matterviz 0.3.6 → 0.3.7

package/dist/src/lib/brillouin/compute.ts

@@ -1,529 +0,0 @@
-// Brillouin zone generation via convex hull
-
-import type { Matrix3x3, Vec2, Vec3 } from '$lib/math'
-import * as math from '$lib/math'
-import type { MoyoDataset } from '@spglib/moyo-wasm'
-import { Vector3 } from 'three'
-import { ConvexGeometry } from 'three/examples/jsm/geometries/ConvexGeometry.js'
-import type { BrillouinZoneData, ConvexHullData, IrreducibleBZData } from './types'
-
-const TOL = 1e-8
-
-const normalize = (vec: Vec3): Vec3 => {
-  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
-const is_identity_rotation = (rot: Matrix3x3): boolean =>
-  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: MoyoDataset[`operations`],
-): Matrix3x3[] {
-  const seen = new Set<string>()
-  const unique_rotations: Matrix3x3[] = []
-
-  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)) as Matrix3x3
-    unique_rotations.push(rot)
-  }
-
-  return unique_rotations
-}
-
-// Multiply two 3x3 matrices: C = A · B
-function mat3x3_multiply(A: Matrix3x3, B: Matrix3x3): Matrix3x3 {
-  const result: Matrix3x3 = [
-    [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: Matrix3x3,
-  k_lattice: Matrix3x3,
-): Matrix3x3 {
-  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: Matrix3x3): Matrix3x3 {
-  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)) as Matrix3x3
-}
-
-// Generate k-space grid with size based on BZ order
-function generate_k_space_grid(k_lattice: Matrix3x3, order: number): Vec3[] {
-  const points: Vec3[] = []
-  // 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 {
-  private readonly grid = new Map<string, Vec3[]>()
-  private readonly cell_size: number
-  constructor(cell_size: number) {
-    this.cell_size = cell_size
-  }
-
-  has_duplicate(vertex: Vec3): boolean {
-    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: Vec3): void {
-    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: { normal: Vec3; dist: number },
-  p2: { normal: Vec3; dist: number },
-  p3: { normal: Vec3; dist: number },
-): Vec3 | null {
-  try {
-    const matrix: Matrix3x3 = [p1.normal, p2.normal, p3.normal]
-    const distances: Vec3 = [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: Matrix3x3,
-  order: 1 | 2 | 3 = 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: Record<1 | 2 | 3, number> = { 1: 26, 2: 80, 3: 150 },
-): Vec3[] {
-  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((plane): plane is NonNullable<typeof plane> => plane !== 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((plane) => plane.normal)
-  const distances = planes.map((plane) => plane.dist)
-
-  const dedup = new VertexDeduplicator(TOL * 10)
-  const vertices: Vec3[] = []
-
-  // 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: Vec3[], faces: number[][]): number {
-  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: Vec3[],
-  edge_sharp_angle_deg = 5, // Angle threshold for edge detection: edges between faces with angle > this are rendered
-): ConvexHullData {
-  if (vertices.length < 4) {
-    throw new Error(`Need ≥4 vertices for convex hull, got ${vertices.length}`)
-  }
-
-  const geometry = new ConvexGeometry(vertices.map((vertex) => new Vector3(...vertex)))
-  const pos = geometry.getAttribute(`position`)
-  const geometry_index = geometry.index
-
-  // Deduplicate vertices from Three.js geometry
-  const unique_verts: Vec3[] = []
-  const vert_map = new Map<number, number>()
-
-  for (let idx_vertex = 0; idx_vertex < pos.count; idx_vertex++) {
-    const vert: Vec3 = [pos.getX(idx_vertex), pos.getY(idx_vertex), pos.getZ(idx_vertex)]
-    const existing_idx = unique_verts.findIndex(
-      (unique_vert) =>
-        Math.abs(unique_vert[0] - vert[0]) < TOL &&
-        Math.abs(unique_vert[1] - vert[1]) < TOL &&
-        Math.abs(unique_vert[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: number[][] = []
-  const n_faces = geometry_index ? geometry_index.count / 3 : pos.count / 3
-
-  for (let idx_face = 0; idx_face < n_faces; idx_face++) {
-    const tri = geometry_index
-      ? [
-          geometry_index.getX(idx_face * 3),
-          geometry_index.getX(idx_face * 3 + 1),
-          geometry_index.getX(idx_face * 3 + 2),
-        ]
-      : [idx_face * 3, idx_face * 3 + 1, idx_face * 3 + 2]
-    faces.push(
-      tri.map((vertex_idx) => {
-        const mapped = vert_map.get(vertex_idx)
-        if (mapped === undefined) throw new Error(`Vertex ${vertex_idx} not mapped`)
-        return mapped
-      }),
-    )
-  }
-
-  // Compute face normals and build edge-to-face adjacency
-  const face_normals = faces.map((face) => {
-    const [v0, v1, v2] = face.slice(0, 3).map((vertex_idx) => unique_verts[vertex_idx])
-    return normalize(math.cross_3d(math.subtract(v1, v0), math.subtract(v2, v0)))
-  })
-
-  const edge_to_faces = new Map<string, number[]>()
-  faces.forEach((face, face_idx) => {
-    face.forEach((from_vertex_idx, idx) => {
-      const to_vertex_idx = face[(idx + 1) % face.length]
-      const key =
-        from_vertex_idx < to_vertex_idx
-          ? `${from_vertex_idx},${to_vertex_idx}`
-          : `${to_vertex_idx},${from_vertex_idx}`
-      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: Vec2[] = []
-
-  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) as Vec2)
-  }
-
-  geometry.dispose()
-  return { vertices: unique_verts, faces, edges }
-}
-
-// Compute complete Brillouin zone with topology and volume
-export function compute_brillouin_zone(
-  k_lattice: Matrix3x3,
-  order: 1 | 2 | 3 = 1,
-  edge_sharp_angle_deg = 5, // Angle threshold for edge extraction (default 5°, increase for fewer edges, decrease for more)
-  max_planes_by_order: Record<number, number> = { 1: 26, 2: 80, 3: 150 }, // Customize plane count limits per BZ order
-): BrillouinZoneData {
-  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),
-  }
-}
-
-// Clipping plane defined by normal and distance from origin (n·x = d)
-type ClippingPlane = { normal: Vec3; dist: number }
-
-// 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: Vec3[] = [
-  [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: Matrix3x3[]): ClippingPlane[] {
-  const planes: ClippingPlane[] = []
-  const seen_normals = new Set<string>()
-
-  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: Vec3 = 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 = (plane: ClippingPlane): ClippingPlane => ({
-  normal: math.scale(plane.normal, -1),
-  dist: -plane.dist,
-})
-
-// Clip polyhedron vertices by a half-space, adding intersection points where edges cross
-function clip_polyhedron_by_plane(
-  vertices: Vec3[],
-  faces: number[][],
-  plane: ClippingPlane,
-): Vec3[] {
-  const { normal, dist } = plane
-  const signed_dists = vertices.map((vertex) => math.dot(vertex, 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<string>()
-  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: Vec3[],
-  edge_sharp_angle_deg: number,
-): ConvexHullData | null {
-  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: BrillouinZoneData,
-  point_group_ops: Matrix3x3[],
-  edge_sharp_angle_deg = 5,
-): IrreducibleBZData | null {
-  // 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/src/lib/brillouin/index.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 type * from './types'

