matsci-parse 0.9.0 → 0.12.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. package/README.md +30 -37
  2. package/dist/index.js +9054 -1083
  3. package/dist/index.js.map +1 -1
  4. package/dist/stats.html +1 -1
  5. package/package.json +9 -4
  6. package/dist/__vite-browser-external-DYxpcVy9.js +0 -5
  7. package/dist/__vite-browser-external-DYxpcVy9.js.map +0 -1
package/dist/index.js.map CHANGED
@@ -1 +1 @@
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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/matrix/operations/determinant.ts","../lib/core/structure/operations/symmetry/brilliounzone/generateBZVertices.ts","../lib/core/structure/operations/supercell.ts","../lib/core/structure/operations/distance/utils.ts","../lib/core/structure/operations/distance/getDisplacement.ts","../lib/core/structure/operations/distance/getDistance.ts","../lib/core/structure/operations/distance/getDistances.ts","../lib/core/structure/operations/distance/getDistancesMatrix.ts","../lib/core/structure/operations/query/findSites.ts","../lib/core/structure/operations/query/findSitesBySpecies.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/volumetric/volumetric.ts","../lib/core/volumetric/create/fill.ts","../lib/core/volumetric/create/fromFunction.ts","../lib/core/volumetric/create/fromMatrixSlices.ts","../lib/core/volumetric/create/ones.ts","../lib/core/volumetric/create/zeros.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/units/converter.ts","../lib/core/units/length.ts","../lib/core/io/gro.ts","../lib/core/io/pdb.ts","../lib/core/io/pw.ts","../lib/core/io/json.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 const sites = structure.sites.slice();\n sites.push(site);\n\n return {\n ...structure,\n sites,\n };\n}\n\nexport function appendSites(\n structure: Structure,\n sitesToAppend: readonly Site[],\n): Structure {\n return {\n ...structure,\n sites: [...structure.sites, ...sitesToAppend],\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 const oldSites = structure.sites;\n const sites = new Array(oldSites.length + 1);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n sites[index] = site;\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + 1] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n\nexport function insertSites(\n structure: Structure,\n index: number,\n sitesToInsert: readonly Site[],\n): Structure {\n const oldSites = structure.sites;\n const n = sitesToInsert.length;\n\n const sites = new Array(oldSites.length + n);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n for (let i = 0; i < n; i++) {\n sites[index + i] = sitesToInsert[i];\n }\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + n] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Structure } from \"../../structure\";\n\nexport function removeSite(structure: Structure, index: number): Structure {\n const sites = structure.sites.slice();\n sites.splice(index, 1);\n\n return {\n ...structure,\n sites,\n };\n}\n\nexport function removeSites(\n structure: Structure,\n indices: readonly number[],\n): Structure {\n const remove = new Set(indices);\n\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => !remove.has(i)),\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 const sites = structure.sites.slice();\n sites[index] = site;\n\n return {\n ...structure,\n sites,\n };\n}\n\nexport function replaceSites(\n structure: Structure,\n replacements: readonly {\n index: number;\n site: Site;\n }[],\n): Structure {\n const sites = structure.sites.slice();\n\n for (const { index, site } of replacements) {\n sites[index] = site;\n }\n\n return {\n ...structure,\n sites,\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 interface Lattice {\n basis: Matrix;\n}\n\nexport function createLattice(\n data: number[] | Float64Array | Matrix | [number, number, number],\n): Lattice {\n const values =\n data instanceof Float64Array\n ? Array.from(data)\n : \"data\" in data\n ? Array.from(data.data)\n : data;\n\n let m: Float64Array;\n\n if (values.length === 3) {\n const [a, b, c] = values;\n\n m = new Float64Array([a, 0, 0, 0, b, 0, 0, 0, c]);\n } else if (values.length === 9) {\n m = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n m[i] = clean(values[i]);\n }\n } else {\n throw new Error(\"Lattice requires 3 or 9 values\");\n }\n\n return {\n basis: createMatrix(3, 3, m),\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 { 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 { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { Structure } from \"@/core/structure/structure\";\nimport { dot, mul } from \"@/core/matrix/operations\";\n\nimport { determinant } from \"@/core/matrix/operations\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { Vector } from \"@/core/matrix/vector\";\n\ninterface Plane {\n normal: Float64Array;\n offset: number;\n}\n\nfunction intersectPlanes(\n p1: Plane,\n p2: Plane,\n p3: Plane,\n tolerance = 1e-10,\n): Float64Array | null {\n const A = createMatrix(3, 3, [...p1.normal, ...p2.normal, ...p3.normal]);\n\n const detA = determinant(A);\n\n if (Math.abs(detA) < tolerance) return null;\n\n const invA = inverse3x3(A);\n\n const d = createMatrix(3, 1, [p1.offset, p2.offset, p3.offset]);\n\n const res = mul(invA, d).data;\n\n return new Float64Array([res[0], res[1], res[2]]);\n}\n\nfunction key(v: Float64Array) {\n const nx = v[0],\n ny = v[1],\n nz = v[2];\n const inv = 1 / Math.sqrt(nx * nx + ny * ny + nz * nz);\n\n // normalize direction so ±G collapse\n const x = Math.round(nx * inv * 1e6);\n const y = Math.round(ny * inv * 1e6);\n const z = Math.round(nz * inv * 1e6);\n\n return `${x},${y},${z}`;\n}\n\nfunction vkey(v: Float64Array, eps = 1e-6) {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\nfunction isInside(v: Float64Array, planes: Plane[]) {\n const tolerance = 0.0;\n for (const p of planes) {\n const d = p.normal[0] * v[0] + p.normal[1] * v[1] + p.normal[2] * v[2];\n\n if (d > p.offset + tolerance) return false;\n }\n return true;\n}\n\nexport async function generateBZVertices(\n structure: Structure,\n tolerance: number = 1e-4,\n): Promise<Float64Array[]> {\n const reciprocalLattice = reciprocalLatticeCrystallographic(\n structure.lattice,\n );\n\n const rcLD = reciprocalLattice.basis.data;\n\n const aStar = [rcLD[0], rcLD[1], rcLD[2]];\n const bStar = [rcLD[3], rcLD[4], rcLD[5]];\n const cStar = [rcLD[6], rcLD[7], rcLD[8]];\n\n const range = 2;\n const points: Vector[] = [];\n\n for (let h = -range; h <= range; h++) {\n for (let k = -range; k <= range; k++) {\n for (let l = -range; l <= range; l++) {\n const point = new Float64Array(3);\n\n point[0] = h * aStar[0] + k * bStar[0] + l * cStar[0];\n\n point[1] = h * aStar[1] + k * bStar[1] + l * cStar[1];\n\n point[2] = h * aStar[2] + k * bStar[2] + l * cStar[2];\n\n points.push(point);\n }\n }\n }\n\n // remove center point\n const neighbors = points.filter(\n (p) =>\n Math.abs(p[0]) > tolerance ||\n Math.abs(p[1]) > tolerance ||\n Math.abs(p[2]) > tolerance,\n );\n\n // sort by distance from origin\n neighbors.sort((a, b) => {\n const da = a[0] * a[0] + a[1] * a[1] + a[2] * a[2];\n\n const db = b[0] * b[0] + b[1] * b[1] + b[2] * b[2];\n\n return da - db;\n });\n\n const map = new Map<string, Float64Array>();\n\n for (const p of neighbors) {\n const k = key(p);\n if (!map.has(k)) map.set(k, p);\n }\n\n const uniqueNeighbors = [...map.values()];\n\n // console.log(uniqueNeighbors); // all neighbor recip points\n\n const planes = uniqueNeighbors.slice(0, 26).map((G) => ({\n normal: G,\n offset: dot(G, G) / 2,\n }));\n\n const candidateBZCorners: Float64Array[] = [];\n\n for (let i = 0; i < planes.length; i++) {\n for (let j = i + 1; j < planes.length; j++) {\n for (let k = j + 1; k < planes.length; k++) {\n const v = intersectPlanes(planes[i], planes[j], planes[k], tolerance);\n\n if (!v) continue;\n\n if (isInside(v, planes)) {\n candidateBZCorners.push(v);\n }\n }\n }\n }\n\n const vertexMap = new Map<string, Float64Array>();\n\n for (const v of candidateBZCorners) {\n const k = vkey(v);\n if (!vertexMap.has(k)) {\n vertexMap.set(k, v);\n }\n }\n\n const hullVertices = [...vertexMap.values()];\n\n return hullVertices;\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","export type Vec3 = Float64Array;\n\n// TODO: these are sort of generic geomtery utils\n// perhaps they would be better served higher up.\n\nexport function minimumImage(df: Vec3): Float64Array {\n return new Float64Array([\n df[0] - Math.round(df[0]),\n df[1] - Math.round(df[1]),\n df[2] - Math.round(df[2]),\n ]);\n}\n// flat metric tensor dot product: d^2 = x^T G x\nexport function distanceSquared(mic: Vec3, G: Float64Array): number {\n const x = mic[0],\n y = mic[1],\n z = mic[2];\n\n return (\n x * (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z)\n );\n}\n","import { Structure } from \"../../structure\";\nimport { minimumImage } from \"./utils\";\nexport type Vec3 = Float64Array;\n\nexport function getDisplacement(\n structure: Structure,\n idx1: number,\n idx2: number,\n): Vec3 {\n const s1 = structure.sites[idx1];\n const s2 = structure.sites[idx2];\n\n return minimumImage([\n s2.frac[0] - s1.frac[0],\n s2.frac[1] - s1.frac[1],\n s2.frac[2] - s1.frac[2],\n ]);\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\nexport function getDistance(\n structure: Structure,\n idx1: number,\n idx2: number,\n): number {\n const displacement = getDisplacement(structure, idx1, idx2);\n\n const G = metricTensor(structure.lattice).data;\n\n return Math.sqrt(distanceSquared(displacement, G));\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\nexport function getDistances(structure: Structure, idx: number): Float64Array {\n const n = structure.sites.length;\n const out = new Float64Array(n);\n\n const G = metricTensor(structure.lattice).data;\n\n for (let j = 0; j < n; j++) {\n if (j === idx) {\n out[j] = 0;\n continue;\n }\n\n const disp = getDisplacement(structure, idx, j);\n\n out[j] = Math.sqrt(distanceSquared(disp, G));\n }\n\n return out;\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\nexport function getDistancesMatrix(structure: Structure): Float64Array[] {\n const n = structure.sites.length;\n\n const matrix: Float64Array[] = Array.from(\n { length: n },\n () => new Float64Array(n),\n );\n\n const G = metricTensor(structure.lattice).data;\n\n for (let i = 0; i < n; i++) {\n matrix[i][i] = 0;\n\n for (let j = i + 1; j < n; j++) {\n const disp = getDisplacement(structure, i, j);\n\n const d = Math.sqrt(distanceSquared(disp, G));\n\n matrix[i][j] = d;\n matrix[j][i] = d;\n }\n }\n\n return matrix;\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n// generic method for finding sites on a given condition.