matsci-parse 0.8.0 → 0.8.1

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Files changed (4) hide show
  1. package/dist/index.js +641 -433
  2. package/dist/index.js.map +1 -1
  3. package/dist/stats.html +1 -1
  4. package/package.json +1 -1
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sources":["../lib/core/structure/operations/canonicalize.ts","../lib/core/structure/operations/hashStructure.ts","../lib/core/structure/operations/sites/appendSite.ts","../lib/core/structure/operations/sites/insertSite.ts","../lib/core/structure/operations/sites/removeSite.ts","../lib/core/structure/operations/sites/replaceSite.ts","../lib/core/matrix/matrix.ts","../lib/core/lattice/lattice.ts","../lib/core/matrix/operations/vector/dot.ts","../lib/core/matrix/operations/vector/norm.ts","../lib/core/lattice/angles.ts","../lib/core/matrix/operations/inverse/inverse3x3.ts","../lib/core/lattice/inverse.ts","../lib/core/lattice/lengths.ts","../lib/core/matrix/operations/transpose.ts","../lib/core/matrix/operations/mul.ts","../lib/core/lattice/metricTensor.ts","../lib/core/lattice/parameters.ts","../lib/core/lattice/reciprocalLattice.ts","../lib/core/lattice/reciprocalLatticeCrystallographic.ts","../lib/core/matrix/operations/determinant.ts","../lib/core/lattice/volume.ts","../lib/core/lattice/create/fromParameters.ts","../lib/core/lattice/create/cubic.ts","../lib/core/lattice/create/hexagonal.ts","../lib/core/lattice/create/monoclinic.ts","../lib/core/lattice/create/orthorhombic.ts","../lib/core/lattice/create/rhombohedral.ts","../lib/core/lattice/create/tetragonal.ts","../lib/core/structure/operations/symmetry/spglib.ts","../lib/core/structure/operations/supercell.ts","../lib/core/site/site.ts","../lib/core/site/cartesian.ts","../lib/core/site/fractional.ts","../lib/core/site/distance.ts","../lib/core/site/wrap.ts","../lib/core/species/species.ts","../lib/core/io/cif.ts","../lib/core/io/poscar.ts","../lib/core/io/structuredata.ts","../lib/core/io/xsf.ts","../lib/core/io/xyz.ts","../lib/core/io/optimade.ts","../lib/core/io/json.ts","../lib/core/units/converter.ts","../lib/core/units/length.ts","../lib/core/units/energy.ts","../lib/core/units/angle.ts"],"sourcesContent":["import { Structure } from \"../../structure/structure\";\n\nconst EPS = 1e-12;\n\nfunction wrap(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < EPS ? 0 : v;\n}\n\nfunction clean(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function canonicalize(structure: Structure): Structure {\n return {\n ...structure,\n sites: structure.sites.map((site) => ({\n ...site,\n frac: new Float64Array([\n wrap(clean(site.frac[0])),\n wrap(clean(site.frac[1])),\n wrap(clean(site.frac[2])),\n ]),\n })),\n };\n}\n","import { Structure } from \"../structure\";\nimport { canonicalize } from \"./canonicalize\";\nimport { Vec3 } from \"@/main\";\n\nfunction toFixedArray(v: Vec3, precision = 8): string {\n return Array.from(v)\n .map((x) => x.toFixed(precision))\n .join(\",\");\n}\n\nfunction fnv1a(str: string): number {\n let hash = 2166136261;\n\n for (let i = 0; i < str.length; i++) {\n hash ^= str.charCodeAt(i);\n hash *= 16777619;\n }\n\n return hash >>> 0;\n}\n\nexport function hashStructure(structure: Structure): number {\n const s = canonicalize(structure);\n\n const lattice = s.lattice.basis.data;\n const latticeKey = toFixedArray(lattice);\n\n const sitesKey = s.sites\n .map((site) => {\n return site.species + \":\" + toFixedArray(site.frac);\n })\n .sort()\n .join(\"|\");\n\n const key = latticeKey + \"::\" + sitesKey;\n\n return fnv1a(key);\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function appendSite(structure: Structure, site: Site): Structure {\n return {\n ...structure,\n sites: [...structure.sites, site],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function insertSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n return {\n ...structure,\n sites: [\n ...structure.sites.slice(0, index),\n site,\n ...structure.sites.slice(index),\n ],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function removeSite(structure: Structure, index: number): Structure {\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => i !== index),\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function replaceSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n return {\n ...structure,\n sites: structure.sites.map((s, i) => (i === index ? site : s)),\n };\n}\n","export interface Matrix {\n readonly rows: number;\n readonly cols: number;\n readonly data: Float64Array;\n}\n\nexport function createMatrix(\n rows: number,\n cols: number,\n data?: Iterable<number>,\n): Matrix {\n const size = rows * cols;\n\n const buffer = data ? Float64Array.from(data) : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(`Expected ${size} values, got ${buffer.length}`);\n }\n\n return {\n rows,\n cols,\n data: buffer,\n };\n}\n\nexport function identity(size: number): Matrix {\n const data = new Float64Array(size * size);\n\n for (let i = 0; i < size; i++) {\n data[i * size + i] = 1;\n }\n\n return {\n rows: size,\n cols: size,\n data,\n };\n}\n\nexport function clone(matrix: Matrix): Matrix {\n return {\n rows: matrix.rows,\n cols: matrix.cols,\n data: new Float64Array(matrix.data),\n };\n}\n\nexport function index(cols: number, row: number, col: number): number {\n return row * cols + col;\n}\n","import { createMatrix, Matrix } from \"../matrix/matrix\";\n\nconst EPS = 1e-12;\n\nfunction clean(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function createLattice(data: number[] | Float64Array | Matrix): Lattice {\n const values =\n data instanceof Float64Array ? data : \"data\" in data ? data.data : data;\n\n if (values.length !== 9) {\n throw new Error(\"Lattice requires 9 values (3x3)\");\n }\n\n const cleaned = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n cleaned[i] = clean(values[i]);\n }\n\n return {\n basis: createMatrix(3, 3, cleaned),\n };\n}\n","import { Vector } from \"../../vector\";\n\nexport function dot(a: Vector, b: Vector): number {\n if (a.length !== b.length) {\n throw new Error(\"Dot product requires same-length vectors\");\n }\n\n let sum = 0;\n\n for (let i = 0; i < a.length; i++) {\n sum += a[i] * b[i];\n }\n\n return sum;\n}\n","import { Vector } from \"../../vector\";\n\nconst EPS = 1e-12;\n\nexport function norm(v: Vector): number {\n let sum = 0;\n\n for (let i = 0; i < v.length; i++) {\n const x = v[i];\n sum += x * x;\n }\n\n return Math.sqrt(sum);\n}\n","import { dot } from \"../matrix/operations/vector/dot\";\nimport { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n\nimport { Vector } from \"../matrix/vector\";\n\nfunction angle(u: Vector, v: Vector) {\n const denom = norm(u) * norm(v);\n if (denom === 0) throw new Error(\"Zero-length lattice vector\");\n\n const c = dot(u, v) / denom;\n const clamped = Math.max(-1, Math.min(1, c));\n\n return Math.acos(clamped);\n}\n\nexport function angles(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Vector = new Float64Array([m[0], m[1], m[2]]);\n const b: Vector = new Float64Array([m[3], m[4], m[5]]);\n const c: Vector = new Float64Array([m[6], m[7], m[8]]);\n\n const alpha = angle(b, c);\n const beta = angle(a, c);\n const gamma = angle(a, b);\n\n return [alpha, beta, gamma];\n}\n","import { Matrix, createMatrix } from \"../../matrix\";\n\nexport function inverse3x3(m: Matrix): Matrix {\n if (m.rows !== 3 || m.cols !== 3) {\n throw new Error(\"Expected 3x3 matrix\");\n }\n\n const a00 = m.data[0],\n a01 = m.data[1],\n a02 = m.data[2];\n const a10 = m.data[3],\n a11 = m.data[4],\n a12 = m.data[5];\n const a20 = m.data[6],\n a21 = m.data[7],\n a22 = m.data[8];\n\n const c00 = a11 * a22 - a12 * a21;\n const c01 = a12 * a20 - a10 * a22;\n const c02 = a10 * a21 - a11 * a20;\n\n const c10 = a02 * a21 - a01 * a22;\n const c11 = a00 * a22 - a02 * a20;\n const c12 = a01 * a20 - a00 * a21;\n\n const c20 = a01 * a12 - a02 * a11;\n const c21 = a02 * a10 - a00 * a12;\n const c22 = a00 * a11 - a01 * a10;\n\n const det = a00 * c00 + a01 * c01 + a02 * c02;\n\n if (det === 0) {\n throw new Error(\"Singular matrix\");\n }\n\n const invDet = 1 / det;\n\n const out = createMatrix(3, 3);\n\n out.data[0] = c00 * invDet;\n out.data[1] = c10 * invDet;\n out.data[2] = c20 * invDet;\n\n out.data[3] = c01 * invDet;\n out.data[4] = c11 * invDet;\n out.data[5] = c21 * invDet;\n\n out.data[6] = c02 * invDet;\n out.data[7] = c12 * invDet;\n out.data[8] = c22 * invDet;\n\n return out;\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse3x3 } from \"../matrix/operations/inverse/inverse3x3\";\nimport { Matrix } from \"../matrix/matrix\";\n\nexport function inverse(lattice: Lattice): Matrix {\n return inverse3x3(lattice.basis);\n}\n","import { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\nexport function lengths(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Float64Array = new Float64Array([m[0], m[1], m[2]]);\n const b: Float64Array = new Float64Array([m[3], m[4], m[5]]);\n const c: Float64Array = new Float64Array([m[6], m[7], m[8]]);\n\n return [norm(a), norm(b), norm(c)];\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nexport function transpose(matrix: Matrix): Matrix {\n const out = createMatrix(matrix.cols, matrix.rows);\n\n for (let row = 0; row < matrix.rows; row++) {\n for (let col = 0; col < matrix.cols; col++) {\n out.data[index(out.cols, col, row)] =\n matrix.data[index(matrix.cols, row, col)];\n }\n }\n\n return out;\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nexport function mul(a: Matrix, b: Matrix): Matrix {\n if (a.cols !== b.rows) {\n throw new Error(\"Invalid matrix multiplication dimensions\");\n }\n\n const out = createMatrix(a.rows, b.cols);\n\n const aRows = a.rows;\n const aCols = a.cols;\n const bCols = b.cols;\n\n for (let row = 0; row < aRows; row++) {\n for (let col = 0; col < bCols; col++) {\n let sum = 0;\n\n for (let k = 0; k < aCols; k++) {\n sum += a.data[index(a.cols, row, k)] * b.data[index(b.cols, k, col)];\n }\n\n out.data[index(out.cols, row, col)] = sum;\n }\n }\n\n return out;\n}\n","import { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Lattice } from \"./lattice\";\nimport { Matrix } from \"../matrix/matrix\";\n\nexport function metricTensor(lattice: Lattice): Matrix {\n const A = lattice.basis;\n\n const AT = transpose(A);\n return mul(AT, A);\n}\n","import { lengths } from \"./lengths\";\nimport { angles } from \"./angles\";\nimport { Lattice } from \"./lattice\";\n\nconst RAD2DEG = 180 / Math.PI;\n\nexport function parameters(\n lattice: Lattice,\n): [number, number, number, number, number, number] {\n const [a, b, c] = lengths(lattice);\n const [alpha, beta, gamma] = angles(lattice);\n\n return [a, b, c, alpha * RAD2DEG, beta * RAD2DEG, gamma * RAD2DEG];\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { createLattice } from \"./lattice\";\n\nconst TWO_PI = 2 * Math.PI;\n\nexport function reciprocalLattice(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const data = invT.data.map((v) => v * TWO_PI);\n\n return createLattice(data);\n}\n","import { Lattice, createLattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nexport function reciprocalLatticeCrystallographic(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n return createLattice(invT.data);\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nfunction minor(matrix: Matrix, skipRow: number, skipCol: number): Matrix {\n const out = createMatrix(matrix.rows - 1, matrix.cols - 1);\n\n let ptr = 0;\n\n for (let row = 0; row < matrix.rows; row++) {\n if (row === skipRow) continue;\n\n for (let col = 0; col < matrix.cols; col++) {\n if (col === skipCol) continue;\n\n out.data[ptr++] = matrix.data[index(matrix.cols, row, col)];\n }\n }\n\n return out;\n}\n\nexport function determinant(matrix: Matrix): number {\n if (matrix.rows !== matrix.cols) {\n throw new Error(\"Determinant requires a square matrix\");\n }\n\n const n = matrix.rows;\n\n // fast path for BZ / geometry\n if (n === 3) {\n const m = matrix.data;\n\n return (\n m[0] * (m[4] * m[8] - m[5] * m[7]) -\n m[1] * (m[3] * m[8] - m[5] * m[6]) +\n m[2] * (m[3] * m[7] - m[4] * m[6])\n );\n }\n\n if (n === 1) {\n return matrix.data[0];\n }\n\n if (n === 2) {\n return matrix.data[0] * matrix.data[3] - matrix.data[1] * matrix.data[2];\n }\n\n let det = 0;\n\n for (let col = 0; col < n; col++) {\n const sign = col % 2 === 0 ? 