp)
-            edges.push(key.split(`,`).map(Number));
-    }
-    geometry.dispose();
-    return { vertices: unique_verts, faces, edges };
-}
-// Compute complete Brillouin zone with topology and volume
-export function compute_brillouin_zone(k_lattice, order = 1, edge_sharp_angle_deg = 5, // Angle threshold for edge extraction (default 5°, increase for fewer edges, decrease for more)
-max_planes_by_order = { 1: 26, 2: 80, 3: 150 }) {
-    const vertices = generate_bz_vertices(k_lattice, order, max_planes_by_order);
-    if (vertices.length < 4) {
-        throw new Error(`Insufficient vertices for BZ (got ${vertices.length}, need ≥4)`);
-    }
-    const hull = compute_convex_hull(vertices, edge_sharp_angle_deg);
-    return {
-        order,
-        vertices: hull.vertices,
-        faces: hull.faces,
-        edges: hull.edges.map(([i1, i2]) => [hull.vertices[i1], hull.vertices[i2]]),
-        k_lattice,
-        volume: compute_hull_volume(hull.vertices, hull.faces),
-    };
-}
-// Test points for IBZ plane detection. These are chosen to:
-// 1. Avoid common rotation axes (2-fold, 3-fold, 4-fold, 6-fold)
-// 2. Span different directions to catch all symmetry operations
-// 3. Include a generic point [1,2,3] that lies on no special axis
-const IBZ_TEST_POINTS = [
-    [1, 0, 0],
-    [0, 1, 0],
-    [0, 0, 1], // basis vectors (avoid 4-fold axes)
-    [1, 1, 0],
-    [1, 0, 1],
-    [0, 1, 1], // face diagonals (avoid 2-fold axes)
-    [1, 1, 1], // body diagonal (avoid 3-fold axis)
-    [1, 2, 3], // generic point on no special axis
-];
-// Compute clipping planes from point group operations.
-// For each non-identity rotation, we define a plane that selects one representative
-// from each equivalence class.
-export function compute_ibz_clipping_planes(point_group_ops) {
-    const planes = [];
-    const seen_normals = new Set();
-    for (const rot of point_group_ops) {
-        if (is_identity_rotation(rot))
-            continue;
-        for (const test_pt of IBZ_TEST_POINTS) {
-            const rotated = math.mat3x3_vec3_multiply(rot, test_pt);
-            const diff = math.subtract(rotated, test_pt);
-            if (Math.hypot(...diff) < TOL)
-                continue; // point on rotation axis
-            const plane_normal = normalize(diff);
-            const key = plane_normal.map((val) => Math.round(val * 1000)).join(`,`);
-            const neg_key = plane_normal.map((val) => Math.round(-val * 1000)).join(`,`);
-            if (!seen_normals.has(key) && !seen_normals.has(neg_key)) {
-                seen_normals.add(key);
-                planes.push({ normal: plane_normal, dist: 0 });
-            }
-            break;
-        }
-    }
-    return planes;
-}
-// Flip a clipping plane to the opposite half-space
-const flip_plane = (p) => ({
-    normal: math.scale(p.normal, -1),
-    dist: -p.dist,
-});
-// Clip polyhedron vertices by a half-space, adding intersection points where edges cross
-function clip_polyhedron_by_plane(vertices, faces, plane) {
-    const { normal, dist } = plane;
-    const signed_dists = vertices.map((v) => math.dot(v, normal) - dist);
-    // Keep vertices inside the half-space
-    const result = vertices.filter((_, idx) => signed_dists[idx] <= TOL);
-    // Build edge set from faces
-    const edge_set = new Set();
-    for (const face of faces) {
-        for (let idx = 0; idx < face.length; idx++) {
-            const i1 = face[idx];
-            const i2 = face[(idx + 1) % face.length];
-            edge_set.add(i1 < i2 ? `${i1},${i2}` : `${i2},${i1}`);
-        }
-    }
-    // Add intersection points where edges cross the plane
-    for (const key of edge_set) {
-        const [i1, i2] = key.split(`,`).map(Number);
-        const d1 = signed_dists[i1];
-        const d2 = signed_dists[i2];
-        // Edge crosses plane if exactly one endpoint is inside the half-space
-        const inside1 = d1 <= TOL;
-        const inside2 = d2 <= TOL;
-        if (inside1 !== inside2) {
-            const denom = d1 - d2;
-            // Skip if denominator too small (tighter than TOL for numerical stability)
-            if (Math.abs(denom) < 1e-12)
-                continue;
-            const t = d1 / denom;
-            // Only add intersection if it's not at an endpoint (which is already kept)
-            if (t > TOL && t < 1 - TOL) {
-                const [v1, v2] = [vertices[i1], vertices[i2]];
-                result.push([
-                    v1[0] + t * (v2[0] - v1[0]),
-                    v1[1] + t * (v2[1] - v1[1]),
-                    v1[2] + t * (v2[2] - v1[2]),
-                ]);
-            }
-        }
-    }
-    return result;
-}
-// Try to build hull from vertices, returns null on failure
-function try_build_hull(vertices, edge_sharp_angle_deg) {
-    if (vertices.length < 4)
-        return null;
-    try {
-        return compute_convex_hull(vertices, edge_sharp_angle_deg);
-    }
-    catch {
-        return null;
-    }
-}
-// Compute the irreducible Brillouin zone by clipping the full BZ with symmetry planes
-export function compute_irreducible_bz(bz_data, point_group_ops, edge_sharp_angle_deg = 5) {
-    // Convert fractional rotations to Cartesian k-space rotations
-    // R_cart = B · W^{-T} · B^{-1}, where B is k_lattice and W^{-T} is inverse-transpose
-    const cartesian_ops = point_group_ops.map((W) => fractional_to_cartesian_rotation(W, bz_data.k_lattice));
-    const clipping_planes = compute_ibz_clipping_planes(cartesian_ops);
-    if (clipping_planes.length === 0) {
-        // No symmetry (P1), IBZ = full BZ
-        return {
-            vertices: [...bz_data.vertices],
-            faces: [...bz_data.faces],
-            edges: [...bz_data.edges],
-            volume: bz_data.volume,
-        };
-    }
-    let current_vertices = [...bz_data.vertices];
-    let current_faces = [...bz_data.faces];
-    for (const plane of clipping_planes) {
-        // Try clipping with plane, then flipped plane if needed
-        let clipped_successfully = false;
-        for (const try_plane of [plane, flip_plane(plane)]) {
-            const clipped = clip_polyhedron_by_plane(current_vertices, current_faces, try_plane);
-            const hull = try_build_hull(clipped, edge_sharp_angle_deg);
-            if (hull) {
-                current_vertices = hull.vertices;
-                current_faces = hull.faces;
-                clipped_successfully = true;
-                break;
-            }
-        }
-        // If both orientations failed, vertices unchanged - continue with best effort
-        if (!clipped_successfully) {
-            console.warn(`IBZ clipping: plane orientation failed, continuing with current geometry`);
-        }
-    }
-    const hull = try_build_hull(current_vertices, edge_sharp_angle_deg);
-    if (!hull)
-        return null;
-    return {
-        vertices: hull.vertices,
-        faces: hull.faces,
-        edges: hull.edges.map(([i1, i2]) => [hull.vertices[i1], hull.vertices[i2]]),
-        volume: compute_hull_volume(hull.vertices, hull.faces),
-    };
-}