\n\nexport function findSites(\n structure: Structure,\n predicate: (site: Site, index: number) => boolean,\n): number[] {\n const indices: number[] = [];\n\n for (let i = 0; i < structure.sites.length; i++) {\n if (predicate(structure.sites[i], i)) {\n indices.push(i);\n }\n }\n\n return indices;\n}\n","import { Species } from \"@/main\";\nimport { Structure } from \"@/main\";\nimport { findSites } from \"./findSites\";\n\nexport function findSitesBySpecies(\n structure: Structure,\n species: Species,\n): number[] {\n return findSites(structure, (site) => site.species.symbol === species.symbol);\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 { Matrix } from \"../matrix\";\nimport { identity } from \"../matrix\";\n\nexport interface VolumetricData {\n readonly data: Float64Array;\n readonly shape: [number, number, number];\n readonly channels: number;\n readonly basis?: Matrix;\n readonly origin: [number, number, number];\n readonly field?: string;\n readonly metadata?: Record<string, unknown>;\n}\n\ntype ReduceAxis = \"all\" | \"channels\";\n\nexport interface ReduceOptions {\n axis?: ReduceAxis;\n}\n\nexport function createVolumetricData(params: {\n shape: [number, number, number];\n channels?: number;\n\n /**\n * Flat voxel-major buffer.\n *\n * Layout:\n * [v000c0, v000c1, ..., v001c0, v001c1, ...]\n */\n data?: Float64Array | Iterable<number>;\n\n basis?: Matrix;\n origin?: [number, number, number];\n\n field?: string;\n metadata?: Record<string, unknown>;\n}): VolumetricData {\n const {\n shape,\n channels = 1,\n data,\n basis,\n origin = [0, 0, 0],\n field,\n metadata,\n } = params;\n\n const [D, H, W] = shape;\n const size = D * H * W * channels;\n\n const buffer =\n data instanceof Float64Array\n ? data\n : data\n ? Float64Array.from(data)\n : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(\n `VolumetricData mismatch: expected ${size}, got ${buffer.length}`,\n );\n }\n\n return {\n data: buffer,\n shape,\n channels,\n basis: basis ?? identity(3),\n origin,\n field,\n metadata,\n };\n}\n\nexport function index(\n vol: VolumetricData,\n x: number,\n y: number,\n z: number,\n c: number,\n) {\n const [D, H, W] = vol.shape;\n const { channels } = vol;\n\n return ((z * H + y) * W + x) * channels + c;\n}\n","import { createVolumetricData } from \"../volumetric\";\n\nexport function fill(\n shape: [number, number, number],\n value: number,\n channels = 1,\n) {\n const size = shape[0] * shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size).fill(value),\n });\n}\n","import { createVolumetricData } from \"../volumetric\";\n\nexport function fromFunction(\n shape: [number, number, number],\n fn: (x: number, y: number, z: number, c: number) => number,\n channels = 1,\n) {\n const [D, H, W] = shape;\n const data = new Float64Array(D * H * W * channels);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n for (let y = 0; y < H; y++) {\n for (let x = 0; x < W; x++) {\n for (let c = 0; c < channels; c++) {\n data[i++] = fn(x, y, z, c);\n }\n }\n }\n }\n\n return createVolumetricData({\n shape,\n channels,\n data,\n });\n}\n","import { Matrix } from \"../../matrix\";\nimport { createVolumetricData } from \"../volumetric\";\n\nexport function fromMatrixSlices(slices: Matrix[]) {\n if (slices.length === 0) {\n throw new Error(\"No slices provided\");\n }\n\n const H = slices[0].rows;\n const W = slices[0].cols;\n const D = slices.length;\n\n const data = new Float64Array(D * H * W);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n const m = slices[z];\n\n if (m.rows !== H || m.cols !== W) {\n throw new Error(\"Inconsistent matrix slice dimensions\");\n }\n\n data.set(m.data, i);\n i += m.data.length;\n }\n\n return createVolumetricData({\n shape: [D, H, W],\n data,\n });\n}\n","import { fill } from \"./fill\";\n\n// special case of fill that sets all to one\nexport function ones(shape: [number, number, number], channels = 1) {\n return fill(shape, 1, channels);\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n// data creation is by default filled with 0s so we can just early return\nexport function zeros(shape: [number, number, number], channels = 1) {\n const size = shape[0] * shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size),\n });\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\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 _cursorEnd: cursor,\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 ${section}`);\n }\n\n return idx;\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\nexport function fromXSF(text: string): Structure {\n const lines = text\n .split(\"\\n\")\n .map((x) => x.trim())\n .filter(Boolean);\n\n const vecStart = findSection(lines, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...lines[vecStart + 1].split(/\\s+/).map(Number),\n ...lines[vecStart + 2].split(/\\s+/).map(Number),\n ...lines[vecStart + 3].split(/\\s+/).map(Number),\n ]);\n\n const coordStart = findSection(lines, \"PRIMCOORD\");\n\n const [nAtoms] = lines[coordStart + 1].split(/\\s+/).map(Number);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = lines[coordStart + 2 + i].split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n const frac = fractional(lattice, new Float64Array([x, y, z]));\n\n sites.push({\n species: { symbol },\n frac,\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n lines.push(`${site.species.symbol} ${c[0]} ${c[1]} ${c[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice, Lattice } from \"../lattice/lattice\";\nimport { cartesian, fractional } from \"../site\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\nfunction parseHeader(comment: string): ExtendedXYZInfo {\n const info: ExtendedXYZInfo = {};\n const kvRegex = /(\\w+)=(\".*?\"|\\S+)/g;\n\n for (const match of comment.matchAll(kvRegex)) {\n let value = match[2];\n if (value.startsWith('\"')) value = value.slice(1, -1);\n info[match[1]] = value;\n }\n\n return info;\n}\n\nfunction parseLattice(info: ExtendedXYZInfo) {\n if (!info.Lattice) {\n throw new Error(\"Extended XYZ must contain Lattice\");\n }\n\n const v = info.Lattice.split(/\\s+/).map(Number);\n if (v.length !== 9) throw new Error(\"Invalid Lattice\");\n\n return createLattice([v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]]);\n}\n\nexport function fromXYZ(text: string) {\n const lines = text.trim().split(\"\\n\");\n\n const n = Number(lines[0]);\n const comment = lines[1];\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const sites: Site[] = [];\n\n for (let i = 0; i < n; i++) {\n const [symbol, x, y, z] = lines[2 + i].split(/\\s+/);\n\n const cart = new Float64Array([+x, +y, +z]);\n\n const frac = fractional(lattice, cart);\n\n sites.push({\n species: { symbol },\n frac,\n });\n }\n\n return { lattice, sites };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n // row-major flattening assumption (consistent with your matrix code)\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\nexport function toXYZ(structure: Structure): string {\n const lines: string[] = [];\n\n const sites = structure.sites;\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n lines.push(`Lattice=\"${latticeStr}\" Properties=species:S:1:pos:R:3`);\n\n for (const site of sites) {\n const cart = cartesian(structure.lattice, site);\n\n lines.push(`${site.species.symbol} ${cart[0]} ${cart[1]} ${cart[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","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","// derived from https://manual.gromacs.org/current/reference-manual/file-formats.html#gro\n\n// NOTE: GROMACS stores all lengths (coordinates and box vectors) in nm.\n// Internally matsci-parse uses Å.\n\n// Its common convention for GROMACs to use Hw or Ow for water, we dont try to fix this at-all\n// therefore cross format parsing (to a software that needs elemental indication) will probably fail.\n\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LengthUnitSystem } from \"../units/length\";\n\nfunction pad5(str: string) {\n return str.length > 5 ? str.slice(0, 5) : str.padStart(5);\n}\n\nfunction formatCoord(x: number) {\n return x.toFixed(3).padStart(8);\n}\n\nexport function fromGRO(text: string): Structure {\n const lines = text.split(/\\r?\\n/).filter((l) => l.length > 0);\n\n let cursor = 0;\n\n const title = lines[cursor++];\n\n const timeMatch = title.match(/t=\\s*([-+]?[0-9]*\\.?[0-9]+)/i);\n const time = timeMatch ? Number(timeMatch[1]) : undefined;\n\n const nAtoms = Number(lines[cursor++]);\n\n if (!Number.isFinite(nAtoms)) {\n throw new Error(\"Invalid GRO atom count\");\n }\n\n type Atom = {\n symbol: string;\n cart: Float64Array;\n };\n\n const atoms: Atom[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const line = lines[cursor++];\n\n const x = Number(line.slice(20, 28));\n const y = Number(line.slice(28, 36));\n const z = Number(line.slice(36, 44));\n\n let atomName = line.slice(10, 15).trim();\n\n let symbol = atomName.replace(/[0-9]/g, \"\");\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n\n atoms.push({\n symbol,\n cart: new Float64Array(\n LengthUnitSystem.convertArray([x, y, z], \"nm\", \"angstrom\"),\n ),\n });\n }\n\n let lattice = null;\n\n const boxLine = lines[cursor];\n\n if (boxLine) {\n const vals = boxLine.trim().split(/\\s+/).map(Number);\n\n const matrix = LengthUnitSystem.convertArray(\n [\n vals[0] ?? 0,\n vals[3] ?? 0,\n vals[4] ?? 0,\n vals[5] ?? 0,\n vals[1] ?? 0,\n vals[6] ?? 0,\n vals[7] ?? 0,\n vals[8] ?? 0,\n vals[2] ?? 0,\n ],\n \"nm\",\n \"angstrom\",\n );\n\n const hasOffDiagonal =\n matrix[1] !== 0 ||\n matrix[2] !== 0 ||\n matrix[3] !== 0 ||\n matrix[5] !== 0 ||\n matrix[6] !== 0 ||\n matrix[7] !== 0;\n\n lattice = hasOffDiagonal\n ? createLattice(matrix)\n : createLattice([matrix[0], matrix[4], matrix[8]]);\n }\n\n const sites: Site[] = atoms.map((atom) => ({\n species: { symbol: atom.symbol },\n frac: lattice\n ? fractional(lattice, atom.cart)\n : new Float64Array([NaN, NaN, NaN]),\n }));\n\n return {\n lattice,\n sites,\n time,\n };\n}\n\nexport function toGRO(\n structure: Structure,\n options?: {\n title?: string;\n time?: number;\n },\n): string {\n const title =\n options?.title ??\n (options?.time !== undefined\n ? `Generated structure, t=${options.time}`\n : \"Generated by matsci-parse\");\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(structure.sites.length));\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n\n const [x, y, z] = LengthUnitSystem.convertArray(\n Array.from(cart),\n \"angstrom\",\n \"nm\",\n );\n\n lines.push(\n pad5(\"1\") +\n pad5(\"RES\") +\n pad5(site.species.symbol) +\n pad5(String(i + 1)) +\n formatCoord(x) +\n formatCoord(y) +\n formatCoord(z),\n );\n }\n\n const m = structure.lattice.basis.data;\n\n const [a, b, c] = LengthUnitSystem.convertArray(\n [m[0], m[4], m[8]],\n \"angstrom\",\n \"nm\",\n );\n\n lines.push([a, b, c].map((v) => v.toFixed(5)).join(\" \"));\n\n return lines.join(\"\\n\");\n}\n","import { fromParameters } from \"../lattice\";\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nconst DEFAULT_PADDING = 10.0;\n\nfunction parseCRYST1(line: string) {\n const a = Number(line.slice(6, 15));\n const b = Number(line.slice(15, 24));\n const c = Number(line.slice(24, 33));\n\n const alpha = Number(line.slice(33, 40));\n const beta = Number(line.slice(40, 47));\n const gamma = Number(line.slice(47, 54));\n\n return { a, b, c, alpha, beta, gamma };\n}\n\nfunction isCRYST1Sane(\n a: number,\n b: number,\n c: number,\n extentX: number,\n extentY: number,\n extentZ: number,\n): boolean {\n // reject degenerate or identity cells\n if (a <= 1e-3 || b <= 1e-3 || c <= 1e-3) return false;\n\n // reject clearly too small cells\n const margin = 1.2; // allow small packing inefficiency\n\n if (a < extentX * margin) return false;\n if (b < extentY * margin) return false;\n if (c < extentZ * margin) return false;\n\n // also reject ridiculous huge identity placeholders\n if (a === 1 && b === 1 && c === 1) return false;\n\n return true;\n}\n\nexport function fromPDB(text: string): Structure {\n const lines = text.split(/\\r?