1 : -1;\n\n det += sign * matrix.data[col] * determinant(minor(matrix, 0, col));\n }\n\n return det;\n}\n","import { determinant } from \"../matrix/operations/determinant\";\nimport { Lattice } from \"./lattice\";\n\nexport function volume(lattice: Lattice): number {\n return Math.abs(determinant(lattice.basis));\n}\n","import { createLattice } from \"../lattice\";\n\nconst DEG2RAD = Math.PI / 180;\nconst EPS = 1e-12;\n\nfunction clean(x: number) {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function fromParameters(\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n) {\n const alphaR = alpha * DEG2RAD;\n const betaR = beta * DEG2RAD;\n const gammaR = gamma * DEG2RAD;\n\n const cosA = Math.cos(alphaR);\n const cosB = Math.cos(betaR);\n const cosG = Math.cos(gammaR);\n const sinG = Math.sin(gammaR);\n\n // lattice vectors\n const v1 = [a, 0, 0];\n\n const v2 = [b * cosG, b * sinG, 0];\n\n // guard against degenerate gamma\n if (Math.abs(sinG) < EPS) {\n throw new Error(\"Invalid lattice: gamma too close to 0 or 180 degrees\");\n }\n\n const cx = c * cosB;\n\n const cy = (c * (cosA - cosB * cosG)) / sinG;\n\n const czSquared = c * c - cx * cx - cy * cy;\n\n const cz = Math.sqrt(Math.max(0, czSquared));\n\n return createLattice([\n clean(v1[0]),\n clean(v1[1]),\n clean(v1[2]),\n clean(v2[0]),\n clean(v2[1]),\n clean(v2[2]),\n clean(cx),\n clean(cy),\n clean(cz),\n ]);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function cubic(a: number) {\n return fromParameters(a, a, a, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function hexagonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 120);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function monoclinic(a: number, b: number, c: number, beta: number) {\n return fromParameters(a, b, c, 90, beta, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function orthorhombic(a: number, b: number, c: number) {\n return fromParameters(a, b, c, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function rhombohedral(a: number, alpha: number) {\n return fromParameters(a, a, a, alpha, alpha, alpha);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function tetragonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 90);\n}\n","import init, { analyze_cell, type MoyoDataset } from \"@spglib/moyo-wasm\";\n\nimport { createLattice } from \"@/core/lattice\";\nimport { Structure } from \"../../structure\";\n\nlet ready: Promise<void> | null = null;\n\nexport function initMoyo() {\n if (!ready) {\n ready = (async () => {\n // In Node.js (tests), load from filesystem\n if (typeof process !== \"undefined\" && process.versions?.node) {\n try {\n const { readFileSync } = await import(\"fs\");\n const { join } = await import(\"path\");\n const wasmPath = join(\n process.cwd(),\n \"node_modules/@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n );\n const wasmBuffer = readFileSync(wasmPath);\n await init(wasmBuffer);\n } catch (e) {\n console.error(\"Failed to load WASM in Node:\", e);\n throw e;\n }\n } else {\n // In browser, use dynamic import to get the URL\n const wasmUrl = new URL(\n \"@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n import.meta.url,\n ).toString();\n\n await init(wasmUrl);\n }\n })();\n }\n return ready;\n}\n\nexport async function getSymmetry(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Standard\",\n): Promise<{\n primitive: Structure;\n conventional: Structure;\n calculationResults: any;\n}> {\n await initMoyo();\n\n // -----------------------------\n // 1. Build reversible mapping\n // -----------------------------\n const symbolToId = new Map<string, number>();\n const idToSymbol = new Map<number, string>();\n\n let counter = 0;\n\n const positions: number[][] = [];\n const numbers: number[] = [];\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n idToSymbol.set(counter, symbol);\n counter++;\n }\n\n positions.push(Array.from(site.frac));\n numbers.push(symbolToId.get(symbol)!);\n }\n\n // -----------------------------\n // 2. Build Moyo input\n // -----------------------------\n const moyoInput = {\n lattice: {\n basis: Array.from(structure.lattice.basis.data),\n },\n positions,\n numbers,\n };\n\n // -----------------------------\n // 3. Run symmetry engine\n // -----------------------------\n const results = await analyze_cell(\n JSON.stringify(moyoInput),\n tolerance,\n setting,\n );\n\n // -----------------------------\n // 4. Convert Moyo cell → Structure\n // -----------------------------\n function build(cell: {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n }): Structure {\n const { lattice, positions, numbers } = cell;\n\n const species = [...new Set(numbers)].map((n: number) => ({\n symbol: idToSymbol.get(n)!,\n }));\n\n const sites = positions.map((pos: number[], i: number) => ({\n species: {\n symbol: idToSymbol.get(numbers[i])!,\n },\n frac: new Float64Array(pos),\n }));\n\n return {\n lattice: createLattice(lattice.basis),\n species,\n sites,\n };\n }\n\n // -----------------------------\n // 5. Return both structures\n // -----------------------------\n return {\n primitive: build(results.prim_std_cell),\n conventional: build(results.std_cell),\n calculationResults: results,\n };\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport type { Structure } from \"../structure\";\nimport type { Site } from \"@/core/site/site\";\n\ntype SupercellSize = number | [number, number, number];\n\nexport function supercell(\n structure: Structure,\n size: SupercellSize,\n): Structure {\n const [nx, ny, nz] = typeof size === \"number\" ? [size, size, size] : size;\n\n if (\n nx < 1 ||\n ny < 1 ||\n nz < 1 ||\n !Number.isInteger(nx) ||\n !Number.isInteger(ny) ||\n !Number.isInteger(nz)\n ) {\n throw new Error(\"Supercell dimensions must be positive integers\");\n }\n\n const m = structure.lattice.basis.data;\n\n // row-major scaling\n const newBasis = [\n m[0] * nx,\n m[1] * nx,\n m[2] * nx,\n\n m[3] * ny,\n m[4] * ny,\n m[5] * ny,\n\n m[6] * nz,\n m[7] * nz,\n m[8] * nz,\n ];\n\n const sites: Site[] = [];\n\n for (const site of structure.sites) {\n const [x, y, z] = site.frac;\n\n for (let i = 0; i < nx; i++) {\n for (let j = 0; j < ny; j++) {\n for (let k = 0; k < nz; k++) {\n sites.push({\n species: site.species,\n\n frac: new Float64Array([(x + i) / nx, (y + j) / ny, (z + k) / nz]),\n });\n }\n }\n }\n }\n\n return {\n lattice: createLattice(newBasis),\n sites,\n };\n}\n","import { Species } from \"../species/species\";\n\nexport type SiteProperties = Record<string, any>;\n\nexport type Vec3 = [number, number, number] | Float64Array | number[];\n\nexport type Site<P extends SiteProperties = SiteProperties> = {\n species: Species;\n frac: Vec3;\n properties?: P;\n};\n\nexport function createSite<P extends SiteProperties>(\n species: Species,\n frac: Vec3,\n properties?: P,\n): Site<P> {\n return {\n species,\n frac,\n properties,\n };\n}\n","import { mul } from \"../matrix/operations/mul\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nimport { Site } from \"./site\";\nimport { Lattice } from \"../lattice/lattice\";\nimport { Vector } from \"../matrix/vector\";\n\nexport function cartesian(lattice: Lattice, site: Site): Vector {\n const [x, y, z] = site.frac;\n\n const frac = {\n rows: 3,\n cols: 1,\n data: new Float64Array([x, y, z]),\n };\n\n const basisT = transpose(lattice.basis);\n const result = mul(basisT, frac);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { inverse } from \"../lattice/inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Vector } from \"../matrix/vector\";\nimport { Lattice } from \"../lattice/lattice\";\n\nexport function fractional(lattice: Lattice, cart: Vector): Vector {\n const vec = {\n rows: 3,\n cols: 1,\n data: cart,\n };\n\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const result = mul(invT, vec);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { Lattice } from \"../lattice/lattice\";\nimport { Site } from \"./site\";\nimport { cartesian } from \"./cartesian\";\n\nimport { norm } from \"../matrix/operations/vector/norm\";\n\nexport function distance(lattice: Lattice, a: Site, b: Site): number {\n const dFrac: [number, number, number] = [\n b.frac[0] - a.frac[0],\n b.frac[1] - a.frac[1],\n b.frac[2] - a.frac[2],\n ];\n\n for (let i = 0; i < 3; i++) {\n dFrac[i] -= Math.round(dFrac[i]);\n }\n\n const displaced: Site = {\n species: a.species,\n frac: dFrac,\n };\n\n const dCart = cartesian(lattice, displaced);\n\n return norm(dCart);\n}\n","import { Site, SiteProperties } from \"./site\";\n\nfunction wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n}\n\nexport function wrap<T extends SiteProperties>(site: Site<T>): Site<T> {\n return {\n ...site,\n frac: [\n wrapValue(site.frac[0]),\n wrapValue(site.frac[1]),\n wrapValue(site.frac[2]),\n ],\n };\n}\n","export type Species<P extends Record<string, any> = Record<string, any>> = {\n symbol: string;\n properties?: P;\n};\n\nexport function createSpecies<P extends Record<string, any>>(\n symbol: string,\n properties?: P,\n): Species<P> {\n return { symbol, properties };\n}\n","import { fromParameters } from \"../lattice/create/fromParameters\";\nimport { parameters } from \"../lattice/parameters\";\nimport { Structure } from \"../structure/structure\";\n\nfunction cleanValue(value: string): number {\n // remove uncertainty notation:\n // 5.432(1) -> 5.432\n return Number(value.replace(/\\(.+\\)/, \"\"));\n}\n\nfunction tokenize(line: string): string[] {\n return line.match(/'[^']*'|\"[^\"]*\"|\\S+/g) ?? [];\n}\n\nfunction warnUnsupportedSymmetry(spaceGroup: string) {\n console.warn(\n `Space group \"${spaceGroup}\" detected. ` +\n `Symmetry operations are not currently applied; ` +\n `only asymmetric-unit sites will be parsed.`,\n );\n}\n\n/**\n * Parses a crystal structure from CIF (Crystallographic Information File) format.\n *\n * Extracts lattice parameters, atomic positions, and species information from a CIF file.\n * Assumes the file contains a single crystal structure block.\n *\n * @param text - The CIF file content as a string\n * @returns A Structure object parsed from the CIF data\n * @throws Error if required CIF fields are missing\n *\n * @remarks\n * - Currently reads only the asymmetric unit (symmetry operations are NOT applied)\n * - Warnings are issued if space group symmetry information is detected but not used\n * - Uncertainty values in CIF are stripped (e.g., 5.432(1) → 5.432)\n * - Only the first data block is processed\n * - Supports quoted values and multiple formatting styles\n *\n * @example\n * ```typescript\n * const cifText = `\n * data_structure\n * _cell_length_a 4.05\n * _cell_length_b 4.05\n * _cell_length_c 4.05\n * _cell_angle_alpha 90\n * _cell_angle_beta 90\n * _cell_angle_gamma 90\n * _atom_site_label Al1\n * _atom_site_fract_x 0\n * _atom_site_fract_y 0\n * _atom_site_fract_z 0\n * `;\n * const structure = fromCIF(cifText);\n * ```\n */\nexport function fromCIF(text: string): Structure {\n const lines = text\n .split(\"\\n\")\n .map((x) => x.trim())\n .filter(Boolean);\n\n let a = 0;\n let b = 0;\n let c = 0;\n\n let alpha = 0;\n let beta = 0;\n let gamma = 0;\n\n let spaceGroup = \"P1\";\n\n let atomHeaders: string[] = [];\n const atomRows: string[][] = [];\n\n let inLoop = false;\n let currentHeaders: string[] = [];\n let collectingAtoms = false;\n\n for (const line of lines) {\n if (line.startsWith(\"_symmetry_space_group_name_H-M\")) {\n const tokens = tokenize(line);\n spaceGroup = tokens.at(-1)?.replace(/['\"]/g, \"\") ?? \"P1\";\n } else if (line.startsWith(\"_space_group_name_H-M_alt\")) {\n const tokens = tokenize(line);\n spaceGroup = tokens.at(-1)?.replace(/['\"]/g, \"\") ?? \"P1\";\n } else if (line.startsWith(\"_cell_length_a\")) {\n a = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_b\")) {\n b = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_c\")) {\n c = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_alpha\")) {\n alpha = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_beta\")) {\n beta = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_gamma\")) {\n gamma = cleanValue(tokenize(line)[1]);\n } else if (line === \"loop_\") {\n inLoop = true;\n currentHeaders = [];\n collectingAtoms = false;\n continue;\n }\n\n if (inLoop && line.startsWith(\"_\")) {\n currentHeaders.push(line);\n\n if (line.includes(\"_atom_site_\")) {\n collectingAtoms = true;\n }\n\n continue;\n }\n\n if (inLoop && collectingAtoms) {\n