package/dist/src/lib/brillouin/types.ts

@@ -1,51 +0,0 @@
-import type { Matrix3x3, Point2D, Vec3 } from '$lib/math'
-import type { Crystal } from '$lib/structure'
-import type { TooltipConfig, TooltipProp } from '$lib/tooltip'
-
-// Hover data for BZ tooltip
-export type BZHoverData = {
-  position_cartesian: Vec3 // k-point in Cartesian coords (Å⁻¹)
-  position_fractional: Vec3 | null // k-point in fractional coords
-  screen_position: Point2D // for tooltip positioning
-  is_ibz: boolean // true if hovering the IBZ mesh
-  bz_order: number
-  bz_volume: number
-  ibz_volume: number | null // only when IBZ is shown
-  symmetry_multiplicity: number | null // BZ volume / IBZ volume (e.g., 48 for cubic)
-}
-
-// Tooltip configuration for prefix/suffix customization
-export type BZTooltipConfig = TooltipConfig<BZHoverData>
-
-// Tooltip prop can be a snippet for full customization or config for prefix/suffix
-export type BZTooltipProp = TooltipProp<BZHoverData, [{ hover_data: BZHoverData }]>
-
-type BZMeshData = {
-  vertices: Vec3[]
-  faces: number[][] // Face indices for mesh rendering
-  edges: Vec3[][] // Edge segments for boundary rendering
-}
-
-// Data structure for the irreducible Brillouin zone wedge
-export type IrreducibleBZData = BZMeshData & { volume: number } // IBZ volume in Å⁻³
-
-export type BrillouinZoneData = BZMeshData & {
-  order: number // 1st, 2nd, 3rd BZ
-  k_lattice: Matrix3x3 // reciprocal lattice vectors
-  volume: number // BZ volume in Å⁻³
-}
-
-export type BrillouinZoneProps = {
-  structure: Crystal
-  bz_order?: number // default 1
-  // Styling
-  surface_color?: string
-  surface_opacity?: number
-  edge_color?: string
-  edge_width?: number
-  show_vectors?: boolean // show b₁, b₂, b₃
-}
-
-export type ConvexHullData = Pick<BZMeshData, `vertices` | `faces`> & {
-  edges: [number, number][] // pairs of vertex indices
-}