\\n/);\n\n let crystal: {\n a: number;\n b: number;\n c: number;\n alpha: number;\n beta: number;\n gamma: number;\n } | null = null;\n\n type ParsedAtom = {\n symbol: string;\n x: number;\n y: number;\n z: number;\n };\n\n const atoms: ParsedAtom[] = [];\n\n let xmin = Infinity;\n let ymin = Infinity;\n let zmin = Infinity;\n\n let xmax = -Infinity;\n let ymax = -Infinity;\n let zmax = -Infinity;\n\n for (const line of lines) {\n if (line.startsWith(\"CRYST1\")) {\n crystal = parseCRYST1(line);\n continue;\n }\n\n if (!line.startsWith(\"ATOM \") && !line.startsWith(\"HETATM\")) {\n continue;\n }\n\n const x = Number(line.slice(30, 38));\n const y = Number(line.slice(38, 46));\n const z = Number(line.slice(46, 54));\n\n let symbol = line.slice(76, 78).trim();\n\n if (!symbol) {\n symbol = line.slice(12, 16).replace(/[0-9]/g, \"\").trim();\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n }\n\n atoms.push({ symbol, x, y, z });\n\n xmin = Math.min(xmin, x);\n ymin = Math.min(ymin, y);\n zmin = Math.min(zmin, z);\n\n xmax = Math.max(xmax, x);\n ymax = Math.max(ymax, y);\n zmax = Math.max(zmax, z);\n }\n\n if (atoms.length === 0) {\n throw new Error(\"No ATOM/HETATM records found.\");\n }\n\n const extentX = xmax - xmin;\n const extentY = ymax - ymin;\n const extentZ = zmax - zmin;\n\n let lattice = createLattice([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n\n let originX = xmin - DEFAULT_PADDING;\n let originY = ymin - DEFAULT_PADDING;\n let originZ = zmin - DEFAULT_PADDING;\n\n const useCrystal =\n crystal !== null &&\n isCRYST1Sane(crystal.a, crystal.b, crystal.c, extentX, extentY, extentZ);\n\n if (useCrystal) {\n lattice = fromParameters(\n crystal.a,\n crystal.b,\n crystal.c,\n crystal.alpha,\n crystal.beta,\n crystal.gamma,\n );\n\n originX = 0;\n originY = 0;\n originZ = 0;\n } else {\n const a = Math.max(extentX + 2 * DEFAULT_PADDING, 1.0);\n const b = Math.max(extentY + 2 * DEFAULT_PADDING, 1.0);\n const c = Math.max(extentZ + 2 * DEFAULT_PADDING, 1.0);\n\n lattice = createLattice([a, 0, 0, 0, b, 0, 0, 0, c]);\n }\n\n const sites: Site[] = atoms.map(({ symbol, x, y, z }) => ({\n species: { symbol },\n frac: fractional(\n lattice,\n new Float64Array([x - originX, y - originY, z - originZ]),\n ),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toPDB(\n structure: Structure,\n options?: {\n title?: string;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n\n const lines: string[] = [];\n\n lines.push(`HEADER ${title}`);\n\n let index = 1;\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n const symbol = site.species.symbol;\n\n lines.push(\n [\n \"ATOM \",\n index.toString().padStart(5),\n \" \",\n symbol.padEnd(4),\n \" MOL \",\n \"A\",\n \" 1 \",\n c[0].toFixed(3).padStart(8),\n c[1].toFixed(3).padStart(8),\n c[2].toFixed(3).padStart(8),\n \" 1.00\",\n \" 0.00\",\n \" \",\n symbol.padStart(2),\n ].join(\"\"),\n );\n\n index++;\n }\n\n lines.push(\"END\");\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { fractional } from \"../site\";\nimport { cartesian } from \"../site/cartesian\";\nimport type { Site } from \"../site/site\";\nimport type { Structure } from \"../structure/structure\";\n\ntype CoordinateMode = \"crystal\" | \"angstrom\";\n\n// NOTE / TODO:\n// PW is a very complex file format, it would be good if i can do some intense reading.\n// It might take a while to get a nice representation of these things...\n\nexport function fromPW(text: string): Structure {\n const lines = text.split(\"\\n\").map((x) => x.trim());\n\n let latticeRows: number[][] = [];\n const atomLines: string[] = [];\n\n // ---------- lattice ----------\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i];\n\n if (/^CELL_PARAMETERS/i.test(line)) {\n for (let j = 1; j <= 3; j++) {\n latticeRows.push(lines[i + j].split(/\\s+/).map(Number));\n }\n\n break;\n }\n }\n\n if (latticeRows.length !== 3) {\n throw new Error(\"CELL_PARAMETERS block not found\");\n }\n\n const lattice = createLattice([\n ...latticeRows[0],\n ...latticeRows[1],\n ...latticeRows[2],\n ]);\n\n // ---------- atomic positions ----------\n let atomUnits = \"angstrom\";\n let inAtomicBlock = false;\n\n for (const line of lines) {\n if (/^ATOMIC_POSITIONS/i.test(line)) {\n inAtomicBlock = true;\n\n const match = line.match(\n /^ATOMIC_POSITIONS\\s*(?:\\{|\\()?(\\w+)(?:\\}|\\))?/i,\n );\n\n atomUnits = match?.[1]?.toLowerCase() ?? \"angstrom\";\n\n continue;\n }\n\n if (!inAtomicBlock) continue;\n\n const parts = line.split(/\\s+/);\n\n if (\n parts.length < 4 ||\n !/^[A-Za-z]/.test(parts[0]) ||\n parts.slice(1, 4).some((x) => Number.isNaN(+x))\n ) {\n break;\n }\n\n atomLines.push(line);\n }\n\n if (atomLines.length === 0) {\n throw new Error(\"ATOMIC_POSITIONS block not found\");\n }\n\n const isCrystal = atomUnits === \"crystal\";\n\n const sites: Site[] = [];\n\n for (const line of atomLines) {\n const [symbol, x, y, z] = line.split(/\\s+/);\n\n let frac: Float64Array;\n\n if (isCrystal) {\n frac = new Float64Array([+x, +y, +z]);\n } else {\n // convert cartesian → fractional\n\n frac = fractional(lattice, new Float64Array([+x, +y, +z]));\n }\n\n sites.push({\n species: { symbol },\n frac,\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nexport function toPW(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"&SYSTEM\");\n lines.push(\"/\");\n\n lines.push(\"\");\n\n lines.push(`CELL_PARAMETERS angstrom`);\n\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]} ${m[8]}`);\n\n lines.push(\"\");\n\n lines.push(`ATOMIC_POSITIONS crystal`);\n\n for (const site of structure.sites) {\n const coords = site.frac;\n\n lines.push(\n `${site.species.symbol} ` + `${coords[0]} ${coords[1]} ${coords[2]}`,\n );\n }\n\n return lines.join(\"\\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","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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A matrix backed by a row-major Float64Array. */\nexport interface Matrix {\n readonly rows: number;\n readonly cols: number;\n readonly data: Float64Array;\n}\n\n/** Create a new Matrix with the given dimensions, optionally populated from an iterable.\n * @param rows - Number of rows.\n * @param cols - Number of columns.\n * @param data - Optional iterable of values to fill the matrix.\n * @returns A new Matrix. */\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\n/** Return an identity matrix of the given size.\n * @param size - Number of rows and columns.\n * @returns A square identity matrix. */\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\n/** Return a deep copy of the given matrix.\n * @param matrix - Matrix to clone.\n * @returns A new Matrix with copied data. */\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\n/** Compute the linear index for the given (row, col) in a row-major layout.\n * @param cols - Number of columns in the matrix.\n * @param row - Row index.\n * @param col - Column index.\n * @returns Linear index into the data array. */\nexport function index(cols: number, row: number, col: number): number {\n return row * cols + col;\n}\n","/** Shared floating-point comparison threshold. */\nexport const EPSILON = 1e-12;\n","import { EPSILON } from \"./constants\";\n\n/** Zero-out values within EPSILON of zero. */\nexport function clean(x: number): number {\n return Math.abs(x) < EPSILON ? 0 : x;\n}\n\n/** Greatest common divisor. */\nexport function gcd(a: number, b: number): number {\n a = Math.abs(a);\n b = Math.abs(b);\n while (b !== 0) {\n [a, b] = [b, a % b];\n }\n return a;\n}\n\n/** Least common multiple. */\nexport function lcm(a: number, b: number): number {\n return (Math.abs(a) / gcd(a, b)) * Math.abs(b);\n}\n","import { createMatrix, Matrix } from \"../matrix/matrix\";\nimport { clean } from \"../math/numeric\";\n\n/** A lattice defined by a 3x3 basis matrix (row vectors). */\nexport interface Lattice {\n basis: Matrix;\n}\n\n/** Create a Lattice from 3 diagonal lengths, 9 matrix values, or a Matrix. */\nexport function createLattice(\n data: number[] | Float64Array | Matrix | [number, number, number],\n): Lattice {\n const values =\n data instanceof Float64Array\n ? Array.from(data)\n : \"data\" in data\n ? Array.from(data.data)\n : data;\n\n let m: Float64Array;\n\n if (values.length === 3) {\n const [a, b, c] = values;\n\n m = new Float64Array([a, 0, 0, 0, b, 0, 0, 0, c]);\n } else if (values.length === 9) {\n m = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n m[i] = clean(values[i]);\n }\n } else {\n throw new Error(\"Lattice requires 3 or 9 values\");\n }\n\n return {\n basis: createMatrix(3, 3, m),\n };\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\n/** Multiply two matrices (matrix product).\n * @param a - Left matrix.\n * @param b - Right matrix.\n * @returns A new Matrix containing the product. */\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 { Matrix, createMatrix } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a 3x3 matrix using cofactors.\n * @param m - A 3x3 matrix.\n * @returns The inverse Matrix. */\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 (Math.abs(det) < EPSILON) {\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 { Matrix, createMatrix, index } from \"../matrix\";\n\n/** Transpose the given matrix (swap rows and columns).\n * @param matrix - Input matrix.\n * @returns A new transposed Matrix. */\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 { createLattice } from \"@/core/lattice/lattice\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Site } from \"@/core/site/site\";\nimport type { Structure } from \"../structure\";\n\n/** Apply a transformation basis matrix to a structure.\n * The new lattice is P * oldBasis and fractional coordinates are P^{-T} * oldFrac,\n * preserving Cartesian positions.\n * @param structure - The input structure.\n * @param basis - A 3x3 transformation matrix.\n * @returns A new Structure with transformed lattice and sites. */\nexport function applyTransformationBasis(\n structure: Structure,\n basis: Matrix,\n): Structure {\n const invP = inverse3x3(basis);\n const newBasis = mul(basis, structure.lattice.basis);\n\n const sites: Site[] = structure.sites.map((site) => {\n const f = site.frac;\n const vec = {\n rows: 3,\n cols: 1,\n data: new Float64Array([f[0], f[1], f[2]]),\n };\n const result = mul(transpose(invP), vec);\n\n return {\n ...site,\n frac: new Float64Array([result.data[0], result.data[1], result.data[2]]),\n };\n });\n\n return {\n lattice: createLattice(newBasis),\n sites,\n };\n}\n","import { Site } from \"../../site/site\";\n\n/** Sort sites by species symbol, then by fractional coordinates (x, y, z). Returns a new array. */\nexport function sortSites(sites: Site[]): Site[] {\n return [...sites].sort((a, b) => {\n const sp = a.species.symbol.localeCompare(b.species.symbol);\n if (sp !== 0) return sp;\n if (a.frac[0] !== b.frac[0]) return a.frac[0] - b.frac[0];\n if (a.frac[1] !