if (atomHeaders.length === 0) {\n atomHeaders = [...currentHeaders];\n }\n\n atomRows.push(tokenize(line));\n }\n }\n\n const isP1 = /^P\\s*1$/i.test(spaceGroup);\n\n if (!isP1) {\n warnUnsupportedSymmetry(spaceGroup);\n }\n\n const lattice = fromParameters(a, b, c, alpha, beta, gamma);\n\n const ix = atomHeaders.findIndex((x) => x.includes(\"fract_x\"));\n\n const iy = atomHeaders.findIndex((x) => x.includes(\"fract_y\"));\n\n const iz = atomHeaders.findIndex((x) => x.includes(\"fract_z\"));\n\n const ispecies = atomHeaders.findIndex((x) => x.includes(\"type_symbol\"));\n\n if (ix < 0 || iy < 0 || iz < 0 || ispecies < 0) {\n throw new Error(\"Missing required atom site columns\");\n }\n\n const sites = atomRows.map((row) => ({\n species: {\n symbol: row[ispecies],\n },\n\n frac: new Float64Array([\n cleanValue(row[ix]),\n cleanValue(row[iy]),\n cleanValue(row[iz]),\n ]),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toCIF(structure: Structure, precision = 6): string {\n const p = parameters(structure.lattice);\n\n const lines: string[] = [];\n\n lines.push(\"data_matsci-parse\");\n lines.push(\"\");\n\n lines.push(\"_symmetry_space_group_name_H-M 'P 1'\");\n lines.push(\"_symmetry_Int_Tables_number 1\");\n\n lines.push(\"\");\n\n lines.push(`_cell_length_a ${p[0].toFixed(precision)}`);\n\n lines.push(`_cell_length_b ${p[1].toFixed(precision)}`);\n\n lines.push(`_cell_length_c ${p[2].toFixed(precision)}`);\n\n lines.push(`_cell_angle_alpha ${p[3].toFixed(precision)}`);\n\n lines.push(`_cell_angle_beta ${p[4].toFixed(precision)}`);\n\n lines.push(`_cell_angle_gamma ${p[5].toFixed(precision)}`);\n\n lines.push(\"\");\n\n lines.push(\"loop_\");\n lines.push(\"_atom_site_label\");\n lines.push(\"_atom_site_type_symbol\");\n lines.push(\"_atom_site_fract_x\");\n lines.push(\"_atom_site_fract_y\");\n lines.push(\"_atom_site_fract_z\");\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n lines.push(\n `${site.species.symbol}${i + 1} ` +\n `${site.species.symbol} ` +\n `${site.frac[0].toFixed(precision)} ` +\n `${site.frac[1].toFixed(precision)} ` +\n `${site.frac[2].toFixed(precision)}`,\n );\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { fractional } from \"../site/fractional\";\n\nimport { cartesian } from \"../site\";\n\nfunction isSelective(line: string): boolean {\n return line.toLowerCase().startsWith(\"selective\");\n}\n\nfunction isCartesian(line: string): boolean {\n const l = line.trim().toLowerCase();\n return l.startsWith(\"c\") || l.startsWith(\"k\");\n}\n\n// TODO: Currently nukes the selective dynamics flag from the input file.\n// It would be good to restore this.\n// TODO: would be good to ensure that the title is also optionally\n// maintained.\n/**\n * Parses a crystal structure from POSCAR (VASP) format.\n *\n * Reads lattice vectors, atomic positions, and species from VASP's POSCAR/CONTCAR format.\n * Supports both Cartesian and fractional coordinates.\n *\n * @param text - The POSCAR file content as a string\n * @returns A Structure object parsed from the POSCAR data\n * @throws Error if required POSCAR fields are missing or malformed\n *\n * @remarks\n * - Line 1: Comment/title line (ignored)\n * - Line 2: Scaling factor\n * - Lines 3-5: Lattice vectors (in Ångströms or scaled units)\n * - Line 6: Element symbols\n * - Line 7: Number of atoms per element\n * - Line 8+: Atomic positions (Cartesian or fractional)\n * - Selective dynamics flags are currently stripped\n * - Structure title is not preserved in the output\n *\n * @example\n * ```typescript\n * const poscarText = `Cubic structure\n * 1.0\n * 4.05 0 0\n * 0 4.05 0\n * 0 0 4.05\n * Al\n * 2\n * Fractional\n * 0 0 0\n * 0.5 0.5 0.5`;\n * const structure = fromPOSCAR(poscarText);\n * ```\n */\nexport function fromPOSCAR(text: string): Structure {\n const lines = text.split(\"\\n\").map((x) => x.trim());\n\n let cursor = 0;\n\n // comment/title\n cursor++;\n\n // scale factor\n const scale = Number(lines[cursor++]);\n\n // lattice vectors (row-major)\n const latticeData: number[] = [];\n\n for (let i = 0; i < 3; i++) {\n const v = lines[cursor++].split(/\\s+/).map(Number);\n\n if (v.length !== 3) {\n throw new Error(\"Invalid POSCAR lattice\");\n }\n\n latticeData.push(v[0] * scale, v[1] * scale, v[2] * scale);\n }\n\n const lattice = createLattice(latticeData);\n\n // VASP5 species names\n const symbols = lines[cursor++].split(/\\s+/);\n\n // atom counts\n const counts = lines[cursor++].split(/\\s+/).map(Number);\n\n if (symbols.length !== counts.length) {\n throw new Error(\"Species/count mismatch\");\n }\n\n // optional selective dynamics\n if (isSelective(lines[cursor])) {\n cursor++;\n }\n\n // direct is true unless cartesian is.\n let direct = true;\n direct = !isCartesian(lines[cursor]);\n\n cursor++;\n\n const sites: Site[] = [];\n\n let speciesIndex = 0;\n let remaining = counts[0];\n\n const latticeInv = !direct ? inverse(lattice) : null;\n\n const totalAtoms = counts.reduce((a, b) => a + b, 0);\n\n for (let i = 0; i < totalAtoms; i++) {\n const tokens = lines[cursor++].split(/\\s+/);\n\n const coords = tokens.slice(0, 3).map(Number);\n\n const frac = direct\n ? new Float64Array(coords)\n : fractional(lattice, new Float64Array(coords));\n\n sites.push({\n species: {\n symbol: symbols[speciesIndex],\n },\n frac,\n });\n\n remaining--;\n\n if (remaining === 0 && speciesIndex < counts.length - 1) {\n speciesIndex++;\n remaining = counts[speciesIndex];\n }\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toPOSCAR(\n structure: Structure,\n options?: {\n title?: string;\n scale?: number;\n direct?: boolean;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n const scale = options?.scale ?? 1.0;\n const direct = options?.direct ?? true;\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(scale));\n\n // lattice\n const m = structure.lattice.basis.data;\n\n lines.push(`${m[0]} ${m[1]} ${m[2]}`);\n lines.push(`${m[3]} ${m[4]} ${m[5]}`);\n lines.push(`${m[6]} ${m[7]} ${m[8]}`);\n\n // preserve order of first appearance\n const grouped = new Map<string, typeof structure.sites>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!grouped.has(symbol)) {\n grouped.set(symbol, []);\n }\n\n grouped.get(symbol)!.push(site);\n }\n\n const species = [...grouped.keys()];\n const sites = [...grouped.values()].flat();\n\n lines.push(species.join(\" \"));\n lines.push(species.map((s) => grouped.get(s)!.length).join(\" \"));\n\n lines.push(direct ? \"Direct\" : \"Cartesian\");\n\n for (const site of sites) {\n const coords = direct ? site.frac : cartesian(structure.lattice, site);\n\n lines.push(`${coords[0]} ${coords[1]} ${coords[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\nexport interface AiiDASite {\n position: [number, number, number];\n kind_name: string[];\n}\n\nexport interface StructureData {\n cell: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ];\n kinds: [];\n sites: AiiDASite[];\n}\n\nexport function fromStructureData(data: StructureData): Structure {\n const lattice = createLattice([\n ...data.cell[0],\n ...data.cell[1],\n ...data.cell[2],\n ]);\n\n const kindMap = new Map(data.kinds.map((kind: any) => [kind.name, kind]));\n\n const sites = data.sites.map((site: any) => {\n const kind = kindMap.get(site.kind_name);\n\n if (!kind) {\n throw new Error(`Unknown kind \"${site.kind_name}\"`);\n }\n\n return {\n species: {\n symbol: kind.symbols[0],\n },\n\n frac: fractional(lattice, new Float64Array(site.position)),\n };\n });\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toStructureData(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const symbols = [...new Set(structure.sites.map((s) => s.species.symbol))];\n\n const kinds = symbols.map((symbol) => ({\n name: symbol,\n symbols: [symbol],\n }));\n\n return {\n cell: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n kinds,\n\n sites: structure.sites.map((site) => ({\n kind_name: site.species.symbol,\n\n position: Array.from(cartesian(structure.lattice, site)),\n })),\n\n pbc1: true,\n pbc2: true,\n pbc3: true,\n };\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { fractional } from \"../site/fractional\";\nimport { cartesian } from \"../site/cartesian\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nfunction findSection(lines: string[], section: string): number {\n const idx = lines.findIndex((line) => line.trim().toUpperCase() === section);\n\n if (idx === -1) {\n throw new Error(`Missing ${section}`);\n }\n\n return idx;\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\n/**\n * Parses a crystal structure from XSF (XCrySDen Structure File) format.\n *\n * Reads lattice vectors and atomic positions from XSF format.\n * Supports both PRIMVEC (primitive) and CONVVEC (conventional) cells.\n *\n * @param text - The XSF file content as a string\n * @returns A Structure object parsed from the XSF data\n * @throws Error if required sections (PRIMVEC, ATOMS) are missing\n *\n * @remarks\n * - XSF format is human-readable and widely used in visualization software\n * - PRIMVEC section defines the lattice vectors\n * - ATOMS section lists atomic positions and species\n * - Atomic numbers are currently not supported (symbols required)\n * - CONVVEC (conventional cell) is not currently used\n *\n * @example\n * ```typescript\n * const xsfText = `\n * PRIMVEC\n * 4.05 0.00 0.00\n * 0.00 4.05 0.00\n * 0.00 0.00 4.05\n * PRIMCOORD\n * 2 1\n * Al 0.00 0.00 0.00 0 0 0\n * Al 2.025 2.025 2.025 0 0 0\n * `;\n * const structure = fromXSF(xsfText);\n * ```\n */\nexport function fromXSF(text: string): Structure {\n const lines = text\n .split(\"\\n\")\n .map((x) => x.trim())\n .filter(Boolean);\n\n const vecStart = findSection(lines, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...lines[vecStart + 1].split(/\\s+/).map(Number),\n ...lines[vecStart + 2].split(/\\s+/).map(Number),\n ...lines[vecStart + 3].split(/\\s+/).map(Number),\n ]);\n\n const coordStart = findSection(lines, \"PRIMCOORD\");\n\n const [nAtoms] = lines[coordStart + 1].split(/\\s+/).map(Number);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = lines[coordStart + 2 + i].split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n const frac = fractional(lattice, new Float64Array([x, y, z]));\n\n sites.push({\n species: { symbol },\n frac,\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n\n lines.push(\"\");\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n lines.push(`${site.species.symbol} ${c[0]} ${c[1]} ${c[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice, Lattice } from \"../lattice/lattice\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\nfunction parseHeader(comment: string): ExtendedXYZInfo {\n const info: ExtendedXYZInfo = {};\n const kvRegex = /(\\w+)=(\".*?\"|\\S+)/g;\n\n for (const match of comment.matchAll(kvRegex)) {\n let value = match[2];\n if (value.startsWith('\"')) value = value.slice(1, -1);\n info[match[1]] = value;\n }\n\n return info;\n}\n\nfunction parseLattice(info: ExtendedXYZInfo) {\n if (!info.Lattice) {\n throw new Error(\"Extended XYZ must contain Lattice\");\n }\n\n const v = info.Lattice.split(/\\s+/).map(Number);\n if (v.length !== 9) throw new Error(\"Invalid Lattice\");\n\n return createLattice([v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]]);\n}\n\n/**\n * Parses a crystal structure from extended XYZ format.\n *\n * Reads atomic structure from XYZ format with extended headers containing\n * lattice information (Extended XYZ format used by ASE and other tools).\n *\n * @param text - The XYZ file content as a string\n * @returns A Structure object parsed from the XYZ data\n * @throws Error if lattice information or required fields are missing\n *\n * @remarks\n * - First line: number of atoms\n * - Second line: properties header in key=value format (must include \"Lattice\")\n * - Remaining lines: atomic species and Cartesian positions\n * - Lattice must be specified in extended header as 9 space-separated values\n * - Standard XYZ format (without lattice) is not supported\n *\n * @example\n * ```typescript\n * const xyzText = `2\n * Lattice=\"4.05 0 0 0 4.05 0 0 0 4.05\" Properties=species:S:1:pos:R:3\n * Al 0.0 0.0 0.0\n * Al 2.025 2.025 2.025`;\n * const structure = fromXYZ(xyzText);\n * ```\n */\nexport function fromXYZ(text: string) {\n const lines = text.trim().split(\"\\n\");\n\n const n = Number(lines[0]);\n const comment = lines[1];\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < n; i++) {\n const [symbol, x, y, z] = lines[2 + i].split(/\\s+/);\n\n sites.push({\n species: { symbol },\n frac: new Float64Array([+x, +y, +z]),\n });\n }\n\n return { lattice, sites };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n // row-major flattening assumption (consistent with your matrix code)\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\n/**\n * Serializes a structure to extended XYZ format.