package/dist/brillouin/index.d.ts

@@ -1,8 +0,0 @@
-export { default as BrillouinZone } from './BrillouinZone.svelte';
-export { default as BrillouinZoneControls } from './BrillouinZoneControls.svelte';
-export { default as BrillouinZoneExportPane } from './BrillouinZoneExportPane.svelte';
-export { default as BrillouinZoneInfoPane } from './BrillouinZoneInfoPane.svelte';
-export { default as BrillouinZoneScene } from './BrillouinZoneScene.svelte';
-export { default as BrillouinZoneTooltip } from './BrillouinZoneTooltip.svelte';
-export * from './compute';
-export * from './types';

package/dist/brillouin/index.js

@@ -1,8 +0,0 @@
-export { default as BrillouinZone } from './BrillouinZone.svelte';
-export { default as BrillouinZoneControls } from './BrillouinZoneControls.svelte';
-export { default as BrillouinZoneExportPane } from './BrillouinZoneExportPane.svelte';
-export { default as BrillouinZoneInfoPane } from './BrillouinZoneInfoPane.svelte';
-export { default as BrillouinZoneScene } from './BrillouinZoneScene.svelte';
-export { default as BrillouinZoneTooltip } from './BrillouinZoneTooltip.svelte';
-export * from './compute';
-export * from './types';

package/dist/brillouin/types.d.ts

@@ -1,48 +0,0 @@
-import type { Matrix3x3, Vec3 } from '../math';
-import type { Crystal } from '../structure';
-import type { TooltipConfig, TooltipProp } from '../tooltip';
-export type BZHoverData = {
-    position_cartesian: Vec3;
-    position_fractional: Vec3 | null;
-    screen_position: {
-        x: number;
-        y: number;
-    };
-    is_ibz: boolean;
-    bz_order: number;
-    bz_volume: number;
-    ibz_volume: number | null;
-    symmetry_multiplicity: number | null;
-};
-export type BZTooltipConfig = TooltipConfig<BZHoverData>;
-export type BZTooltipProp = TooltipProp<BZHoverData, [{
-    hover_data: BZHoverData;
-}]>;
-export type IrreducibleBZData = {
-    vertices: Vec3[];
-    faces: number[][];
-    edges: Vec3[][];
-    volume: number;
-};
-export type BrillouinZoneData = {
-    order: number;
-    vertices: Vec3[];
-    faces: number[][];
-    edges: Vec3[][];
-    k_lattice: Matrix3x3;
-    volume: number;
-};
-export type BrillouinZoneProps = {
-    structure: Crystal;
-    bz_order?: number;
-    surface_color?: string;
-    surface_opacity?: number;
-    edge_color?: string;
-    edge_width?: number;
-    show_vectors?: boolean;
-};
-export type ConvexHullData = {
-    vertices: Vec3[];
-    faces: number[][];
-    edges: [number, number][];
-};

package/dist/brillouin/types.js

@@ -1 +0,0 @@
-export {};