== b.frac[1]) return a.frac[1] - b.frac[1];\n return a.frac[2] - b.frac[2];\n });\n}\n","import { Structure } from \"../../structure/structure\";\nimport { sortSites } from \"./sortSites\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nfunction wrap(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < EPSILON ? 0 : v;\n}\n\n/** Return a copy with fractional coordinates wrapped to [0, 1), near-zero values cleaned, and sites sorted by species then coordinates. */\nexport function canonicalize(structure: Structure): Structure {\n const 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 return { ...structure, sites: sortSites(sites) };\n}\n","import { Structure } from \"../structure\";\nimport { canonicalize } from \"./canonicalize\";\nimport { Vec3 } from \"../../site/site\";\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\n/** FNV-1a hash of a canonicalized structure (lattice + sorted sites). */\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.symbol + \":\" + 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\n/** Append a single site to the structure. */\nexport function appendSite(structure: Structure, site: Site): Structure {\n const sites = structure.sites.slice();\n sites.push(site);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/** Append multiple sites to the structure. */\nexport function appendSites(\n structure: Structure,\n sitesToAppend: readonly Site[],\n): Structure {\n return {\n ...structure,\n sites: [...structure.sites, ...sitesToAppend],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/** Insert a single site at the given index. */\nexport function insertSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const oldSites = structure.sites;\n const sites = new Array(oldSites.length + 1);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n sites[index] = site;\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + 1] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n\n/** Insert multiple sites starting at the given index. */\nexport function insertSites(\n structure: Structure,\n index: number,\n sitesToInsert: readonly Site[],\n): Structure {\n const oldSites = structure.sites;\n const n = sitesToInsert.length;\n\n const sites = new Array(oldSites.length + n);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n for (let i = 0; i < n; i++) {\n sites[index + i] = sitesToInsert[i];\n }\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + n] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Structure } from \"../../structure\";\n\n/** Remove the site at the given index. */\nexport function removeSite(structure: Structure, index: number): Structure {\n const sites = structure.sites.slice();\n sites.splice(index, 1);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/** Remove sites at the given indices. */\nexport function removeSites(\n structure: Structure,\n indices: readonly number[],\n): Structure {\n const remove = new Set(indices);\n\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => !remove.has(i)),\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/** Replace a single site at the given index. */\nexport function replaceSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const sites = structure.sites.slice();\n sites[index] = site;\n\n return {\n ...structure,\n sites,\n };\n}\n\n/** Replace multiple sites at the given indices. */\nexport function replaceSites(\n structure: Structure,\n replacements: readonly {\n index: number;\n site: Site;\n }[],\n): Structure {\n const sites = structure.sites.slice();\n\n for (const { index, site } of replacements) {\n sites[index] = site;\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the 3D cross product of two vectors.\n * @param a - First 3D vector.\n * @param b - Second 3D vector.\n * @returns The cross product vector. */\nexport function cross(a: Vector, b: Vector): Vector {\n if (a.length !== 3 || b.length !== 3) {\n throw new Error(\"Cross product requires 3D vectors\");\n }\n\n return new Float64Array([\n a[1] * b[2] - a[2] * b[1],\n a[2] * b[0] - a[0] * b[2],\n a[0] * b[1] - a[1] * b[0],\n ]);\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the Euclidean norm (magnitude) of a vector.\n * @param v - Input vector.\n * @returns The Euclidean norm. */\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 { Vector } from \"../../vector\";\nimport { norm } from \"./norm\";\n\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Return a unit vector in the direction of v.\n * @param v - Input vector.\n * @returns A normalized unit vector. */\nexport function normalize(v: Vector): Vector {\n const n = norm(v);\n\n if (n < EPSILON) {\n throw new Error(\"Cannot normalize zero vector\");\n }\n\n const out = new Float64Array(v.length);\n\n for (let i = 0; i < v.length; i++) {\n out[i] = v[i] / n;\n }\n\n return out;\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { cross } from \"@/core/matrix/operations/vector/cross\";\nimport { normalize } from \"@/core/matrix/operations/vector/normalize\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/**\n * Rotate the lattice so that the given Cartesian direction maps to the new c-axis\n * (third lattice vector). Atom Cartesian positions are preserved exactly.\n *\n * NOTE: this only guarantees the new c-axis aligns with `normal` when the original\n * third lattice vector is parallel to `normal`. For slab construction, the caller\n * must first apply `calculateScaleFactor` + `supercell` to orient the cell.\n *\n * @param structure - The input structure.\n * @param normal - A 3D Cartesian direction vector (need not be unit).\n * @returns A new Structure with rotated lattice and sites.\n */\nexport function reorientToNormal(\n structure: Structure,\n normal: Float64Array | number[],\n): Structure {\n const n = normalize(new Float64Array(normal));\n\n let e1: Float64Array;\n const ref = new Float64Array([1, 0, 0]);\n\n if (Math.abs(Math.abs(n[0]) - 1) < EPSILON) {\n e1 = normalize(cross(n, new Float64Array([0, 1, 0])));\n } else {\n e1 = normalize(cross(n, ref));\n }\n\n const e2 = cross(n, e1);\n\n const R = createMatrix(3, 3, [\n e1[0], e2[0], n[0],\n e1[1], e2[1], n[1],\n e1[2], e2[2], n[2],\n ]);\n\n return applyTransformationBasis(structure, R);\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/**\n * Add vacuum along the c-axis by stretching the c-vector.\n * Atom Cartesian positions are preserved exactly.\n * @param structure - The input structure (should already be reoriented with surface normal along c).\n * @param thickness - Vacuum thickness in the same length units as the lattice.\n * @returns A new Structure with extended c-vector.\n */\nexport function addVacuum(structure: Structure, thickness: number): Structure {\n if (thickness <= 0) return structure;\n\n const b = structure.lattice.basis.data;\n const cVec = new Float64Array([b[6], b[7], b[8]]);\n const cLength = norm(cVec);\n\n if (cLength < EPSILON) {\n throw new Error(\"c-vector has zero length\");\n }\n\n const scale = (cLength + thickness) / cLength;\n const P = createMatrix(3, 3, [1, 0, 0, 0, 1, 0, 0, 0, scale]);\n\n return applyTransformationBasis(structure, P);\n}\n","import { Matrix, clone } from \"../matrix\";\n\nimport { EPSILON } from \"../../math/constants\";\n\nexport interface LUDecomposition {\n readonly LU: Matrix;\n readonly piv: Int32Array;\n readonly sign: number;\n readonly singular: boolean;\n}\n\n/** Compute the LU decomposition of a square matrix with partial pivoting.\n * @param A - A square matrix.\n * @returns The LU decomposition. */\nexport function lu(A: Matrix): LUDecomposition {\n if (A.rows !== A.cols) {\n throw new Error(\"LU decomposition requires a square matrix\");\n }\n\n const n = A.rows;\n const LU = clone(A);\n const data = LU.data;\n const piv = new Int32Array(n);\n\n for (let i = 0; i < n; i++) piv[i] = i;\n\n let sign = 1;\n\n for (let k = 0; k < n; k++) {\n let pivot = k;\n let max = Math.abs(data[k * n + k]);\n\n for (let i = k + 1; i < n; i++) {\n const v = Math.abs(data[i * n + k]);\n\n if (v > max) {\n max = v;\n pivot = i;\n }\n }\n\n if (max < EPSILON) {\n return { LU, piv, sign, singular: true };\n }\n\n if (pivot !== k) {\n const rowK = k * n;\n const rowP = pivot * n;\n\n for (let j = 0; j < n; j++) {\n const tmp = data[rowK + j];\n data[rowK + j] = data[rowP + j];\n data[rowP + j] = tmp;\n }\n\n const tmp = piv[k];\n piv[k] = piv[pivot];\n piv[pivot] = tmp;\n sign = -sign;\n }\n\n const rowK = k * n;\n const pivotVal = data[rowK + k];\n\n for (let i = k + 1; i < n; i++) {\n const rowI = i * n;\n\n data[rowI + k] /= pivotVal;\n const factor = data[rowI + k];\n\n for (let j = k + 1; j < n; j++) {\n data[rowI + j] -= factor * data[rowK + j];\n }\n }\n }\n\n return { LU, piv, sign, singular: false };\n}\n","import { Matrix } from \"../matrix\";\nimport { lu } from \"./lu\";\n\n/** Compute the determinant of a square matrix using LU decomposition (O(n³)).\n * @param matrix - A square matrix.\n * @returns The determinant value. */\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 const { LU, sign, singular } = lu(matrix);\n\n if (singular) return 0;\n\n const data = LU.data;\n let det = sign;\n\n for (let i = 0; i < n; i++) {\n det *= data[i * n + i];\n }\n\n return det;\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the dot product of two vectors.\n * @param a - First vector.\n * @param b - Second vector.\n * @returns The dot product. */\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 { Lattice } from \"./lattice\";\nimport { inverse3x3 } from \"../matrix/operations/inverse/inverse3x3\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/** Compute the inverse of the lattice basis matrix. */\nexport function inverse(lattice: Lattice): Matrix {\n return inverse3x3(lattice.basis);\n}\n","import { Lattice, createLattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\n/** Compute the crystallographic reciprocal lattice (without 2*pi scaling). */\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 { createMatrix, type Matrix } from \"@/core/matrix/matrix\";\nimport { determinant } from \"@/core/matrix/operations/determinant\";\nimport { dot } from \"@/core/matrix/operations/vector/dot\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport type { Lattice } from \"@/core/lattice/lattice\";\nimport { EPSILON } from \"@/core/math/constants\";\nimport { gcd, lcm } from \"@/core/math/numeric\";\n\nfunction reduceVector(v: number[]): number[] {\n let g = 0;\n for (const x of v) {\n g = gcd(g, Math.abs(Math.round(x)));\n }\n if (g <= 1) return v;\n return v.map((x) => Math.round(x / g));\n}\n\n/**\n * Calculate the slab scale factor following pymatgen's `calculate_scaling_factor` algorithm.\n *\n * Given Miller indices (h, k, l), builds a 3×3 integer matrix U such that:\n * - Rows 0 and 1 are real-space vectors perpendicular to the surface normal (in-plane).\n * - Row 2 is a real-space vector with maximal projection onto the surface normal (c-direction).\n *\n * The key insight: a real-space vector v = r·lattice is perpendicular to the (hkl) surface\n * normal iff r·[h,k,l] = 0. In-plane rows are built as LCM combinations of lattice vectors\n * whose integer coefficients cancel the dot product with the Miller index.\n *\n * @param millerIndex - The Miller indices [h, k, l].