\n *\n * Converts a Structure to extended XYZ format suitable for visualization\n * and exchange with other materials science tools (ASE, OVITO, etc.).\n *\n * @param structure - The structure to serialize\n * @returns The structure as an extended XYZ formatted string\n *\n * @remarks\n * - Line 1: Number of atoms\n * - Line 2: Header with lattice information in extended XYZ format\n * - Remaining lines: Atomic species and fractional coordinates\n * - Lattice is specified as 9 space-separated values in row-major order\n * - The output uses fractional coordinates as given in the structure\n *\n * @example\n * ```typescript\n * const structure = { lattice: cubic(4.05), sites: [...] };\n * const xyzString = toXYZ(structure);\n * // Output can be written to file and opened in visualization software\n * ```\n */\nexport function toXYZ(structure: Structure): string {\n const sites = structure.sites;\n\n const lines: string[] = [];\n\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n lines.push(`Lattice=\"${latticeStr}\"`);\n\n for (const site of sites) {\n const f = site.frac;\n\n lines.push(`${site.species.symbol} ${f[0]} ${f[1]} ${f[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice\";\n\nimport { fractional, cartesian } from \"../site\";\nimport { Structure } from \"../structure\";\n\nexport function fromOptimade(data: any): Structure {\n const lattice = createLattice([\n ...data.attributes.lattice_vectors[0],\n ...data.attributes.lattice_vectors[1],\n ...data.attributes.lattice_vectors[2],\n ]);\n\n const positions = data.attributes.cartesian_site_positions;\n const species = data.attributes.species_at_sites;\n\n const sites = positions.map((position: number[], i: number) => ({\n species: {\n symbol: species[i],\n },\n\n frac: fractional(lattice, new Float64Array(position)),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toOptimade(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const species_at_sites = structure.sites.map((site) => site.species.symbol);\n\n const elements = [...new Set(species_at_sites)].sort();\n\n return {\n attributes: {\n lattice_vectors: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n species_at_sites,\n\n cartesian_site_positions: structure.sites.map((site) =>\n Array.from(cartesian(structure.lattice, site)),\n ),\n\n dimension_types: [1, 1, 1],\n\n nsites: structure.sites.length,\n\n nelements: elements.length,\n\n elements,\n },\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\n/**\n * Serializes a structure to JSON format.\n *\n * Converts a Structure to a plain JavaScript object suitable for JSON stringification.\n *\n * @param structure - The structure to serialize\n * @returns An object with `lattice` (flattened array) and `sites` (with species and fractional coordinates)\n *\n * @remarks\n * - Lattice is serialized as a flat array [a1x, a1y, a1z, ...]\n * - Fractional coordinates are converted from Float64Array to regular arrays\n * - Use with JSON.stringify() for string serialization\n *\n * @example\n * ```typescript\n * const structure = { lattice: cubic(4), sites: [...] };\n * const json = toJSON(structure);\n * const jsonString = JSON.stringify(json);\n * ```\n */\nexport function toJSON(structure: Structure) {\n return {\n lattice: structure.lattice.basis.data,\n sites: structure.sites.map((s) => ({\n species: s.species,\n frac: Array.from(s.frac),\n })),\n };\n}\n\n/**\n * Deserializes a structure from JSON format.\n *\n * Reconstructs a Structure from a JSON object (typically parsed from JSON string).\n *\n * @param data - An object with `lattice` (9-element array) and `sites` array\n * @returns A new Structure object\n *\n * @remarks\n * - Lattice array must have exactly 9 elements\n * - Fractional coordinates are converted to Float64Array\n * - Inverse operation of toJSON()\n * - No validation is performed on the input data\n *\n * @example\n * ```typescript\n * const jsonData = {\n * lattice: [4, 0, 0, 0, 4, 0, 0, 0, 4],\n * sites: [{ species: 'Al', frac: [0, 0, 0] }]\n * };\n * const structure = fromJSON(jsonData);\n * ```\n */\nexport function fromJSON(data: any): Structure {\n return {\n lattice: createLattice(data.lattice),\n sites: data.sites.map((s: any) => ({\n species: s.species,\n frac: new Float64Array(s.frac),\n })),\n };\n}\n","export function convertMeasurement<T extends string>(\n value: number,\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number {\n const resolve = (u: string) => (aliases?.[u] ?? u) as T;\n\n const fromUnit = resolve(from);\n const toUnit = resolve(to);\n\n if (fromUnit === toUnit) return value;\n\n const valueInBase = value * conversions[fromUnit];\n return valueInBase / conversions[toUnit];\n}\n\nexport function convertMeasurementArray<T extends string>(\n arr: number[],\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number[] {\n return arr.map((v) => 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+ {"version":3,"file":"index.js","sources":["../lib/core/structure/operations/canonicalize.ts","../lib/core/structure/operations/hashStructure.ts","../lib/core/structure/operations/sites/appendSite.ts","../lib/core/structure/operations/sites/insertSite.ts","../lib/core/structure/operations/sites/removeSite.ts","../lib/core/structure/operations/sites/replaceSite.ts","../lib/core/matrix/matrix.ts","../lib/core/lattice/lattice.ts","../lib/core/matrix/operations/vector/dot.ts","../lib/core/matrix/operations/vector/norm.ts","../lib/core/lattice/angles.ts","../lib/core/matrix/operations/inverse/inverse3x3.ts","../lib/core/lattice/inverse.ts","../lib/core/lattice/lengths.ts","../lib/core/matrix/operations/transpose.ts","../lib/core/matrix/operations/mul.ts","../lib/core/lattice/metricTensor.ts","../lib/core/lattice/parameters.ts","../lib/core/lattice/reciprocalLattice.ts","../lib/core/lattice/reciprocalLatticeCrystallographic.ts","../lib/core/lattice/create/fromParameters.ts","../lib/core/lattice/create/cubic.ts","../lib/core/lattice/create/hexagonal.ts","../lib/core/lattice/create/monoclinic.ts","../lib/core/lattice/create/orthorhombic.ts","../lib/core/lattice/create/rhombohedral.ts","../lib/core/lattice/create/tetragonal.ts","../lib/core/structure/operations/symmetry/spglib.ts","../lib/core/structure/operations/supercell.ts","../lib/core/matrix/operations/determinant.ts","../lib/core/lattice/volume.ts","../lib/core/structure/properties/volume.ts","../lib/core/structure/properties/formula.ts","../lib/core/data/periodictable/atomicData.ts","../lib/core/structure/properties/cellMass.ts","../lib/core/structure/properties/density.ts","../lib/core/site/site.ts","../lib/core/site/cartesian.ts","../lib/core/site/fractional.ts","../lib/core/site/distance.ts","../lib/core/site/wrap.ts","../lib/core/species/species.ts","../lib/core/io/cif.ts","../lib/core/io/poscar.ts","../lib/core/io/structuredata.ts","../lib/core/io/xsf.ts","../lib/core/io/xyz.ts","../lib/core/io/optimade.ts","../lib/core/io/json.ts","../lib/core/units/converter.ts","../lib/core/units/length.ts","../lib/core/units/energy.ts","../lib/core/units/angle.ts"],"sourcesContent":["import { Structure } from \"../../structure/structure\";\n\nconst EPS = 1e-12;\n\nfunction wrap(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < EPS ? 0 : v;\n}\n\nfunction clean(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function canonicalize(structure: Structure): Structure {\n return {\n ...structure,\n sites: structure.sites.map((site) => ({\n ...site,\n frac: new Float64Array([\n wrap(clean(site.frac[0])),\n wrap(clean(site.frac[1])),\n wrap(clean(site.frac[2])),\n ]),\n })),\n };\n}\n","import { Structure } from \"../structure\";\nimport { canonicalize } from \"./canonicalize\";\nimport { Vec3 } from \"@/main\";\n\nfunction toFixedArray(v: Vec3, precision = 8): string {\n return Array.from(v)\n .map((x) => x.toFixed(precision))\n .join(\",\");\n}\n\nfunction fnv1a(str: string): number {\n let hash = 2166136261;\n\n for (let i = 0; i < str.length; i++) {\n hash ^= str.charCodeAt(i);\n hash *= 16777619;\n }\n\n return hash >>> 0;\n}\n\nexport function hashStructure(structure: Structure): number {\n const s = canonicalize(structure);\n\n const lattice = s.lattice.basis.data;\n const latticeKey = toFixedArray(lattice);\n\n const sitesKey = s.sites\n .map((site) => {\n return site.species + \":\" + toFixedArray(site.frac);\n })\n .sort()\n .join(\"|\");\n\n const key = latticeKey + \"::\" + sitesKey;\n\n return fnv1a(key);\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function appendSite(structure: Structure, site: Site): Structure {\n return {\n ...structure,\n sites: [...structure.sites, site],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function insertSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n return {\n ...structure,\n sites: [\n ...structure.sites.slice(0, index),\n site,\n ...structure.sites.slice(index),\n ],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function removeSite(structure: Structure, index: number): Structure {\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => i !== index),\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\nexport function replaceSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n return {\n ...structure,\n sites: structure.sites.map((s, i) => (i === index ? site : s)),\n };\n}\n","export interface Matrix {\n readonly rows: number;\n readonly cols: number;\n readonly data: Float64Array;\n}\n\nexport function createMatrix(\n rows: number,\n cols: number,\n data?: Iterable<number>,\n): Matrix {\n const size = rows * cols;\n\n const buffer = data ? Float64Array.from(data) : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(`Expected ${size} values, got ${buffer.length}`);\n }\n\n return {\n rows,\n cols,\n data: buffer,\n };\n}\n\nexport function identity(size: number): Matrix {\n const data = new Float64Array(size * size);\n\n for (let i = 0; i < size; i++) {\n data[i * size + i] = 1;\n }\n\n return {\n rows: size,\n cols: size,\n data,\n };\n}\n\nexport function clone(matrix: Matrix): Matrix {\n return {\n rows: matrix.rows,\n cols: matrix.cols,\n data: new Float64Array(matrix.data),\n };\n}\n\nexport function index(cols: number, row: number, col: number): number {\n return row * cols + col;\n}\n","import { createMatrix, Matrix } from \"../matrix/matrix\";\n\nconst EPS = 1e-12;\n\nfunction clean(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function createLattice(data: number[] | Float64Array | Matrix): Lattice {\n const values =\n data instanceof Float64Array ? data : \"data\" in data ? data.data : data;\n\n if (values.length !== 9) {\n throw new Error(\"Lattice requires 9 values (3x3)\");\n }\n\n const cleaned = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n cleaned[i] = clean(values[i]);\n }\n\n return {\n basis: createMatrix(3, 3, cleaned),\n };\n}\n","import { Vector } from \"../../vector\";\n\nexport function dot(a: Vector, b: Vector): number {\n if (a.length !== b.length) {\n throw new Error(\"Dot product requires same-length vectors\");\n }\n\n let sum = 0;\n\n for (let i = 0; i < a.length; i++) {\n sum += a[i] * b[i];\n }\n\n return sum;\n}\n","import { Vector } from \"../../vector\";\n\nconst EPS = 1e-12;\n\nexport function norm(v: Vector): number {\n let sum = 0;\n\n for (let i = 0; i < v.length; i++) {\n const x = v[i];\n sum += x * x;\n }\n\n return Math.sqrt(sum);\n}\n","import { dot } from \"../matrix/operations/vector/dot\";\nimport { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n\nimport { Vector } from \"../matrix/vector\";\n\nfunction angle(u: Vector, v: Vector) {\n const denom = norm(u) * norm(v);\n if (denom === 0) throw new Error(\"Zero-length lattice vector\");\n\n const c = dot(u, v) / denom;\n const clamped = Math.max(-1, Math.min(1, c));\n\n return Math.acos(clamped);\n}\n\nexport function angles(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Vector = new Float64Array([m[0], m[1], m[2]]);\n const b: Vector = new Float64Array([m[3], m[4], m[5]]);\n const c: Vector = new Float64Array([m[6], m[7], m[8]]);\n\n const alpha = angle(b, c);\n const beta = angle(a, c);\n const gamma = angle(a, b);\n\n return [alpha, beta, gamma];\n}\n","import { Matrix, createMatrix } from \"../../matrix\";\n\nexport function inverse3x3(m: Matrix): Matrix {\n if (m.rows !== 3 || m.cols !== 3) {\n throw new Error(\"Expected 3x3 matrix\");\n }\n\n const a00 = m.data[0],\n a01 = m.data[1],\n a02 = m.data[2];\n const a10 = m.data[3],\n a11 = m.data[4],\n a12 = m.data[5];\n const a20 = m.data[6],\n a21 = m.data[7],\n a22 = m.data[8];\n\n const c00 = a11 * a22 - a12 * a21;\n const c01 = a12 * a20 - a10 * a22;\n const c02 = a10 * a21 - a11 * a20;\n\n const c10 = a02 * a21 - a01 * a22;\n const c11 = a00 * a22 - a02 * a20;\n const c12 = a01 * a20 - a00 * a21;\n\n const c20 = a01 * a12 - a02 * a11;\n const c21 = a02 * a10 - a00 * a12;\n const c22 = a00 * a11 - a01 * a10;\n\n const det = a00 * c00 + a01 * c01 + a02 * c02;\n\n if (det === 0) {\n throw new Error(\"Singular matrix\");\n }\n\n const invDet = 1 / det;\n\n const out = createMatrix(3, 3);\n\n out.data[0] = c00 * invDet;\n out.data[1] = c10 * invDet;\n out.data[2] = c20 * invDet;\n\n out.data[3] = c01 * invDet;\n out.data[4] = c11 * invDet;\n out.data[5] = c21 * invDet;\n\n out.data[6] = c02 * invDet;\n out.data[7] = c12 * invDet;\n out.data[8] = c22 * invDet;\n\n return out;\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse3x3 } from \"../matrix/operations/inverse/inverse3x3\";\nimport { Matrix } from \"../matrix/matrix\";\n\nexport function inverse(lattice: Lattice): Matrix {\n return inverse3x3(lattice.basis);\n}\n","import { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\nexport function lengths(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Float64Array = new Float64Array([m[0], m[1], m[2]]);\n const b: Float64Array = new Float64Array([m[3], m[4], m[5]]);\n const c: Float64Array = new Float64Array([m[6], m[7], m[8]]);\n\n return [norm(a), norm(b), norm(c)];\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nexport function transpose(matrix: Matrix): Matrix {\n const out = createMatrix(matrix.cols, matrix.rows);\n\n for (let row = 0; row < matrix.rows; row++) {\n for (let col = 0; col < matrix.cols; col++) {\n out.data[index(out.cols, col, row)] =\n matrix.data[index(matrix.cols, row, col)];\n }\n }\n\n return out;\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nexport function mul(a: Matrix, b: Matrix): Matrix {\n if (a.cols !== b.rows) {\n throw new Error(\"Invalid matrix multiplication dimensions\");\n }\n\n const out = createMatrix(a.rows, b.cols);\n\n const aRows = a.rows;\n const aCols = a.cols;\n const bCols = b.cols;\n\n for (let row = 0; row < aRows; row++) {\n for (let col = 0; col < bCols; col++) {\n let sum = 0;\n\n for (let k = 0; k < aCols; k++) {\n sum += a.data[index(a.cols, row, k)] * b.data[index(b.cols, k, col)];\n }\n\n out.data[index(out.cols, row, col)] = sum;\n }\n }\n\n return out;\n}\n","import { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Lattice } from \"./lattice\";\nimport { Matrix } from \"../matrix/matrix\";\n\nexport function metricTensor(lattice: Lattice): Matrix {\n const A = lattice.basis;\n\n const AT = transpose(A);\n return mul(AT, A);\n}\n","import { lengths } from \"./lengths\";\nimport { angles } from \"./angles\";\nimport { Lattice } from \"./lattice\";\n\nconst RAD2DEG = 180 / Math.PI;\n\nexport function parameters(\n lattice: Lattice,\n): [number, number, number, number, number, number] {\n const [a, b, c] = lengths(lattice);\n const [alpha, beta, gamma] = angles(lattice);\n\n return [a, b, c, alpha * RAD2DEG, beta * RAD2DEG, gamma * RAD2DEG];\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { createLattice } from \"./lattice\";\n\nconst TWO_PI = 2 * Math.PI;\n\nexport function reciprocalLattice(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const data = invT.data.map((v) => v * TWO_PI);\n\n return createLattice(data);\n}\n","import { Lattice, createLattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nexport function reciprocalLatticeCrystallographic(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n return createLattice(invT.data);\n}\n","import { createLattice } from \"../lattice\";\n\nconst DEG2RAD = Math.PI / 180;\nconst EPS = 1e-12;\n\nfunction clean(x: number) {\n return Math.abs(x) < EPS ? 0 : x;\n}\n\nexport function fromParameters(\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n) {\n const alphaR = alpha * DEG2RAD;\n const betaR = beta * DEG2RAD;\n const gammaR = gamma * DEG2RAD;\n\n const cosA = Math.cos(alphaR);\n const cosB = Math.cos(betaR);\n const cosG = Math.cos(gammaR);\n const sinG = Math.sin(gammaR);\n\n // lattice vectors\n const v1 = [a, 0, 0];\n\n const v2 = [b * cosG, b * sinG, 0];\n\n // guard against degenerate gamma\n if (Math.abs(sinG) < EPS) {\n throw new Error(\"Invalid lattice: gamma too close to 0 or 180 degrees\");\n }\n\n const cx = c * cosB;\n\n const cy = (c * (cosA - cosB * cosG)) / sinG;\n\n const czSquared = c * c - cx * cx - cy * cy;\n\n const cz = Math.sqrt(Math.max(0, czSquared));\n\n return createLattice([\n clean(v1[0]),\n clean(v1[1]),\n clean(v1[2]),\n clean(v2[0]),\n clean(v2[1]),\n clean(v2[2]),\n clean(cx),\n clean(cy),\n clean(cz),\n ]);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function cubic(a: number) {\n return fromParameters(a, a, a, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function hexagonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 120);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function monoclinic(a: number, b: number, c: number, beta: number) {\n return fromParameters(a, b, c, 90, beta, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function orthorhombic(a: number, b: number, c: number) {\n return fromParameters(a, b, c, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function rhombohedral(a: number, alpha: number) {\n return fromParameters(a, a, a, alpha, alpha, alpha);\n}\n","import { fromParameters } from \"./fromParameters\";\n\nexport function tetragonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 90);\n}\n","import init, { analyze_cell, type MoyoDataset } from \"@spglib/moyo-wasm\";\n\nimport { createLattice } from \"@/core/lattice\";\nimport { Structure } from \"../../structure\";\n\nlet ready: Promise<void> | null = null;\n\nexport function initMoyo() {\n if (!ready) {\n ready = (async () => {\n // In Node.js (tests), load from filesystem\n if (typeof process !== \"undefined\" && process.versions?.node) {\n try {\n const { readFileSync } = await import(\"fs\");\n const { join } = await import(\"path\");\n const wasmPath = join(\n process.cwd(),\n \"node_modules/@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n );\n const wasmBuffer = readFileSync(wasmPath);\n await init(wasmBuffer);\n } catch (e) {\n console.error(\"Failed to load WASM in Node:\", e);\n throw e;\n }\n } else {\n // In browser, use dynamic import to get the URL\n const wasmUrl = new URL(\n \"@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n import.meta.url,\n ).toString();\n\n await init(wasmUrl);\n }\n })();\n }\n return ready;\n}\n\nexport async function getSymmetry(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Standard\",\n): Promise<{\n primitive: Structure;\n conventional: Structure;\n calculationResults: any;\n}> {\n await initMoyo();\n\n // -----------------------------\n // 1. Build reversible mapping\n // -----------------------------\n const symbolToId = new Map<string, number>();\n const idToSymbol = new Map<number, string>();\n\n let counter = 0;\n\n const positions: number[][] = [];\n const numbers: number[] = [];\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n idToSymbol.set(counter, symbol);\n counter++;\n }\n\n positions.push(Array.from(site.frac));\n numbers.push(symbolToId.get(symbol)!);\n }\n\n // -----------------------------\n // 2. Build Moyo input\n // -----------------------------\n const moyoInput = {\n lattice: {\n basis: Array.from(structure.lattice.basis.data),\n },\n positions,\n numbers,\n };\n\n // -----------------------------\n // 3. Run symmetry engine\n // -----------------------------\n const results = await analyze_cell(\n JSON.stringify(moyoInput),\n tolerance,\n setting,\n );\n\n // -----------------------------\n // 4. Convert Moyo cell → Structure\n // -----------------------------\n function build(cell: {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n }): Structure {\n const { lattice, positions, numbers } = cell;\n\n const species = [...new Set(numbers)].map((n: number) => ({\n symbol: idToSymbol.get(n)!,\n }));\n\n const sites = positions.map((pos: number[], i: number) => ({\n species: {\n symbol: idToSymbol.get(numbers[i])!,\n },\n frac: new Float64Array(pos),\n }));\n\n return {\n lattice: createLattice(lattice.basis),\n species,\n sites,\n };\n }\n\n // -----------------------------\n // 5. Return both structures\n // -----------------------------\n return {\n primitive: build(results.prim_std_cell),\n conventional: build(results.std_cell),\n calculationResults: results,\n };\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport type { Structure } from \"../structure\";\nimport type { Site } from \"@/core/site/site\";\n\ntype SupercellSize = number | [number, number, number];\n\nexport function supercell(\n structure: Structure,\n size: SupercellSize,\n): Structure {\n const [nx, ny, nz] = typeof size === \"number\" ? [size, size, size] : size;\n\n if (\n nx < 1 ||\n ny < 1 ||\n nz < 1 ||\n !Number.isInteger(nx) ||\n !Number.isInteger(ny) ||\n !Number.isInteger(nz)\n ) {\n throw new Error(\"Supercell dimensions must be positive integers\");\n }\n\n const m = structure.lattice.basis.data;\n\n // row-major scaling\n const newBasis = [\n m[0] * nx,\n m[1] * nx,\n m[2] * nx,\n\n m[3] * ny,\n m[4] * ny,\n m[5] * ny,\n\n m[6] * nz,\n m[7] * nz,\n m[8] * nz,\n ];\n\n const sites: Site[] = [];\n\n for (const site of structure.sites) {\n const [x, y, z] = site.frac;\n\n for (let i = 0; i < nx; i++) {\n for (let j = 0; j < ny; j++) {\n for (let k = 0; k < nz; k++) {\n sites.push({\n species: site.species,\n\n frac: new Float64Array([(x + i) / nx, (y + j) / ny, (z + k) / nz]),\n });\n }\n }\n }\n }\n\n return {\n lattice: createLattice(newBasis),\n sites,\n };\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\nfunction minor(matrix: Matrix, skipRow: number, skipCol: number): Matrix {\n const out = createMatrix(matrix.rows - 1, matrix.cols - 1);\n\n let ptr = 0;\n\n for (let row = 0; row < matrix.rows; row++) {\n if (row === skipRow) continue;\n\n for (let col = 0; col < matrix.cols; col++) {\n if (col === skipCol) continue;\n\n out.data[ptr++] = matrix.data[index(matrix.cols, row, col)];\n }\n }\n\n return out;\n}\n\nexport function determinant(matrix: Matrix): number {\n if (matrix.rows !== matrix.cols) {\n throw new Error(\"Determinant requires a square matrix\");\n }\n\n const n = matrix.rows;\n\n // fast path for BZ / geometry\n if (n === 3) {\n const m = matrix.data;\n\n return (\n m[0] * (m[4] * m[8] - m[5] * m[7]) -\n m[1] * (m[3] * m[8] - m[5] * m[6]) +\n m[2] * (m[3] * m[7] - m[4] * m[6])\n );\n }\n\n if (n === 1) {\n return matrix.data[0];\n }\n\n if (n === 2) {\n return matrix.data[0] * matrix.data[3] - matrix.data[1] * matrix.data[2];\n }\n\n let det = 0;\n\n for (let col = 0; col < n; col++) {\n const sign = col % 2 === 0 ? 1 : -1;\n\n det += sign * matrix.data[col] * determinant(minor(matrix, 0, col));\n }\n\n return det;\n}\n","import { determinant } from \"../matrix/operations/determinant\";\nimport { Lattice } from \"./lattice\";\n\nexport function volume(lattice: Lattice): number {\n return Math.abs(determinant(lattice.basis));\n}\n","import { Structure } from \"../structure\";\nimport { volume as latticeVolume } from \"../../lattice/volume\";\n\nexport function volume(structure: Structure): number {\n return latticeVolume(structure.lattice);\n}\n","import { Structure } from \"../structure\";\n\nfunction gcd(a: number, b: number): number {\n while (b !== 0) {\n [a, b] = [b, a % b];\n }\n\n return Math.abs(a);\n}\n\nexport function composition(structure: Structure): Record<string, number> {\n const out: Record<string, number> = {};\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n out[symbol] ??