\n * @param lattice - The crystal lattice.\n * @returns A 3×3 integer Matrix (the scale factor).\n */\nexport function calculateScaleFactor(\n millerIndex: [number, number, number],\n lattice: Lattice,\n): Matrix {\n const [h, k, l] = millerIndex;\n\n // Surface normal in Cartesian from reciprocal lattice\n const recip = reciprocalLatticeCrystallographic(lattice);\n const rb = recip.basis.data;\n const normalRaw = new Float64Array([\n h * rb[0] + k * rb[3] + l * rb[6],\n h * rb[1] + k * rb[4] + l * rb[7],\n h * rb[2] + k * rb[5] + l * rb[8],\n ]);\n const normalLen = norm(normalRaw);\n if (normalLen < EPSILON) {\n throw new Error(\"Miller index [0,0,0] is invalid\");\n }\n const normal = new Float64Array(normalRaw.map((x) => x / normalLen));\n\n const basis = lattice.basis.data;\n const millerArr = [h, k, l];\n\n // Classify lattice vectors: in-plane (miller[i]==0) vs non-orthogonal\n const slabScaleFactor: number[][] = [];\n const nonOrthInd: [number, number][] = []; // [index, projection onto normal]\n\n for (let idx = 0; idx < 3; idx++) {\n if (millerArr[idx] === 0) {\n // Lattice vector is already in the surface plane\n const row = [0, 0, 0];\n row[idx] = 1;\n slabScaleFactor.push(row);\n } else {\n const aIdx = new Float64Array([\n basis[idx * 3],\n basis[idx * 3 + 1],\n basis[idx * 3 + 2],\n ]);\n const aLen = norm(aIdx);\n const d = Math.abs(dot(normal, aIdx)) / aLen;\n nonOrthInd.push([idx, d]);\n }\n }\n\n // Pick the vector with maximum projection onto normal as the c-direction\n let cIndex = nonOrthInd[0][0];\n let maxProj = nonOrthInd[0][1];\n for (const [idx, proj] of nonOrthInd) {\n if (proj > maxProj) {\n cIndex = idx;\n maxProj = proj;\n }\n }\n\n // Build in-plane vectors from non-orthogonal pairs using LCM combinations\n // For pair (ii, jj): row[ii] = -lcm/m[ii], row[jj] = lcm/m[jj]\n // This ensures row·[h,k,l] = (-lcm/m[ii])*m[ii] + (lcm/m[jj])*m[jj] = -lcm + lcm = 0\n if (nonOrthInd.length > 1) {\n const millerNonZero = nonOrthInd.map(([idx]) => Math.abs(millerArr[idx]));\n let lcmVal = millerNonZero[0];\n for (let i = 1; i < millerNonZero.length; i++) {\n lcmVal = lcm(lcmVal, millerNonZero[i]);\n }\n\n for (let ii = 0; ii < nonOrthInd.length; ii++) {\n for (let jj = ii + 1; jj < nonOrthInd.length; jj++) {\n const iiIdx = nonOrthInd[ii][0];\n const jjIdx = nonOrthInd[jj][0];\n const row = [0, 0, 0];\n row[iiIdx] = -Math.round(lcmVal / millerArr[iiIdx]);\n row[jjIdx] = Math.round(lcmVal / millerArr[jjIdx]);\n slabScaleFactor.push(reduceVector(row));\n if (slabScaleFactor.length === 2) break;\n }\n if (slabScaleFactor.length === 2) break;\n }\n }\n\n // Add c-direction vector: use the lattice vector at cIndex (identity row)\n const cRow = [0, 0, 0];\n cRow[cIndex] = 1;\n slabScaleFactor.push(cRow);\n\n // Build matrix\n const flat = slabScaleFactor.flat();\n let mat = createMatrix(3, 3, flat);\n\n // Ensure positive determinant (left-handed → negate first row)\n if (determinant(mat) < 0) {\n mat = createMatrix(\n 3,\n 3,\n flat.map((x, i) => (i < 3 ? -x : x)),\n );\n }\n\n return mat;\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\n/** Convert a site's fractional coordinates to Cartesian.\n * @param lattice - The lattice.\n * @param site - The site.\n * @returns Cartesian coordinate vector. */\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\n/** Convert Cartesian coordinates to fractional.\n * @param lattice - The lattice.\n * @param cart - Cartesian vector.\n * @returns Fractional coordinate vector. */\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 { Matrix, createMatrix } from \"../matrix\";\nimport { inverse3x3 } from \"./inverse/inverse3x3\";\n\n/**\n * Return fractional coordinates (in the original cell) of all lattice points\n * that lie inside the supercell defined by an integer transformation matrix U.\n *\n * The new cell has basis B' = U @ B. A lattice point at integer vector n\n * maps to fractional coordinate inv(U) @ n in the original cell. We collect\n * all n such that inv(U) @ n has every component in [0, 1).\n *\n * The number of returned points equals |det(U)|.\n *\n * @param U - A 3×3 integer transformation matrix.\n * @returns An array of 3-element Float64Arrays, each a fractional coordinate.\n */\nexport function latticePointsInSupercell(U: Matrix): Float64Array[] {\n const invU = inverse3x3(U);\n\n // Determine search range: entries of inv(U) scale the integer vectors,\n // so we need to cover enough range. For typical slab scale factors\n // (entries 0, ±1, ±2), ±4 is ample.\n const maxEntry = Math.max(\n ...Array.from(U.data).map(Math.abs),\n 1,\n );\n const range = maxEntry + 2;\n\n const points: Float64Array[] = [];\n\n for (let i = -range; i <= range; i++) {\n for (let j = -range; j <= range; j++) {\n for (let k = -range; k <= range; k++) {\n // frac = invU @ [i, j, k]\n const d = invU.data;\n const f0 = d[0] * i + d[1] * j + d[2] * k;\n const f1 = d[3] * i + d[4] * j + d[5] * k;\n const f2 = d[6] * i + d[7] * j + d[8] * k;\n\n if (\n f0 >= -1e-10 && f0 < 1 - 1e-10 &&\n f1 >= -1e-10 && f1 < 1 - 1e-10 &&\n f2 >= -1e-10 && f2 < 1 - 1e-10\n ) {\n points.push(\n new Float64Array([\n Math.max(0, f0),\n Math.max(0, f1),\n Math.max(0, f2),\n ]),\n );\n }\n }\n }\n }\n\n return points;\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { cartesian } from \"@/core/site/cartesian\";\nimport { fractional } from \"@/core/site/fractional\";\nimport { latticePointsInSupercell } from \"@/core/matrix/operations/latticePointsInSupercell\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Structure } from \"../structure\";\nimport type { Site } from \"@/core/site/site\";\n\ntype SupercellSize = number | [number, number, number] | Matrix;\n\nfunction isMatrix(size: SupercellSize): size is Matrix {\n return typeof size !== \"number\" && !Array.isArray(size);\n}\n\n/** Create a supercell by applying an integer transformation matrix U.\n *\n * If `size` is a number or [nx, ny, nz], a diagonal supercell is formed by\n * replicating the structure in each lattice direction.\n *\n * If `size` is a 3x3 integer Matrix, the general supercell algorithm from\n * pymatgen's `Structure.__mul__` (make_supercell) is used: the new basis\n * is U @ oldBasis and lattice points are replicated by |det(U)|.\n *\n * @param structure - The input structure.\n * @param size - Supercell size: number (isotropic), [nx, ny, nz], or 3x3 integer matrix.\n * @returns A new Structure with the supercell applied.\n */\nexport function supercell(structure: Structure, size: SupercellSize): Structure {\n let U: Matrix;\n\n if (isMatrix(size)) {\n U = size;\n } else {\n const [nx, ny, nz] = typeof size === \"number\" ? [size, size, size] : size;\n U = createMatrix(3, 3, [nx, 0, 0, 0, ny, 0, 0, 0, nz]);\n }\n\n const newBasis = mul(U, structure.lattice.basis);\n const newLattice = createLattice(newBasis);\n\n const fracPoints = latticePointsInSupercell(U);\n\n const sites: Site[] = [];\n\n for (const site of structure.sites) {\n const siteCart = cartesian(structure.lattice, site);\n\n for (const lp of fracPoints) {\n // Lattice point in Cartesian (using new lattice)\n const lpCart = cartesian(newLattice, {\n species: site.species,\n frac: lp,\n });\n\n const pos = new Float64Array([\n siteCart[0] + lpCart[0],\n siteCart[1] + lpCart[1],\n siteCart[2] + lpCart[2],\n ]);\n\n const frac = fractional(newLattice, pos);\n\n // Wrap to [0, 1)\n for (let d = 0; d < 3; d++) {\n frac[d] = frac[d] - Math.floor(frac[d]);\n if (frac[d] > 1 - 1e-10) frac[d] = 0;\n if (frac[d] < 1e-10) frac[d] = 0;\n }\n\n sites.push({\n species: site.species,\n frac,\n });\n }\n }\n\n return {\n lattice: newLattice,\n sites,\n };\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { calculateScaleFactor } from \"./calculateScaleFactor\";\nimport { supercell } from \"../supercell\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /** Number of unit cell replications along c (surface normal). Default 1. */\n layers?: number;\n /** Vacuum thickness in Angstroms. Default 0. */\n vacuum?: number;\n}\n\n/**\n * Generate a slab oriented along the (hkl) plane, following pymatgen's algorithm.\n *\n * Steps:\n * 1. Calculate an integer scale factor U that puts in-plane vectors perpendicular\n * to the surface normal, and a c-vector with max projection onto the normal.\n * 2. Apply make_supercell(U) to create an oriented unit cell (OUC).\n * 3. Replicate the OUC along c to get the desired number of layers.\n * 4. Add vacuum by stretching the c-vector.\n *\n * @param structure - The bulk input structure.\n * @param h - Miller index h.\n * @param k - Miller index k.\n * @param l - Miller index l.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n */\nexport function slabFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n // Step 1: Calculate the scale factor\n const U = calculateScaleFactor([h, k, l], structure.lattice);\n\n // Step 2: Create the oriented unit cell\n const ouc = supercell(structure, U);\n\n // Step 3: Replicate along c\n const replicated = supercell(ouc, [1, 1, layers]);\n\n // Step 4: Add vacuum\n return addVacuum(replicated, vacuum);\n}\n","/** A 3-component vector. */\nexport type Vec3 = Float64Array;\n\n// TODO: these are sort of generic geomtery utils\n// perhaps they would be better served higher up.\n\n/** Wrap a fractional displacement into the minimum-image convention (components in [-0.5, 0.5]). */\nexport function minimumImage(df: Vec3): Float64Array {\n return new Float64Array([\n df[0] - Math.round(df[0]),\n df[1] - Math.round(df[1]),\n df[2] - Math.round(df[2]),\n ]);\n}\n/** Squared distance from a minimum-image vector using the metric tensor G. */\nexport function distanceSquared(mic: Vec3, G: Float64Array): number {\n const x = mic[0],\n y = mic[1],\n z = mic[2];\n\n return (\n x * (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z)\n );\n}\n","import { Structure } from \"../../structure\";\nimport { minimumImage } from \"./utils\";\n/** A 3-component vector. */\nexport type Vec3 = Float64Array;\n\n/** Minimum-image displacement vector from site idx1 to site idx2. */\nexport function getDisplacement(\n structure: Structure,\n idx1: number,\n idx2: number,\n): Vec3 {\n const s1 = structure.sites[idx1];\n const s2 = structure.sites[idx2];\n\n return minimumImage([\n s2.frac[0] - s1.frac[0],\n s2.frac[1] - s1.frac[1],\n s2.frac[2] - s1.frac[2],\n ]);\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\n/** Compute the reciprocal lattice scaled by 2*pi. */\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 { Structure } from \"../../structure\";\nimport { getDisplacement } from \"../distance/getDisplacement\";\nimport { cross } from \"../../../matrix/operations/vector/cross\";\nimport { norm } from \"../../../matrix/operations/vector/norm\";\nimport { cartesian } from \"../../../site/cartesian\";\n\nimport { reciprocalLattice } from \"../../../lattice/reciprocalLattice\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** A plane defined by a unit normal and a point on the plane (Cartesian). */\nexport interface Plane {\n readonly normal: Float64Array;\n readonly point: Float64Array;\n}\n\n/** Plane equation in the form ax + by + cz + d = 0. */\nexport interface PlaneEquation {\n readonly a: number;\n readonly b: number;\n readonly c: number;\n readonly d: number;\n}\n\n/** Plane through three non-collinear sites. */\nexport function planeFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n): Plane {\n // Cartesian displacement vectors\n const r1 = getDisplacement(structure, i, j);\n const r2 = getDisplacement(structure, i, k);\n\n const n = cross(r1, r2);\n const nNorm = norm(n);\n\n if (nNorm < EPSILON) {\n throw new Error(\"Cannot construct plane from collinear sites\");\n }\n\n const normal = new Float64Array([n[0] / nNorm, n[1] / nNorm, n[2] / nNorm]);\n\n // pick a real point on plane (site i), convert properly\n const point = cartesian(structure.lattice, structure.sites[i]);\n\n return { normal, point };\n}\n\n/** Convert a Plane to PlaneEquation coefficients (ax + by + cz + d = 0). */\nexport function planeEquation(plane: Plane): PlaneEquation {\n const { normal, point } = plane;\n\n const d = -(\n normal[0] * point[0] +\n normal[1] * point[1] +\n normal[2] * point[2]\n );\n\n return {\n a: normal[0],\n b: normal[1],\n c: normal[2],\n d,\n };\n}\n\n/** Signed distance from a Cartesian point to a plane. */\nexport function distanceFromPlane(\n point: Float64Array,\n plane: PlaneEquation,\n): number {\n const { a, b, c, d } = plane;\n\n const denominator = Math.sqrt(a * a + b * b + c * c);\n\n if (denominator < EPSILON) {\n throw new Error(\"Invalid plane normal\");\n }\n\n return (a * point[0] + b * point[1] + c * point[2] + d) / denominator;\n}\n\n/** Signed distance from a site to a plane. */\nexport function distanceFromSiteToPlane(\n structure: Structure,\n siteIndex: number,\n plane: PlaneEquation,\n): number {\n const point = cartesian(structure.lattice, structure.sites[siteIndex]);\n\n return distanceFromPlane(point, plane);\n}\n\n/** Plane from Miller indices (hkl) using the reciprocal lattice. */\nexport function planeFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n): Plane {\n const reciprocal = reciprocalLattice(structure.lattice);\n\n const normal = new Float64Array([\n h * reciprocal.basis.data[0] +\n k * reciprocal.basis.data[3] +\n l * reciprocal.basis.data[6],\n\n h * reciprocal.basis.data[1] +\n k * reciprocal.basis.data[4] +\n l * reciprocal.basis.data[7],\n\n h * reciprocal.basis.data[2] +\n k * reciprocal.basis.data[5] +\n l * reciprocal.basis.data[8],\n ]);\n\n const length = norm(normal);\n\n if (length < EPSILON) {\n throw new Error(\"Invalid Miller index\");\n }\n\n return {\n normal: new Float64Array([\n normal[0] / length,\n normal[1] / length,\n normal[2] / length,\n ]),\n point: new Float64Array([0, 0, 0]),\n };\n}\n","import { planeFromSites } from \"../geometry/plane\";\nimport { canonicalize } from \"../canonicalize\";\nimport { supercell } from \"../supercell\";\nimport { reorientToNormal } from \"./reorientToNormal\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /** Number of unit cell replications along c (surface normal). Default 1. */\n layers?: number;\n /** Vacuum thickness in lattice length units. Default 0. */\n vacuum?: number;\n}\n\n/**\n * Generate a slab oriented so the plane through three sites is the surface.\n *\n * Steps: plane normal → rotation → replicate → add vacuum.\n * Atom Cartesian positions within the slab are preserved exactly.\n *\n * @param structure - The bulk input structure.\n * @param i - Index of first site defining the surface plane.\n * @param j - Index of second site defining the surface plane.\n * @param k - Index of third site defining the surface plane.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n */\nexport function slabFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n const plane = planeFromSites(structure, i, j, k);\n const reoriented = canonicalize(reorientToNormal(structure, plane.normal));\n const replicated = supercell(reoriented, [1, 1, layers]);\n\n return addVacuum(replicated, vacuum);\n}\n","\nvar createModule = (() => {\n var _scriptDir = import.meta.url;\n \n return (\nfunction(createModule) {\n createModule = createModule || {};\n\nvar Module=typeof createModule!=\"undefined\"?createModule:{};var readyPromiseResolve,readyPromiseReject;Module[\"ready\"]=new Promise(function(resolve,reject){readyPromiseResolve=resolve;readyPromiseReject=reject});var moduleOverrides=Object.assign({},Module);var arguments_=[];var thisProgram=\"./this.program\";var quit_=(status,toThrow)=>{throw toThrow};var ENVIRONMENT_IS_WEB=true;var ENVIRONMENT_IS_WORKER=false;var scriptDirectory=\"\";function locateFile(path){if(Module[\"locateFile\"]){return Module[\"locateFile\"](path,scriptDirectory)}return scriptDirectory+path}var read_,readAsync,readBinary,setWindowTitle;if(ENVIRONMENT_IS_WEB||ENVIRONMENT_IS_WORKER){if(ENVIRONMENT_IS_WORKER){scriptDirectory=self.location.href}else if(typeof document!=\"undefined\"&&document.currentScript){scriptDirectory=document.currentScript.src}if(_scriptDir){scriptDirectory=_scriptDir}if(scriptDirectory.indexOf(\"blob:\")!==0){scriptDirectory=scriptDirectory.substr(0,scriptDirectory.replace(/[?#].*/,\"\").lastIndexOf(\"/\")+1)}else{scriptDirectory=\"\"}{read_=(url=>{var xhr=new XMLHttpRequest;xhr.open(\"GET\",url,false);xhr.send(null);return xhr.responseText});if(ENVIRONMENT_IS_WORKER){readBinary=(url=>{var xhr=new XMLHttpRequest;xhr.open(\"GET\",url,false);xhr.responseType=\"arraybuffer\";xhr.send(null);return new Uint8Array(xhr.response)})}readAsync=((url,onload,onerror)=>{var xhr=new XMLHttpRequest;xhr.open(\"GET\",url,true);xhr.responseType=\"arraybuffer\";xhr.onload=(()=>{if(xhr.status==200||xhr.status==0&&xhr.response){onload(xhr.response);return}onerror()});xhr.onerror=onerror;xhr.send(null)})}setWindowTitle=(title=>document.title=title)}else{}var out=Module[\"print\"]||console.log.bind(console);var err=Module[\"printErr\"]||console.warn.bind(console);Object.assign(Module,moduleOverrides);moduleOverrides=null;if(Module[\"arguments\"])arguments_=Module[\"arguments\"];if(Module[\"thisProgram\"])thisProgram=Module[\"thisProgram\"];if(Module[\"quit\"])quit_=Module[\"quit\"];var POINTER_SIZE=4;function warnOnce(text){if(!warnOnce.shown)warnOnce.shown={};if(!warnOnce.shown[text]){warnOnce.shown[text]=1;err(text)}}function convertJsFunctionToWasm(func,sig){if(typeof WebAssembly.Function==\"function\"){var typeNames={\"i\":\"i32\",\"j\":\"i64\",\"f\":\"f32\",\"d\":\"f64\"};var type={parameters:[],results:sig[0]==\"v\"?[]:[typeNames[sig[0]]]};for(var i=1;i<sig.length;++i){type.parameters.push(typeNames[sig[i]])}return new WebAssembly.Function(type,func)}var typeSection=[1,0,1,96];var sigRet=sig.slice(0,1);var sigParam=sig.slice(1);var typeCodes={\"i\":127,\"j\":126,\"f\":125,\"d\":124};typeSection.push(sigParam.length);for(var i=0;i<sigParam.length;++i){typeSection.push(typeCodes[sigParam[i]])}if(sigRet==\"v\"){typeSection.push(0)}else{typeSection=typeSection.concat([1,typeCodes[sigRet]])}typeSection[1]=typeSection.length-2;var bytes=new Uint8Array([0,97,115,109,1,0,0,0].concat(typeSection,[2,7,1,1,101,1,102,0,0,7,5,1,1,102,0,0]));var module=new WebAssembly.Module(bytes);var instance=new WebAssembly.Instance(module,{\"e\":{\"f\":func}});var wrappedFunc=instance.exports[\"f\"];return wrappedFunc}var freeTableIndexes=[];var functionsInTableMap;function getEmptyTableSlot(){if(freeTableIndexes.length){return freeTableIndexes.pop()}try{wasmTable.grow(1)}catch(err){if(!(err instanceof RangeError)){throw err}throw\"Unable to grow wasm table. Set ALLOW_TABLE_GROWTH.\"}return wasmTable.length-1}function updateTableMap(offset,count){for(var i=offset;i<offset+count;i++){var item=getWasmTableEntry(i);if(item){functionsInTableMap.set(item,i)}}}var tempRet0=0;var wasmBinary;if(Module[\"wasmBinary\"])wasmBinary=Module[\"wasmBinary\"];var noExitRuntime=Module[\"noExitRuntime\"]||true;if(typeof WebAssembly!=\"object\"){abort(\"no native wasm support detected\")}function getValue(ptr,type=\"i8\",noSafe){if(type.charAt(type.length-1)===\"*\")type=\"i32\";switch(type){case\"i1\":return HEAP8[ptr>>0];case\"i8\":return HEAP8[ptr>>0];case\"i16\":return HEAP16[ptr>>1];case\"i32\":return HEAP32[ptr>>2];case\"i64\":return HEAP32[ptr>>2];case\"float\":return HEAPF32[ptr>>2];case\"double\":return Number(HEAPF64[ptr>>3]);default:abort(\"invalid type for getValue: \"+type)}return null}var wasmMemory;var ABORT=false;var EXITSTATUS;function assert(condition,text){if(!condition){abort(text)}}function getCFunc(ident){var func=Module[\"_\"+ident];return func}function ccall(ident,returnType,argTypes,args,opts){var toC={\"string\":function(str){var ret=0;if(str!==null&&str!==undefined&&str!==0){var len=(str.length<<2)+1;ret=stackAlloc(len);stringToUTF8(str,ret,len)}return ret},\"array\":function(arr){var ret=stackAlloc(arr.length);writeArrayToMemory(arr,ret);return ret}};function convertReturnValue(ret){if(returnType===\"string\")return UTF8ToString(ret);if(returnType===\"boolean\")return Boolean(ret);return ret}var func=getCFunc(ident);var cArgs=[];var stack=0;if(args){for(var i=0;i<args.length;i++){var converter=toC[argTypes[i]];if(converter){if(stack===0)stack=stackSave();cArgs[i]=converter(args[i])}else{cArgs[i]=args[i]}}}var ret=func.apply(null,cArgs);function onDone(ret){if(stack!==0)stackRestore(stack);return convertReturnValue(ret)}ret=onDone(ret);return ret}var ALLOC_STACK=1;var UTF8Decoder=typeof TextDecoder!=\"undefined\"?new TextDecoder(\"utf8\"):undefined;function UTF8ArrayToString(heap,idx,maxBytesToRead){var endIdx=idx+maxBytesToRead;var endPtr=idx;while(heap[endPtr]&&!(endPtr>=endIdx))++endPtr;if(endPtr-idx>16&&heap.subarray&&UTF8Decoder){return UTF8Decoder.decode(heap.subarray(idx,endPtr))}else{var str=\"\";while(idx<endPtr){var u0=heap[idx++];if(!(u0&128)){str+=String.fromCharCode(u0);continue}var u1=heap[idx++]&63;if((u0&224)==192){str+=String.fromCharCode((u0&31)<<6|u1);continue}var u2=heap[idx++]&63;if((u0&240)==224){u0=(u0&15)<<12|u1<<6|u2}else{u0=(u0&7)<<18|u1<<12|u2<<6|heap[idx++]&63}if(u0<65536){str+=String.fromCharCode(u0)}else{var ch=u0-65536;str+=String.fromCharCode(55296|ch>>10,56320|ch&1023)}}}return str}function UTF8ToString(ptr,maxBytesToRead){return ptr?UTF8ArrayToString(HEAPU8,ptr,maxBytesToRead):\"\"}function stringToUTF8Array(str,heap,outIdx,maxBytesToWrite){if(!