= 0;\n out[symbol]++;\n }\n\n return out;\n}\n\nfunction compositionGCD(comp: Record<string, number>): number {\n const values = Object.values(comp);\n\n return values.reduce((a, b) => gcd(a, b));\n}\n\nfunction hillOrder(elements: string[]): string[] {\n if (!elements.includes(\"C\")) {\n return [...elements].sort();\n }\n\n const rest = elements.filter((e) => e !== \"C\" && e !== \"H\").sort();\n\n return [\"C\", ...(elements.includes(\"H\") ? [\"H\"] : []), ...rest];\n}\n\nfunction formulaFromComposition(\n comp: Record<string, number>,\n ordering: (elements: string[]) => string[],\n): string {\n const elements = ordering(Object.keys(comp));\n\n return elements\n .map((el) => {\n const count = comp[el];\n\n return count === 1 ? el : `${el}${count}`;\n })\n .join(\"\");\n}\n\nfunction reducedComposition(\n comp: Record<string, number>,\n): Record<string, number> {\n const factor = compositionGCD(comp);\n\n const out: Record<string, number> = {};\n\n for (const [element, count] of Object.entries(comp)) {\n out[element] = count / factor;\n }\n\n return out;\n}\n\nexport function hillFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), hillOrder);\n}\n\nexport function reducedFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n );\n}\n","export interface ElementInfo {\n atomicNumber: number;\n symbol: string;\n name: string;\n mass: number;\n [key: string]: unknown;\n}\n\nexport const PeriodicTable: Record<number, ElementInfo> = {\n 1: { atomicNumber: 1, symbol: \"H\", name: \"Hydrogen\", mass: 1.008 },\n 2: { atomicNumber: 2, symbol: \"He\", name: \"Helium\", mass: 4.0026 },\n 3: { atomicNumber: 3, symbol: \"Li\", name: \"Lithium\", mass: 6.94 },\n 4: { atomicNumber: 4, symbol: \"Be\", name: \"Beryllium\", mass: 9.0122 },\n 5: { atomicNumber: 5, symbol: \"B\", name: \"Boron\", mass: 10.81 },\n 6: { atomicNumber: 6, symbol: \"C\", name: \"Carbon\", mass: 12.011 },\n 7: { atomicNumber: 7, symbol: \"N\", name: \"Nitrogen\", mass: 14.007 },\n 8: { atomicNumber: 8, symbol: \"O\", name: \"Oxygen\", mass: 15.999 },\n 9: { atomicNumber: 9, symbol: \"F\", name: \"Fluorine\", mass: 18.998 },\n 10: { atomicNumber: 10, symbol: \"Ne\", name: \"Neon\", mass: 20.18 },\n 11: { atomicNumber: 11, symbol: \"Na\", name: \"Sodium\", mass: 22.99 },\n 12: { atomicNumber: 12, symbol: \"Mg\", name: \"Magnesium\", mass: 24.305 },\n 13: { atomicNumber: 13, symbol: \"Al\", name: \"Aluminum\", mass: 26.982 },\n 14: { atomicNumber: 14, symbol: \"Si\", name: \"Silicon\", mass: 28.085 },\n 15: { atomicNumber: 15, symbol: \"P\", name: \"Phosphorus\", mass: 30.974 },\n 16: { atomicNumber: 16, symbol: \"S\", name: \"Sulfur\", mass: 32.06 },\n 17: { atomicNumber: 17, symbol: \"Cl\", name: \"Chlorine\", mass: 35.45 },\n 18: { atomicNumber: 18, symbol: \"Ar\", name: \"Argon\", mass: 39.948 },\n 19: { atomicNumber: 19, symbol: \"K\", name: \"Potassium\", mass: 39.098 },\n 20: { atomicNumber: 20, symbol: \"Ca\", name: \"Calcium\", mass: 40.078 },\n 21: { atomicNumber: 21, symbol: \"Sc\", name: \"Scandium\", mass: 44.956 },\n 22: { atomicNumber: 22, symbol: \"Ti\", name: \"Titanium\", mass: 47.867 },\n 23: { atomicNumber: 23, symbol: \"V\", name: \"Vanadium\", mass: 50.942 },\n 24: { atomicNumber: 24, symbol: \"Cr\", name: \"Chromium\", mass: 51.996 },\n 25: { atomicNumber: 25, symbol: \"Mn\", name: \"Manganese\", mass: 54.938 },\n 26: { atomicNumber: 26, symbol: \"Fe\", name: \"Iron\", mass: 55.845 },\n 27: { atomicNumber: 27, symbol: \"Co\", name: \"Cobalt\", mass: 58.933 },\n 28: { atomicNumber: 28, symbol: \"Ni\", name: \"Nickel\", mass: 58.693 },\n 29: { atomicNumber: 29, symbol: \"Cu\", name: \"Copper\", mass: 63.546 },\n 30: { atomicNumber: 30, symbol: \"Zn\", name: \"Zinc\", mass: 65.38 },\n 31: { atomicNumber: 31, symbol: \"Ga\", name: \"Gallium\", mass: 69.723 },\n 32: { atomicNumber: 32, symbol: \"Ge\", name: \"Germanium\", mass: 72.63 },\n 33: { atomicNumber: 33, symbol: \"As\", name: \"Arsenic\", mass: 74.922 },\n 34: { atomicNumber: 34, symbol: \"Se\", name: \"Selenium\", mass: 78.971 },\n 35: { atomicNumber: 35, symbol: \"Br\", name: \"Bromine\", mass: 79.904 },\n 36: { atomicNumber: 36, symbol: \"Kr\", name: \"Krypton\", mass: 83.798 },\n 37: { atomicNumber: 37, symbol: \"Rb\", name: \"Rubidium\", mass: 85.468 },\n 38: { atomicNumber: 38, symbol: \"Sr\", name: \"Strontium\", mass: 87.62 },\n 39: { atomicNumber: 39, symbol: \"Y\", name: \"Yttrium\", mass: 88.906 },\n 40: { atomicNumber: 40, symbol: \"Zr\", name: \"Zirconium\", mass: 91.224 },\n 41: { atomicNumber: 41, symbol: \"Nb\", name: \"Niobium\", mass: 92.906 },\n 42: { atomicNumber: 42, symbol: \"Mo\", name: \"Molybdenum\", mass: 95.95 },\n 43: { atomicNumber: 43, symbol: \"Tc\", name: \"Technetium\", mass: 98 },\n 44: { atomicNumber: 44, symbol: \"Ru\", name: \"Ruthenium\", mass: 101.07 },\n 45: { atomicNumber: 45, symbol: \"Rh\", name: \"Rhodium\", mass: 102.91 },\n 46: { atomicNumber: 46, symbol: \"Pd\", name: \"Palladium\", mass: 106.42 },\n 47: { atomicNumber: 47, symbol: \"Ag\", name: \"Silver\", mass: 107.868 },\n 48: { atomicNumber: 48, symbol: \"Cd\", name: \"Cadmium\", mass: 112.414 },\n 49: { atomicNumber: 49, symbol: \"In\", name: \"Indium\", mass: 114.818 },\n 50: { atomicNumber: 50, symbol: \"Sn\", name: \"Tin\", mass: 118.71 },\n 51: { atomicNumber: 51, symbol: \"Sb\", name: \"Antimony\", mass: 121.76 },\n 52: { atomicNumber: 52, symbol: \"Te\", name: \"Tellurium\", mass: 127.6 },\n 53: { atomicNumber: 53, symbol: \"I\", name: \"Iodine\", mass: 126.904 },\n 54: { atomicNumber: 54, symbol: \"Xe\", name: \"Xenon\", mass: 131.293 },\n 55: { atomicNumber: 55, symbol: \"Cs\", name: \"Cesium\", mass: 132.905 },\n 56: { atomicNumber: 56, symbol: \"Ba\", name: \"Barium\", mass: 137.33 },\n 57: { atomicNumber: 57, symbol: \"La\", name: \"Lanthanum\", mass: 138.905 },\n 58: { atomicNumber: 58, symbol: \"Ce\", name: \"Cerium\", mass: 140.12 },\n 59: { atomicNumber: 59, symbol: \"Pr\", name: \"Praseodymium\", mass: 140.91 },\n 60: { atomicNumber: 60, symbol: \"Nd\", name: \"Neodymium\", mass: 144.24 },\n 61: { atomicNumber: 61, symbol: \"Pm\", name: \"Promethium\", mass: 145 },\n 62: { atomicNumber: 62, symbol: \"Sm\", name: \"Samarium\", mass: 150.36 },\n 63: { atomicNumber: 63, symbol: \"Eu\", name: \"Europium\", mass: 151.964 },\n 64: { atomicNumber: 64, symbol: \"Gd\", name: \"Gadolinium\", mass: 157.25 },\n 65: { atomicNumber: 65, symbol: \"Tb\", name: \"Terbium\", mass: 158.93 },\n 66: { atomicNumber: 66, symbol: \"Dy\", name: \"Dysprosium\", mass: 162.5 },\n 67: { atomicNumber: 67, symbol: \"Ho\", name: \"Holmium\", mass: 164.93 },\n 68: { atomicNumber: 68, symbol: \"Er\", name: \"Erbium\", mass: 167.26 },\n 69: { atomicNumber: 69, symbol: \"Tm\", name: \"Thulium\", mass: 168.93 },\n 70: { atomicNumber: 70, symbol: \"Yb\", name: \"Ytterbium\", mass: 173.05 },\n 71: { atomicNumber: 71, symbol: \"Lu\", name: \"Lutetium\", mass: 174.97 },\n 72: { atomicNumber: 72, symbol: \"Hf\", name: \"Hafnium\", mass: 178.49 },\n 73: { atomicNumber: 73, symbol: \"Ta\", name: \"Tantalum\", mass: 180.95 },\n 74: { atomicNumber: 74, symbol: \"W\", name: \"Tungsten\", mass: 183.84 },\n 75: { atomicNumber: 75, symbol: \"Re\", name: \"Rhenium\", mass: 186.207 },\n 76: { atomicNumber: 76, symbol: \"Os\", name: \"Osmium\", mass: 190.23 },\n 77: { atomicNumber: 77, symbol: \"Ir\", name: \"Iridium\", mass: 192.217 },\n 78: { atomicNumber: 78, symbol: \"Pt\", name: \"Platinum\", mass: 195.084 },\n 79: { atomicNumber: 79, symbol: \"Au\", name: \"Gold\", mass: 196.967 },\n 80: { atomicNumber: 80, symbol: \"Hg\", name: \"Mercury\", mass: 200.592 },\n 81: { atomicNumber: 81, symbol: \"Tl\", name: \"Thallium\", mass: 204.38 },\n 82: { atomicNumber: 82, symbol: \"Pb\", name: \"Lead\", mass: 207.2 },\n 83: { atomicNumber: 83, symbol: \"Bi\", name: \"Bismuth\", mass: 208.98 },\n 84: { atomicNumber: 84, symbol: \"Po\", name: \"Polonium\", mass: 209 },\n 85: { atomicNumber: 85, symbol: \"At\", name: \"Astatine\", mass: 210 },\n 86: { atomicNumber: 86, symbol: \"Rn\", name: \"Radon\", mass: 222 },\n 87: { atomicNumber: 87, symbol: \"Fr\", name: \"Francium\", mass: 223 },\n 88: { atomicNumber: 88, symbol: \"Ra\", name: \"Radium\", mass: 226 },\n 89: { atomicNumber: 89, symbol: \"Ac\", name: \"Actinium\", mass: 227 },\n 90: { atomicNumber: 90, symbol: \"Th\", name: \"Thorium\", mass: 232.04 },\n 91: { atomicNumber: 91, symbol: \"Pa\", name: \"Protactinium\", mass: 231.04 },\n 92: { atomicNumber: 92, symbol: \"U\", name: \"Uranium\", mass: 238.03 },\n 93: { atomicNumber: 93, symbol: \"Np\", name: \"Neptunium\", mass: 237 },\n 94: { atomicNumber: 94, symbol: \"Pu\", name: \"Plutonium\", mass: 244 },\n 95: { atomicNumber: 95, symbol: \"Am\", name: \"Americium\", mass: 243 },\n 96: { atomicNumber: 96, symbol: \"Cm\", name: \"Curium\", mass: 247 },\n 97: { atomicNumber: 97, symbol: \"Bk\", name: \"Berkelium\", mass: 247 },\n 98: { atomicNumber: 98, symbol: \"Cf\", name: \"Californium\", mass: 251 },\n 99: { atomicNumber: 99, symbol: \"Es\", name: \"Einsteinium\", mass: 252 },\n 100: { atomicNumber: 100, symbol: \"Fm\", name: \"Fermium\", mass: 257 },\n 101: { atomicNumber: 101, symbol: \"Md\", name: \"Mendelevium\", mass: 258 },\n 102: { atomicNumber: 102, symbol: \"No\", name: \"Nobelium\", mass: 259 },\n 103: { atomicNumber: 103, symbol: \"Lr\", name: \"Lawrencium\", mass: 262 },\n 104: { atomicNumber: 104, symbol: \"Rf\", name: \"Rutherfordium\", mass: 267 },\n 105: { atomicNumber: 105, symbol: \"Db\", name: \"Dubnium\", mass: 270 },\n 106: { atomicNumber: 106, symbol: \"Sg\", name: \"Seaborgium\", mass: 269 },\n 107: { atomicNumber: 107, symbol: \"Bh\", name: \"Bohrium\", mass: 270 },\n 108: { atomicNumber: 108, symbol: \"Hs\", name: \"Hassium\", mass: 277 },\n 109: { atomicNumber: 109, symbol: \"Mt\", name: \"Meitnerium\", mass: 278 },\n 110: { atomicNumber: 110, symbol: \"Ds\", name: \"Darmstadtium\", mass: 281 },\n 111: { atomicNumber: 111, symbol: \"Rg\", name: \"Roentgenium\", mass: 282 },\n 112: { atomicNumber: 112, symbol: \"Cn\", name: \"Copernicium\", mass: 285 },\n 113: { atomicNumber: 113, symbol: \"Nh\", name: \"Nihonium\", mass: 286 },\n 114: { atomicNumber: 114, symbol: \"Fl\", name: \"Flerovium\", mass: 289 },\n 115: { atomicNumber: 115, symbol: \"Mc\", name: \"Moscovium\", mass: 289 },\n 116: { atomicNumber: 116, symbol: \"Lv\", name: \"Livermorium\", mass: 293 },\n 117: { atomicNumber: 117, symbol: \"Ts\", name: \"Tennessine\", mass: 294 },\n 118: { atomicNumber: 118, symbol: \"Og\", name: \"Oganesson\", mass: 294 },\n};\n\nexport const elementBySymbol = Object.values(PeriodicTable).reduce(\n (acc, el) => {\n acc[el.symbol] = el;\n return acc;\n },\n {} as Record<string, ElementInfo>,\n);\n\nexport function getElement(symbol: string): ElementInfo | undefined {\n return elementBySymbol[symbol];\n}\n\n/**\n * Symbol → atomic number lookup (fast + safe)\n */\nexport const SymbolToAtomicNumber = new Map<string, number>(\n Object.values(PeriodicTable).map((el) => [el.symbol, el.atomicNumber]),\n);\n\nexport const AtomicNumberToSymbol = new Map<number, string>(\n Object.values(PeriodicTable).map((el) => [el.atomicNumber, el.symbol]),\n);\n","import { Structure } from \"../structure\";\nimport { Site } from \"../../site/site\";\nimport { getElement } from \"@/core/data/periodictable/atomicData\";\n\nfunction siteMass(site: Site): number {\n const siteMass = site.properties?.mass;\n\n if (typeof siteMass === \"number\") {\n return siteMass;\n }\n\n const speciesMass = site.species.properties?.mass;\n\n if (typeof speciesMass === \"number\") {\n return speciesMass;\n }\n\n const element = getElement(site.species.symbol);\n\n if (!element) {\n throw new Error(`Unknown element: ${site.species.symbol}`);\n }\n\n return element.mass;\n}\n\nexport function cellMass(structure: Structure): number {\n let mass = 0;\n\n for (const site of structure.sites) {\n mass += siteMass(site);\n }\n\n return mass;\n}\n","import { Structure } from \"../structure\";\nimport { volume } from \"./volume\";\nimport { cellMass } from \"./cellMass\";\n\n// in units amu / Ang^3'd\nexport function density(structure: Structure): number {\n return cellMass(structure) / volume(structure);\n}\n","import { Species } from \"../species/species\";\n\nexport type SiteProperties = Record<string, any>;\n\nexport type Vec3 = [number, number, number] | Float64Array | number[];\n\nexport type Site<P extends SiteProperties = SiteProperties> = {\n species: Species;\n frac: Vec3;\n properties?: P;\n};\n\nexport function createSite<P extends SiteProperties>(\n species: Species,\n frac: Vec3,\n properties?: P,\n): Site<P> {\n return {\n species,\n frac,\n properties,\n };\n}\n","import { mul } from \"../matrix/operations/mul\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nimport { Site } from \"./site\";\nimport { Lattice } from \"../lattice/lattice\";\nimport { Vector } from \"../matrix/vector\";\n\nexport function cartesian(lattice: Lattice, site: Site): Vector {\n const [x, y, z] = site.frac;\n\n const frac = {\n rows: 3,\n cols: 1,\n data: new Float64Array([x, y, z]),\n };\n\n const basisT = transpose(lattice.basis);\n const result = mul(basisT, frac);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { inverse } from \"../lattice/inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Vector } from \"../matrix/vector\";\nimport { Lattice } from \"../lattice/lattice\";\n\nexport function fractional(lattice: Lattice, cart: Vector): Vector {\n const vec = {\n rows: 3,\n cols: 1,\n data: cart,\n };\n\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const result = mul(invT, vec);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { Lattice } from \"../lattice/lattice\";\nimport { Site } from \"./site\";\nimport { cartesian } from \"./cartesian\";\n\nimport { norm } from \"../matrix/operations/vector/norm\";\n\nexport function distance(lattice: Lattice, a: Site, b: Site): number {\n const dFrac: [number, number, number] = [\n b.frac[0] - a.frac[0],\n b.frac[1] - a.frac[1],\n b.frac[2] - a.frac[2],\n ];\n\n for (let i = 0; i < 3; i++) {\n dFrac[i] -= Math.round(dFrac[i]);\n }\n\n const displaced: Site = {\n species: a.species,\n frac: dFrac,\n };\n\n const dCart = cartesian(lattice, displaced);\n\n return norm(dCart);\n}\n","import { Site, SiteProperties } from \"./site\";\n\nfunction wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n}\n\nexport function wrap<T extends SiteProperties>(site: Site<T>): Site<T> {\n return {\n ...site,\n frac: [\n wrapValue(site.frac[0]),\n wrapValue(site.frac[1]),\n wrapValue(site.frac[2]),\n ],\n };\n}\n","export type Species<P extends Record<string, any> = Record<string, any>> = {\n symbol: string;\n properties?: P;\n};\n\nexport function createSpecies<P extends Record<string, any>>(\n symbol: string,\n properties?: P,\n): Species<P> {\n return { symbol, properties };\n}\n","import { fromParameters } from \"../lattice/create/fromParameters\";\nimport { parameters } from \"../lattice/parameters\";\nimport { Structure } from \"../structure/structure\";\n\nfunction cleanValue(value: string): number {\n // remove uncertainty notation:\n // 5.432(1) -> 5.432\n return Number(value.replace(/\\(.+\\)/, \"\"));\n}\n\nfunction tokenize(line: string): string[] {\n return line.match(/'[^']*'|\"[^\"]*\"|\\S+/g) ?? [];\n}\n\nfunction warnUnsupportedSymmetry(spaceGroup: string) {\n console.warn(\n `Space group \"${spaceGroup}\" detected. ` +\n `Symmetry operations are not currently applied; ` +\n `only asymmetric-unit sites will be parsed.`,\n );\n}\n\nexport function fromCIF(text: string): Structure {\n const lines = text\n .split(\"\\n\")\n .map((x) => x.trim())\n .filter(Boolean);\n\n let a = 0;\n let b = 0;\n let c = 0;\n\n let alpha = 0;\n let beta = 0;\n let gamma = 0;\n\n let spaceGroup = \"P1\";\n\n let atomHeaders: string[] = [];\n const atomRows: string[][] = [];\n\n let inLoop = false;\n let currentHeaders: string[] = [];\n let collectingAtoms = false;\n\n for (const line of lines) {\n if (line.startsWith(\"_symmetry_space_group_name_H-M\")) {\n const tokens = tokenize(line);\n spaceGroup = tokens.at(-1)?.replace(/['\"]/g, \"\") ?? \"P1\";\n } else if (line.startsWith(\"_space_group_name_H-M_alt\")) {\n const tokens = tokenize(line);\n spaceGroup = tokens.at(-1)?.replace(/['\"]/g, \"\") ?? \"P1\";\n } else if (line.startsWith(\"_cell_length_a\")) {\n a = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_b\")) {\n b = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_c\")) {\n c = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_alpha\")) {\n alpha = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_beta\")) {\n beta = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_gamma\")) {\n gamma = cleanValue(tokenize(line)[1]);\n } else if (line === \"loop_\") {\n inLoop = true;\n currentHeaders = [];\n collectingAtoms = false;\n continue;\n }\n\n if (inLoop && line.startsWith(\"_\")) {\n currentHeaders.push(line);\n\n if (line.includes(\"_atom_site_\")) {\n collectingAtoms = true;\n }\n\n continue;\n }\n\n if (inLoop && collectingAtoms) {\n if (atomHeaders.length === 0) {\n atomHeaders = [...currentHeaders];\n }\n\n atomRows.push(tokenize(line));\n }\n }\n\n const isP1 = /^P\\s*1$/i.test(spaceGroup);\n\n if (!isP1) {\n warnUnsupportedSymmetry(spaceGroup);\n }\n\n const lattice = fromParameters(a, b, c, alpha, beta, gamma);\n\n const ix = atomHeaders.findIndex((x) => x.includes(\"fract_x\"));\n\n const iy = atomHeaders.findIndex((x) => x.includes(\"fract_y\"));\n\n const iz = atomHeaders.findIndex((x) => x.includes(\"fract_z\"));\n\n const ispecies = atomHeaders.findIndex((x) => x.includes(\"type_symbol\"));\n\n if (ix < 0 || iy < 0 || iz < 0 || ispecies < 0) {\n throw new Error(\"Missing required atom site columns\");\n }\n\n const sites = atomRows.map((row) => ({\n species: {\n symbol: row[ispecies],\n },\n\n frac: new Float64Array([\n cleanValue(row[ix]),\n cleanValue(row[iy]),\n cleanValue(row[iz]),\n ]),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toCIF(structure: Structure, precision = 6): string {\n const p = parameters(structure.lattice);\n\n const lines: string[] = [];\n\n lines.push(\"data_matsci-parse\");\n lines.push(\"\");\n\n lines.push(\"_symmetry_space_group_name_H-M 'P 1'\");\n lines.push(\"_symmetry_Int_Tables_number 1\");\n\n lines.push(\"\");\n\n lines.push(`_cell_length_a ${p[0].toFixed(precision)}`);\n\n lines.push(`_cell_length_b ${p[1].toFixed(precision)}`);\n\n lines.push(`_cell_length_c ${p[2].toFixed(precision)}`);\n\n lines.push(`_cell_angle_alpha ${p[3].toFixed(precision)}`);\n\n lines.push(`_cell_angle_beta ${p[4].toFixed(precision)}`);\n\n lines.push(`_cell_angle_gamma ${p[5].toFixed(precision)}`);\n\n lines.push(\"\");\n\n lines.push(\"loop_\");\n lines.push(\"_atom_site_label\");\n lines.push(\"_atom_site_type_symbol\");\n lines.push(\"_atom_site_fract_x\");\n lines.push(\"_atom_site_fract_y\");\n lines.push(\"_atom_site_fract_z\");\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n lines.push(\n `${site.species.symbol}${i + 1} ` +\n `${site.species.symbol} ` +\n `${site.frac[0].toFixed(precision)} ` +\n `${site.frac[1].toFixed(precision)} ` +\n `${site.frac[2].toFixed(precision)}`,\n );\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { fractional } from \"../site/fractional\";\n\nimport { cartesian } from \"../site\";\n\nfunction isSelective(line: string): boolean {\n return line.toLowerCase().startsWith(\"selective\");\n}\n\nfunction isCartesian(line: string): boolean {\n const l = line.trim().toLowerCase();\n return l.startsWith(\"c\") || l.startsWith(\"k\");\n}\n\n// TODO: Currently nukes the selective dynamics flag from the input file.\n// It would be good to restore this.\n// TODO: would be good to ensure that the title is also optionally\n// maintained.\n/**\n * Parses a crystal structure from POSCAR (VASP) format.\n *\n * Reads lattice vectors, atomic positions, and species from VASP's POSCAR/CONTCAR format.\n * Supports both Cartesian and fractional coordinates.\n *\n * @param text - The POSCAR file content as a string\n * @returns A Structure object parsed from the POSCAR data\n * @throws Error if required POSCAR fields are missing or malformed\n *\n * @remarks\n * - Line 1: Comment/title line (ignored)\n * - Line 2: Scaling factor\n * - Lines 3-5: Lattice vectors (in Ångströms or scaled units)\n * - Line 6: Element symbols\n * - Line 7: Number of atoms per element\n * - Line 8+: Atomic positions (Cartesian or fractional)\n * - Selective dynamics flags are currently stripped\n * - Structure title is not preserved in the output\n *\n * @example\n * ```typescript\n * const poscarText = `Cubic structure\n * 1.0\n * 4.05 0 0\n * 0 4.05 0\n * 0 0 4.05\n * Al\n * 2\n * Fractional\n * 0 0 0\n * 0.5 0.5 0.5`;\n * const structure = fromPOSCAR(poscarText);\n * ```\n */\nexport function fromPOSCAR(text: string): Structure {\n const lines = text.split(\"\\n\").map((x) => x.trim());\n\n let cursor = 0;\n\n // comment/title\n cursor++;\n\n // scale factor\n const scale = Number(lines[cursor++]);\n\n // lattice vectors (row-major)\n const latticeData: number[] = [];\n\n for (let i = 0; i < 3; i++) {\n const v = lines[cursor++].split(/\\s+/).map(Number);\n\n if (v.length !== 3) {\n throw new Error(\"Invalid POSCAR lattice\");\n }\n\n latticeData.push(v[0] * scale, v[1] * scale, v[2] * scale);\n }\n\n const lattice = createLattice(latticeData);\n\n // VASP5 species names\n const symbols = lines[cursor++].split(/\\s+/);\n\n // atom counts\n const counts = lines[cursor++].split(/\\s+/).map(Number);\n\n if (symbols.length !== counts.length) {\n throw new Error(\"Species/count mismatch\");\n }\n\n // optional selective dynamics\n if (isSelective(lines[cursor])) {\n cursor++;\n }\n\n // direct is true unless cartesian is.\n let direct = true;\n direct = !isCartesian(lines[cursor]);\n\n cursor++;\n\n const sites: Site[] = [];\n\n let speciesIndex = 0;\n let remaining = counts[0];\n\n const latticeInv = !direct ? inverse(lattice) : null;\n\n const totalAtoms = counts.reduce((a, b) => a + b, 0);\n\n for (let i = 0; i < totalAtoms; i++) {\n const tokens = lines[cursor++].split(/\\s+/);\n\n const coords = tokens.slice(0, 3).map(Number);\n\n const frac = direct\n ? new Float64Array(coords)\n : fractional(lattice, new Float64Array(coords));\n\n sites.push({\n species: {\n symbol: symbols[speciesIndex],\n },\n frac,\n });\n\n remaining--;\n\n if (remaining === 0 && speciesIndex < counts.length - 1) {\n speciesIndex++;\n remaining = counts[speciesIndex];\n }\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toPOSCAR(\n structure: Structure,\n options?: {\n title?: string;\n scale?: number;\n direct?: boolean;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n const scale = options?.scale ?? 1.0;\n const direct = options?.direct ?? true;\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(scale));\n\n // lattice\n const m = structure.lattice.basis.data;\n\n lines.push(`${m[0]} ${m[1]} ${m[2]}`);\n lines.push(`${m[3]} ${m[4]} ${m[5]}`);\n lines.push(`${m[6]} ${m[7]} ${m[8]}`);\n\n // preserve order of first appearance\n const grouped = new Map<string, typeof structure.sites>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!grouped.has(symbol)) {\n grouped.set(symbol, []);\n }\n\n grouped.get(symbol)!.push(site);\n }\n\n const species = [...grouped.keys()];\n const sites = [...grouped.values()].flat();\n\n lines.push(species.join(\" \"));\n lines.push(species.map((s) => grouped.get(s)!.length).join(\" \"));\n\n lines.push(direct ? \"Direct\" : \"Cartesian\");\n\n for (const site of sites) {\n const coords = direct ? site.frac : cartesian(structure.lattice, site);\n\n lines.push(`${coords[0]} ${coords[1]} ${coords[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\nexport interface AiiDASite {\n position: [number, number, number];\n kind_name: string[];\n}\n\nexport interface StructureData {\n cell: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ];\n kinds: [];\n sites: AiiDASite[];\n}\n\nexport function fromStructureData(data: StructureData): Structure {\n const lattice = createLattice([\n ...data.cell[0],\n ...data.cell[1],\n ...data.cell[2],\n ]);\n\n const kindMap = new Map(data.kinds.map((kind: any) => [kind.name, kind]));\n\n const sites = data.sites.map((site: any) => {\n const kind = kindMap.get(site.kind_name);\n\n if (!kind) {\n throw new Error(`Unknown kind \"${site.kind_name}\"`);\n }\n\n return {\n species: {\n symbol: kind.symbols[0],\n },\n\n frac: fractional(lattice, new Float64Array(site.position)),\n };\n });\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toStructureData(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const symbols = [...new Set(structure.sites.map((s) => s.species.symbol))];\n\n const kinds = symbols.map((symbol) => ({\n name: symbol,\n symbols: [symbol],\n }));\n\n return {\n cell: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n kinds,\n\n sites: structure.sites.map((site) => ({\n kind_name: site.species.symbol,\n\n position: Array.from(cartesian(structure.lattice, site)),\n })),\n\n pbc1: true,\n pbc2: true,\n pbc3: true,\n };\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { fractional } from \"../site/fractional\";\nimport { cartesian } from \"../site/cartesian\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nfunction findSection(lines: string[], section: string): number {\n const idx = lines.findIndex((line) => line.trim().toUpperCase() === section);\n\n if (idx === -1) {\n throw new Error(`Missing ${section}`);\n }\n\n return idx;\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\n/**\n * Parses a crystal structure from XSF (XCrySDen Structure File) format.\n *\n * Reads lattice vectors and atomic positions from XSF format.\n * Supports both PRIMVEC (primitive) and CONVVEC (conventional) cells.\n *\n * @param text - The XSF file content as a string\n * @returns A Structure object parsed from the XSF data\n * @throws Error if required sections (PRIMVEC, ATOMS) are missing\n *\n * @remarks\n * - XSF format is human-readable and widely used in visualization software\n * - PRIMVEC section defines the lattice vectors\n * - ATOMS section lists atomic positions and species\n * - Atomic numbers are currently not supported (symbols required)\n * - CONVVEC (conventional cell) is not currently used\n *\n * @example\n * ```typescript\n * const xsfText = `\n * PRIMVEC\n * 4.05 0.00 0.00\n * 0.00 4.05 0.00\n * 0.00 0.00 4.05\n * PRIMCOORD\n * 2 1\n * Al 0.00 0.00 0.00 0 0 0\n * Al 2.025 2.025 2.025 0 0 0\n * `;\n * const structure = fromXSF(xsfText);\n * ```\n */\nexport function fromXSF(text: string): Structure {\n const lines = text\n .split(\"\\n\")\n .map((x) => x.trim())\n .filter(Boolean);\n\n const vecStart = findSection(lines, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...lines[vecStart + 1].split(/\\s+/).map(Number),\n ...lines[vecStart + 2].split(/\\s+/).map(Number),\n ...lines[vecStart + 3].split(/\\s+/).map(Number),\n ]);\n\n const coordStart = findSection(lines, \"PRIMCOORD\");\n\n const [nAtoms] = lines[coordStart + 1].split(/\\s+/).map(Number);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = lines[coordStart + 2 + i].split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n const frac = fractional(lattice, new Float64Array([x, y, z]));\n\n sites.push({\n species: { symbol },\n frac,\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n\n lines.push(\"\");\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n lines.push(`${site.species.symbol} ${c[0]} ${c[1]} ${c[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice, Lattice } from \"../lattice/lattice\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\nfunction parseHeader(comment: string): ExtendedXYZInfo {\n const info: ExtendedXYZInfo = {};\n const kvRegex = /(\\w+)=(\".*?\"|\\S+)/g;\n\n for (const match of comment.matchAll(kvRegex)) {\n let value = match[2];\n if (value.startsWith('\"')) value = value.slice(1, -1);\n info[match[1]] = value;\n }\n\n return info;\n}\n\nfunction parseLattice(info: ExtendedXYZInfo) {\n if (!info.Lattice) {\n throw new Error(\"Extended XYZ must contain Lattice\");\n }\n\n const v = info.Lattice.split(/\\s+/).map(Number);\n if (v.length !== 9) throw new Error(\"Invalid Lattice\");\n\n return createLattice([v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]]);\n}\n\n/**\n * Parses a crystal structure from extended XYZ format.\n *\n * Reads atomic structure from XYZ format with extended headers containing\n * lattice information (Extended XYZ format used by ASE and other tools).\n *\n * @param text - The XYZ file content as a string\n * @returns A Structure object parsed from the XYZ data\n * @throws Error if lattice information or required fields are missing\n *\n * @remarks\n * - First line: number of atoms\n * - Second line: properties header in key=value format (must include \"Lattice\")\n * - Remaining lines: atomic species and Cartesian positions\n * - Lattice must be specified in extended header as 9 space-separated values\n * - Standard XYZ format (without lattice) is not supported\n *\n * @example\n * ```typescript\n * const xyzText = `2\n * Lattice=\"4.05 0 0 0 4.05 0 0 0 4.05\" Properties=species:S:1:pos:R:3\n * Al 0.0 0.0 0.0\n * Al 2.025 2.025 2.025`;\n * const structure = fromXYZ(xyzText);\n * ```\n */\nexport function fromXYZ(text: string) {\n const lines = text.trim().split(\"\\n\");\n\n const n = Number(lines[0]);\n const comment = lines[1];\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < n; i++) {\n const [symbol, x, y, z] = lines[2 + i].split(/\\s+/);\n\n sites.push({\n species: { symbol },\n frac: new Float64Array([+x, +y, +z]),\n });\n }\n\n return { lattice, sites };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n // row-major flattening assumption (consistent with your matrix code)\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\n/**\n * Serializes a structure to extended XYZ format.\n *\n * Converts a Structure to extended XYZ format suitable for visualization\n * and exchange with other materials science tools (ASE, OVITO, etc.).\n *\n * @param structure - The structure to serialize\n * @returns The structure as an extended XYZ formatted string\n *\n * @remarks\n * - Line 1: Number of atoms\n * - Line 2: Header with lattice information in extended XYZ format\n * - Remaining lines: Atomic species and fractional coordinates\n * - Lattice is specified as 9 space-separated values in row-major order\n * - The output uses fractional coordinates as given in the structure\n *\n * @example\n * ```typescript\n * const structure = { lattice: cubic(4.05), sites: [...] };\n * const xyzString = toXYZ(structure);\n * // Output can be written to file and opened in visualization software\n * ```\n */\nexport function toXYZ(structure: Structure): string {\n const sites = structure.sites;\n\n const lines: string[] = [];\n\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n lines.push(`Lattice=\"${latticeStr}\"`);\n\n for (const site of sites) {\n const f = site.frac;\n\n lines.push(`${site.species.symbol} ${f[0]} ${f[1]} ${f[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice\";\n\nimport { fractional, cartesian } from \"../site\";\nimport { Structure } from \"../structure\";\n\nexport function fromOptimade(data: any): Structure {\n const lattice = createLattice([\n ...data.attributes.lattice_vectors[0],\n ...data.attributes.lattice_vectors[1],\n ...data.attributes.lattice_vectors[2],\n ]);\n\n const positions = data.attributes.cartesian_site_positions;\n const species = data.attributes.species_at_sites;\n\n const sites = positions.map((position: number[], i: number) => ({\n species: {\n symbol: species[i],\n },\n\n frac: fractional(lattice, new Float64Array(position)),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toOptimade(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const species_at_sites = structure.sites.map((site) => site.species.symbol);\n\n const elements = [...new Set(species_at_sites)].sort();\n\n return {\n attributes: {\n lattice_vectors: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n species_at_sites,\n\n cartesian_site_positions: structure.sites.map((site) =>\n Array.from(cartesian(structure.lattice, site)),\n ),\n\n dimension_types: [1, 1, 1],\n\n nsites: structure.sites.length,\n\n nelements: elements.length,\n\n elements,\n },\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\n/**\n * Serializes a structure to JSON format.\n *\n * Converts a Structure to a plain JavaScript object suitable for JSON stringification.\n *\n * @param structure - The structure to serialize\n * @returns An object with `lattice` (flattened array) and `sites` (with species and fractional coordinates)\n *\n * @remarks\n * - Lattice is serialized as a flat array [a1x, a1y, a1z, ...]\n * - Fractional coordinates are converted from Float64Array to regular arrays\n * - Use with JSON.stringify() for string serialization\n *\n * @example\n * ```typescript\n * const structure = { lattice: cubic(4), sites: [...] };\n * const json = toJSON(structure);\n * const jsonString = JSON.stringify(json);\n * ```\n */\nexport function toJSON(structure: Structure) {\n return {\n lattice: structure.lattice.basis.data,\n sites: structure.sites.map((s) => ({\n species: s.species,\n frac: Array.from(s.frac),\n })),\n };\n}\n\n/**\n * Deserializes a structure from JSON format.\n *\n * Reconstructs a Structure from a JSON object (typically parsed from JSON string).\n *\n * @param data - An object with `lattice` (9-element array) and `sites` array\n * @returns A new Structure object\n *\n * @remarks\n * - Lattice array must have exactly 9 elements\n * - Fractional coordinates are converted to Float64Array\n * - Inverse operation of toJSON()\n * - No validation is performed on the input data\n *\n * @example\n * ```typescript\n * const jsonData = {\n * lattice: [4, 0, 0, 0, 4, 0, 0, 0, 4],\n * sites: [{ species: 'Al', frac: [0, 0, 0] }]\n * };\n * const structure = fromJSON(jsonData);\n * ```\n */\nexport function fromJSON(data: any): Structure {\n return {\n lattice: createLattice(data.lattice),\n sites: data.sites.map((s: any) => ({\n species: s.species,\n frac: new Float64Array(s.frac),\n })),\n };\n}\n","export function convertMeasurement<T extends string>(\n value: number,\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number {\n const resolve = (u: string) => (aliases?.[u] ?? u) as T;\n\n const fromUnit = resolve(from);\n const toUnit = resolve(to);\n\n if (fromUnit === toUnit) return value;\n\n const valueInBase = value * conversions[fromUnit];\n return valueInBase / conversions[toUnit];\n}\n\nexport function convertMeasurementArray<T extends string>(\n arr: number[],\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number[] {\n return arr.map((v) => convertMeasurement(v, from, to, conversions, aliases));\n}\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\nexport type LengthUnits =\n | \"angstrom\"\n | \"bohr\"\n | \"nm\"\n | \"pm\"\n | \"cm\"\n | \"m\"\n | \"um\"\n | \"fm\";\n\nconst LengthConversions: Record<LengthUnits, number> = {\n angstrom: 1,\n bohr: 0.529177,\n nm: 10,\n pm: 0.01,\n um: 1e4,\n cm: 1e8,\n m: 1e10,\n fm: 1e-5,\n};\n\nconst LengthAliases: Record<string, LengthUnits> = {\n Å: \"angstrom\",\n μm: \"um\",\n};\n\nexport const LengthUnitSystem = {\n conversions: LengthConversions,\n aliases: LengthAliases,\n\n convert(value: number, from: LengthUnits | string, to: LengthUnits | string) {\n return convertMeasurement(\n value,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: LengthUnits | string,\n to: LengthUnits | string,\n ) {\n return convertMeasurementArray(\n arr,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n};\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\nexport type EnergyUnits = \"eV\" | \"Hartree\" | \"kJ/mol\" | \"kcal/mol\";\n\nconst EnergyConversions: Record<EnergyUnits, number> = {\n eV: 1,\n Hartree: 27.2114,\n \"kJ/mol\": 0.0103643,\n \"kcal/mol\": 0.0433641,\n};\n\nconst EnergyAliases: Record<string, EnergyUnits> = {\n Ha: \"Hartree\",\n ev: \"eV\",\n electronvolt: \"eV\",\n};\n\nexport const EnergyUnitSystem = {\n conversions: EnergyConversions,\n aliases: EnergyAliases,\n\n convert(value: number, from: EnergyUnits | string, to: EnergyUnits | string) {\n return convertMeasurement(\n value,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: EnergyUnits | string,\n to: EnergyUnits | string,\n ) {\n return convertMeasurementArray(\n arr,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n};\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\nexport type AngleUnits = \"rad\" | \"deg\" | \"grad\";\n\nconst AngleConversions: Record<AngleUnits, number> = {\n rad: 1,\n deg: Math.PI / 180,\n grad: Math.PI / 200,\n};\n\nconst AngleAliases: Record<string, AngleUnits> = {\n \"°\": \"deg\",\n deg: \"deg\",\n rad: \"rad\",\n gon: \"grad\",\n};\n\nexport const AngleUnitSystem = {\n conversions: AngleConversions,\n aliases: AngleAliases,\n\n convert(value: number, from: AngleUnits | string, to: AngleUnits | string) {\n return convertMeasurement(\n value,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: AngleUnits | string,\n to: AngleUnits | string,\n ) {\n return convertMeasurementArray(\n arr,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n 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