(maxBytesToWrite>0))return 0;var startIdx=outIdx;var endIdx=outIdx+maxBytesToWrite-1;for(var i=0;i<str.length;++i){var 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writeArrayToMemory(array,buffer){HEAP8.set(array,buffer)}function writeAsciiToMemory(str,buffer,dontAddNull){for(var i=0;i<str.length;++i){HEAP8[buffer++>>0]=str.charCodeAt(i)}if(!dontAddNull)HEAP8[buffer>>0]=0}var buffer,HEAP8,HEAPU8,HEAP16,HEAPU16,HEAP32,HEAPU32,HEAPF32,HEAPF64;function updateGlobalBufferAndViews(buf){buffer=buf;Module[\"HEAP8\"]=HEAP8=new Int8Array(buf);Module[\"HEAP16\"]=HEAP16=new Int16Array(buf);Module[\"HEAP32\"]=HEAP32=new Int32Array(buf);Module[\"HEAPU8\"]=HEAPU8=new Uint8Array(buf);Module[\"HEAPU16\"]=HEAPU16=new Uint16Array(buf);Module[\"HEAPU32\"]=HEAPU32=new Uint32Array(buf);Module[\"HEAPF32\"]=HEAPF32=new Float32Array(buf);Module[\"HEAPF64\"]=HEAPF64=new Float64Array(buf)}var INITIAL_MEMORY=Module[\"INITIAL_MEMORY\"]||16777216;var wasmTable;var __ATPRERUN__=[];var __ATINIT__=[];var __ATPOSTRUN__=[];var runtimeInitialized=false;var runtimeExited=false;var runtimeKeepaliveCounter=0;function keepRuntimeAlive(){return 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___assert_fail(condition,filename,line,func){abort(\"Assertion failed: \"+UTF8ToString(condition)+\", at: \"+[filename?UTF8ToString(filename):\"unknown filename\",line,func?UTF8ToString(func):\"unknown function\"])}function _emscripten_memcpy_big(dest,src,num){HEAPU8.copyWithin(dest,src,src+num)}function _emscripten_get_heap_max(){return 2147483648}function emscripten_realloc_buffer(size){try{wasmMemory.grow(size-buffer.byteLength+65535>>>16);updateGlobalBufferAndViews(wasmMemory.buffer);return 1}catch(e){}}function _emscripten_resize_heap(requestedSize){var oldSize=HEAPU8.length;requestedSize=requestedSize>>>0;var maxHeapSize=_emscripten_get_heap_max();if(requestedSize>maxHeapSize){return false}let alignUp=(x,multiple)=>x+(multiple-x%multiple)%multiple;for(var cutDown=1;cutDown<=4;cutDown*=2){var overGrownHeapSize=oldSize*(1+.2/cutDown);overGrownHeapSize=Math.min(overGrownHeapSize,requestedSize+100663296);var 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buffer=SYSCALLS.buffers[stream];if(curr===0||curr===10){(stream===1?out:err)(UTF8ArrayToString(buffer,0));buffer.length=0}else{buffer.push(curr)}},varargs:undefined,get:function(){SYSCALLS.varargs+=4;var ret=HEAP32[SYSCALLS.varargs-4>>2];return ret},getStr:function(ptr){var ret=UTF8ToString(ptr);return ret},get64:function(low,high){return low}};function _environ_get(__environ,environ_buf){var bufSize=0;getEnvStrings().forEach(function(string,i){var ptr=environ_buf+bufSize;HEAP32[__environ+i*4>>2]=ptr;writeAsciiToMemory(string,ptr);bufSize+=string.length+1});return 0}function _environ_sizes_get(penviron_count,penviron_buf_size){var strings=getEnvStrings();HEAP32[penviron_count>>2]=strings.length;var bufSize=0;strings.forEach(function(string){bufSize+=string.length+1});HEAP32[penviron_buf_size>>2]=bufSize;return 0}var ASSERTIONS=false;var asmLibraryArg={\"__assert_fail\":___assert_fail,\"emscripten_memcpy_big\":_emscripten_memcpy_big,\"emscripten_resize_heap\":_emscripten_resize_heap,\"environ_get\":_environ_get,\"environ_sizes_get\":_environ_sizes_get};var asm=createWasm();var ___wasm_call_ctors=Module[\"___wasm_call_ctors\"]=function(){return(___wasm_call_ctors=Module[\"___wasm_call_ctors\"]=Module[\"asm\"][\"__wasm_call_ctors\"]).apply(null,arguments)};var _spglib_analyze_cell=Module[\"_spglib_analyze_cell\"]=function(){return(_spglib_analyze_cell=Module[\"_spglib_analyze_cell\"]=Module[\"asm\"][\"spglib_analyze_cell\"]).apply(null,arguments)};var _malloc=Module[\"_malloc\"]=function(){return(_malloc=Module[\"_malloc\"]=Module[\"asm\"][\"malloc\"]).apply(null,arguments)};var _free=Module[\"_free\"]=function(){return(_free=Module[\"_free\"]=Module[\"asm\"][\"free\"]).apply(null,arguments)};var _spglib_free_string=Module[\"_spglib_free_string\"]=function(){return(_spglib_free_string=Module[\"_spglib_free_string\"]=Module[\"asm\"][\"spglib_free_string\"]).apply(null,arguments)};var _spglib_niggli_reduce=Module[\"_spglib_niggli_reduce\"]=function(){return(_spglib_niggli_reduce=Module[\"_spglib_niggli_reduce\"]=Module[\"asm\"][\"spglib_niggli_reduce\"]).apply(null,arguments)};var ___errno_location=Module[\"___errno_location\"]=function(){return(___errno_location=Module[\"___errno_location\"]=Module[\"asm\"][\"__errno_location\"]).apply(null,arguments)};var stackSave=Module[\"stackSave\"]=function(){return(stackSave=Module[\"stackSave\"]=Module[\"asm\"][\"stackSave\"]).apply(null,arguments)};var stackRestore=Module[\"stackRestore\"]=function(){return(stackRestore=Module[\"stackRestore\"]=Module[\"asm\"][\"stackRestore\"]).apply(null,arguments)};var stackAlloc=Module[\"stackAlloc\"]=function(){return(stackAlloc=Module[\"stackAlloc\"]=Module[\"asm\"][\"stackAlloc\"]).apply(null,arguments)};Module[\"getValue\"]=getValue;Module[\"UTF8ToString\"]=UTF8ToString;var calledRun;function ExitStatus(status){this.name=\"ExitStatus\";this.message=\"Program terminated with exit(\"+status+\")\";this.status=status}dependenciesFulfilled=function runCaller(){if(!calledRun)run();if(!calledRun)dependenciesFulfilled=runCaller};function run(args){args=args||arguments_;if(runDependencies>0){return}preRun();if(runDependencies>0){return}function doRun(){if(calledRun)return;calledRun=true;Module[\"calledRun\"]=true;if(ABORT)return;initRuntime();readyPromiseResolve(Module);if(Module[\"onRuntimeInitialized\"])Module[\"onRuntimeInitialized\"]();postRun()}if(Module[\"setStatus\"]){Module[\"setStatus\"](\"Running...\");setTimeout(function(){setTimeout(function(){Module[\"setStatus\"](\"\")},1);doRun()},1)}else{doRun()}}Module[\"run\"]=run;function procExit(code){EXITSTATUS=code;if(!keepRuntimeAlive()){if(Module[\"onExit\"])Module[\"onExit\"](code);ABORT=true}quit_(code,new ExitStatus(code))}if(Module[\"preInit\"]){if(typeof Module[\"preInit\"]==\"function\")Module[\"preInit\"]=[Module[\"preInit\"]];while(Module[\"preInit\"].length>0){Module[\"preInit\"].pop()()}}run();\n\n\n return createModule.ready\n}\n);\n})();\nexport default createModule;","/**\n * Runtime bindings for the self-contained spglib WASM build.\n *\n * Exposes the same MoyoDataset-shaped interface as `@spglib/moyo-wasm` so the\n * rest of the library can swap engines without changing its API.\n */\n\nimport initWasm from \"./spglib_wasm.js\";\n\nexport interface Lattice {\n basis: [\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n ];\n}\n\nexport interface MoyoCell {\n lattice: Lattice;\n positions: [number, number, number][];\n numbers: number[];\n}\n\nexport interface MoyoDataset {\n number: number;\n hall_number: number;\n hm_symbol: string;\n operations: MoyoOperation[];\n orbits: number[];\n wyckoffs: string[];\n site_symmetry_symbols: string[];\n std_cell: MoyoCell;\n std_linear: [\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n ];\n std_origin_shift: [number, number, number];\n std_rotation_matrix: [\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n ];\n pearson_symbol: string;\n prim_std_cell: MoyoCell;\n prim_std_linear: [\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n ];\n prim_std_origin_shift: [number, number, number];\n mapping_std_prim: number[];\n symprec: number;\n angle_tolerance: { type: \"Default\" };\n}\n\nexport interface MoyoOperation {\n rotation: [\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n number,\n ];\n translation: [number, number, number];\n}\n\ntype Module = Awaited<ReturnType<typeof initWasm>> | null;\n\nlet ready: Promise<Module> | null = null;\n\n/** Instantiate (and cache) the WASM module. Idempotent. */\nexport function init(): Promise<Module> {\n if (!ready) {\n ready = (async () => {\n const wasmUrl = new URL(\"spglib_wasm.wasm\", import.meta.url);\n\n if (typeof process !== \"undefined\" && process.versions?.node) {\n const { readFileSync } = await import(\"fs\");\n const { fileURLToPath } = await import(\"url\");\n const wasmPath = fileURLToPath(wasmUrl);\n const wasmBinary = readFileSync(wasmPath);\n return (await initWasm({ wasmBinary })) as Module;\n }\n\n return (await initWasm({\n locateFile: () => wasmUrl.toString(),\n })) as Module;\n })();\n }\n return ready;\n}\n\ninterface CellInput {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n}\n\n/** Analyze a cell and return a MoyoDataset-shaped result. */\nexport async function analyze_cell(\n cell_json: string,\n symprec: number,\n _setting = \"Standard\",\n): Promise<MoyoDataset> {\n const mod = await init();\n if (!mod) throw new Error(\"spglib WASM module failed to initialize\");\n\n const cell = JSON.parse(cell_json) as CellInput;\n const lattice = cell.lattice.basis;\n const positions = cell.positions;\n const numbers = cell.numbers;\n const n = positions.length;\n\n if (lattice.length !== 9 || positions.length !== n || numbers.length !== n) {\n throw new Error(\"spglib analyze_cell: malformed cell input\");\n }\n\n const latPtr = mod._malloc(9 * 8);\n const posPtr = mod._malloc(n * 3 * 8);\n const numPtr = mod._malloc(n * 4);\n\n try {\n new Float64Array(mod.HEAP8.buffer, latPtr, 9).set(lattice);\n const posArr = new Float64Array(mod.HEAP8.buffer, posPtr, n * 3);\n for (let i = 0; i < n; i++) posArr.set(positions[i], i * 3);\n new Int32Array(mod.HEAP8.buffer, numPtr, n).set(numbers);\n\n const jsonPtr = mod._spglib_analyze_cell(\n latPtr,\n posPtr,\n numPtr,\n n,\n symprec,\n );\n if (!jsonPtr) throw new Error(\"spglib analyze_cell returned null\");\n const json = mod.UTF8ToString(jsonPtr);\n mod._spglib_free_string(jsonPtr);\n return JSON.parse(json) as MoyoDataset;\n } finally {\n mod._free(latPtr);\n mod._free(posPtr);\n mod._free(numPtr);\n }\n}\n\n/**\n * Niggli-reduce a 3x3 lattice given row-major.\n * Returns the reduced lattice basis (9 numbers), or null on failure.\n */\nexport async function niggli_reduce(\n lattice: number[],\n): Promise<number[] | null> {\n if (lattice.length !== 9)\n throw new Error(\"niggli_reduce: expected 9 numbers\");\n const mod = await init();\n if (!mod) throw new Error(\"spglib WASM module failed to initialize\");\n\n const latPtr = mod._malloc(9 * 8);\n try {\n new Float64Array(mod.HEAP8.buffer, latPtr, 9).set(lattice);\n const ok = mod._spglib_niggli_reduce(latPtr);\n if (!ok) return null;\n return Array.from(new Float64Array(mod.HEAP8.buffer, latPtr, 9));\n } finally {\n mod._free(latPtr);\n }\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 (Math.abs(denom) < 1e-300) 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\n/** Compute the three inter-vector angles (alpha, beta, gamma) in radians. */\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 { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n/** Compute the three lattice vector lengths (a, b, c). */\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 { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Lattice } from \"./lattice\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/** Compute the metric tensor G = A A^T for the lattice basis (row vectors). */\nexport function metricTensor(lattice: Lattice): Matrix {\n const A = lattice.basis;\n\n const AT = transpose(A);\n return mul(A, AT);\n}\n","import { lengths } from \"./lengths\";\nimport { angles } from \"./angles\";\nimport { Lattice } from \"./lattice\";\n\nconst RAD2DEG = 180 / Math.PI;\n\n/** Return lattice parameters (a, b, c, alpha, beta, gamma) with angles in degrees. */\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 { reciprocalLatticeCrystallographic } from \"./reciprocalLatticeCrystallographic\";\nimport { lengths } from \"./lengths\";\n\n/** Compute k-point grid [Nx, Ny, Nz] from desired spacing in Å⁻¹. */\nexport function kspacingToGrid(\n lattice: Lattice,\n spacing: number,\n): [number, number, number] {\n if (spacing <= 0) {\n throw new Error(\"k-spacing must be positive\");\n }\n\n const rec = reciprocalLatticeCrystallographic(lattice);\n const [b1, b2, b3] = lengths(rec);\n\n return [\n Math.max(1, Math.ceil((b1 * 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b2 * 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b3 * 2 * Math.PI) / spacing)),\n ];\n}\n","import { createLattice } from \"../lattice\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nconst DEG2RAD = Math.PI / 180;\n\n/** Create a Lattice from conventional cell parameters (angles in degrees). */\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) < EPSILON) {\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\n/** Create a cubic lattice with side length a. */\nexport function cubic(a: number) {\n return fromParameters(a, a, a, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/** Create a hexagonal lattice with side a and height c. */\nexport function hexagonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 120);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/** Create a monoclinic lattice (alpha=gamma=90, beta given in degrees). */\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\n/** Create an orthorhombic lattice with sides a, b, c and all angles 90. */\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\n/** Create a rhombohedral lattice with side a and equal angles alpha (degrees). */\nexport function rhombohedral(a: number, alpha: number) {\n return fromParameters(a, a, a, alpha, alpha, alpha);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/** Create a tetragonal lattice with a=b, c, and all angles 90. */\nexport function tetragonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 90);\n}\n","import { init, analyze_cell } from \"./spglib-wasm\";\n\nimport { createLattice } from \"@/core/lattice\";\nimport { Structure } from \"../../structure\";\n\n/** Ensure the WASM module is loaded (idempotent). */\nexport function initMoyo() {\n return init();\n}\n\n/** Compute primitive and conventional structures plus calculation results via Moyo/SPGLIB. */\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 { Matrix, createMatrix } from \"../matrix\";\n\n/** Multiply every element of matrix m by scalar k.\n * @param m - Input matrix.\n * @param k - Scalar multiplier.\n * @returns A new scaled Matrix. */\nexport function scale(m: Matrix, k: number): Matrix {\n const out = createMatrix(m.rows, m.cols);\n\n const size = m.data.length;\n\n for (let i = 0; i < size; i++) {\n out.data[i] = m.data[i] * k;\n }\n\n return out;\n}\n","import { Matrix, createMatrix, clone, index } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a square matrix using Gauss-Jordan elimination with partial pivoting.\n * @param m - A square matrix.\n * @returns The inverse Matrix. */\nexport function gjInverse(m: Matrix): Matrix {\n if (m.rows !== m.cols) {\n throw new Error(\"Inverse requires square matrix\");\n }\n\n const n = m.rows;\n const A = clone(m);\n const I = createMatrix(n, n);\n const Adata = A.data;\n const Idata = I.data;\n\n // Initialize identity\n for (let i = 0; i < n; i++) {\n Idata[i * n + i] = 1;\n }\n\n for (let i = 0; i < n; i++) {\n let pivotIdx = i * n + i;\n\n // Pivoting\n if (Math.abs(Adata[pivotIdx]) < EPSILON) {\n let swapRow = -1;\n for (let r = i + 1; r < n; r++) {\n if (Math.abs(Adata[r * n + i]) > EPSILON) {\n swapRow = r;\n break;\n }\n }\n if (swapRow === -1) {\n throw new Error(\"Singular matrix\");\n }\n\n // performant inline swap\n const r1Offset = i * n;\n const r2Offset = swapRow * n;\n for (let c = 0; c < n; c++) {\n let tmp = Adata[r1Offset + c];\n Adata[r1Offset + c] = Adata[r2Offset + c];\n Adata[r2Offset + c] = tmp;\n\n tmp = Idata[r1Offset + c];\n Idata[r1Offset + c] = Idata[r2Offset + c];\n Idata[r2Offset + c] = tmp;\n }\n\n pivotIdx = i * n + i;\n }\n\n const pivot = Adata[pivotIdx];\n const invPivot = 1 / pivot;\n\n // Normalize pivot row\n const pivotOffset = i * n;\n for (let c = 0; c < n; c++) {\n Adata[pivotOffset + c] *= invPivot;\n Idata[pivotOffset + c] *= invPivot;\n }\n\n // Eliminate other rows\n for (let r = 0; r < n; r++) {\n if (r === i) continue;\n\n const factor = Adata[r * n + i];\n if (Math.abs(factor) < EPSILON) continue;\n\n const rOffset = r * n;\n for (let c = 0; c < n; c++) {\n Adata[rOffset + c] -= Adata[pivotOffset + c] * factor;\n Idata[rOffset + c] -= Idata[pivotOffset + c] * factor;\n }\n }\n }\n\n return I;\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { Structure } from \"@/core/structure/structure\";\nimport { dot, mul } from \"@/core/matrix/operations\";\n\nimport { determinant } from \"@/core/matrix/operations\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { Vector } from \"@/core/matrix/vector\";\n\ninterface Plane {\n normal: Float64Array;\n offset: number;\n}\n\nfunction intersectPlanes(\n p1: Plane,\n p2: Plane,\n p3: Plane,\n tolerance = 1e-10,\n): Float64Array | null {\n const A = createMatrix(3, 3, [...p1.normal, ...p2.normal, ...p3.normal]);\n\n const detA = determinant(A);\n\n if (Math.abs(detA) < tolerance) return null;\n\n const invA = inverse3x3(A);\n\n const d = createMatrix(3, 1, [p1.offset, p2.offset, p3.offset]);\n\n const res = mul(invA, d).data;\n\n return new Float64Array([res[0], res[1], res[2]]);\n}\n\nfunction key(v: Float64Array) {\n const nx = v[0],\n ny = v[1],\n nz = v[2];\n const inv = 1 / Math.sqrt(nx * nx + ny * ny + nz * nz);\n\n // normalize direction so ±G collapse\n const x = Math.round(nx * inv * 1e6);\n const y = Math.round(ny * inv * 1e6);\n const z = Math.round(nz * inv * 1e6);\n\n return `${x},${y},${z}`;\n}\n\nfunction vkey(v: Float64Array, eps = 1e-6) {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\nfunction isInside(v: Float64Array, planes: Plane[]) {\n const tolerance = 0.0;\n for (const p of planes) {\n const d = p.normal[0] * v[0] + p.normal[1] * v[1] + p.normal[2] * v[2];\n\n if (d > p.offset + tolerance) return false;\n }\n return true;\n}\n\n/** Generate Brillouin zone vertices from the reciprocal crystallographic lattice. */\nexport async function generateBZVertices(\n structure: Structure,\n tolerance: number = 1e-4,\n): Promise<Float64Array[]> {\n const reciprocalLattice = reciprocalLatticeCrystallographic(\n structure.lattice,\n );\n\n const rcLD = reciprocalLattice.basis.data;\n\n const aStar = [rcLD[0], rcLD[1], rcLD[2]];\n const bStar = [rcLD[3], rcLD[4], rcLD[5]];\n const cStar = [rcLD[6], rcLD[7], rcLD[8]];\n\n const range = 2;\n const points: Vector[] = [];\n\n for (let h = -range; h <= range; h++) {\n for (let k = -range; k <= range; k++) {\n for (let l = -range; l <= range; l++) {\n const point = new Float64Array(3);\n\n point[0] = h * aStar[0] + k * bStar[0] + l * cStar[0];\n\n point[1] = h * aStar[1] + k * bStar[1] + l * cStar[1];\n\n point[2] = h * aStar[2] + k * bStar[2] + l * cStar[2];\n\n points.push(point);\n }\n }\n }\n\n // remove center point\n const neighbors = points.filter(\n (p) =>\n Math.abs(p[0]) > tolerance ||\n Math.abs(p[1]) > tolerance ||\n Math.abs(p[2]) > tolerance,\n );\n\n // sort by distance from origin\n neighbors.sort((a, b) => {\n const da = a[0] * a[0] + a[1] * a[1] + a[2] * a[2];\n\n const db = b[0] * b[0] + b[1] * b[1] + b[2] * b[2];\n\n return da - db;\n });\n\n const map = new Map<string, Float64Array>();\n\n for (const p of neighbors) {\n const k = key(p);\n if (!map.has(k)) map.set(k, p);\n }\n\n const uniqueNeighbors = [...map.values()];\n\n // console.log(uniqueNeighbors); // all neighbor recip points\n\n const planes = uniqueNeighbors.slice(0, 26).map((G) => ({\n normal: G,\n offset: dot(G, G) / 2,\n }));\n\n const candidateBZCorners: Float64Array[] = [];\n\n for (let i = 0; i < planes.length; i++) {\n for (let j = i + 1; j < planes.length; j++) {\n for (let k = j + 1; k < planes.length; k++) {\n const v = intersectPlanes(planes[i], planes[j], planes[k], tolerance);\n\n if (!v) continue;\n\n if (isInside(v, planes)) {\n candidateBZCorners.push(v);\n }\n }\n }\n }\n\n const vertexMap = new Map<string, Float64Array>();\n\n for (const v of candidateBZCorners) {\n const k = vkey(v);\n if (!vertexMap.has(k)) {\n vertexMap.set(k, v);\n }\n }\n\n const hullVertices = [...vertexMap.values()];\n\n return hullVertices;\n}\n","/**\n * Compute the triangulated polyhedron of the first Brillouin zone from the\n * reciprocal lattice vectors, mirroring `seekpath.brillouinzone.BZ`.\n *\n * The output matches the `faces_data` consumed by the\n * `brillouinzone-visualizer` web widget:\n * - `triangles_vertices`: all polyhedron vertices\n * - `triangles`: index triples (fan-triangulated convex faces)\n * - `faces`: the flat faces as lists of vertex coordinates\n */\n\nimport { Vector } from \"@/core/matrix/vector\";\nimport { dot, cross, norm } from \"@/core/matrix/operations/vector\";\n\n/** Round a vector direction to a stable key so ±parallel G-vectors collide. */\nfunction directionKey(v: Vector): string {\n const n = norm(v);\n const x = Math.round((v[0] / n) * 1e6);\n const y = Math.round((v[1] / n) * 1e6);\n const z = Math.round((v[2] / n) * 1e6);\n return `${x},${y},${z}`;\n}\n\nfunction vertexKey(v: Vector, eps = 1e-6): string {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\n/**\n * Solve the 3x3 system A x = d via Cramer's rule. Returns null if singular.\n * Kept local: the lib `solve` throws on singular matrices, but the corner\n * search needs a null result for near-degenerate plane intersections.\n */\nfunction solve3(A: Vector[], d: number[], tolerance: number): Vector | null {\n const det = A[0][0] * (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n if (Math.abs(det) < tolerance) return null;\n\n const detX = d[0] * (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (d[1] * A[2][2] - A[1][2] * d[2]) +\n A[0][2] * (d[1] * A[2][1] - A[1][1] * d[2]);\n const detY = A[0][0] * (d[1] * A[2][2] - A[1][2] * d[2]) -\n d[0] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * d[2] - d[1] * A[2][0]);\n const detZ = A[0][0] * (A[1][1] * d[2] - d[1] * A[2][1]) -\n A[0][1] * (A[1][0] * d[2] - d[1] * A[2][0]) +\n d[0] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n return new Float64Array([detX / det, detY / det, detZ / det]);\n}\n\nexport interface BZPolyhedron {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n}\n\n/**\n * Compute the first Brillouin zone polyhedron from the reciprocal lattice\n * vectors b1, b2, b3 (rows of the reciprocal lattice matrix).\n */\nexport function getBZPolyhedron(\n b1: number[],\n b2: number[],\n b3: number[],\n supercellSize = 3,\n): BZPolyhedron {\n const r1 = new Float64Array(b1);\n const r2 = new Float64Array(b2);\n const r3 = new Float64Array(b3);\n\n // Reciprocal lattice points, keeping the shortest G-vector per direction\n const best: Map<string, { g: Vector; length2: number }> = new Map();\n for (let i = -supercellSize; i <= supercellSize; i++) {\n for (let j = -supercellSize; j <= supercellSize; j++) {\n for (let k = -supercellSize; k <= supercellSize; k++) {\n if (i === 0 && j === 0 && k === 0) continue;\n const g = new Float64Array([\n i * r1[0] + j * r2[0] + k * r3[0],\n i * r1[1] + j * r2[1] + k * r3[1],\n i * r1[2] + j * r2[2] + k * r3[2],\n ]);\n const key = directionKey(g);\n const length2 = dot(g, g);\n const existing = best.get(key);\n if (!existing || length2 < existing.length2) {\n best.set(key, { g, length2 });\n }\n }\n }\n }\n\n // Planes: perpendicular bisectors of the G-vectors (normals g, offset |g|^2/2).\n // The faces of the BZ are always among the nearest reciprocal lattice\n // directions, so restricting to the shortest ones is safe and fast.\n const MAX_PLANES = 40;\n const planes: { g: Vector; offset: number }[] = [...best.values()]\n .sort((a, b) => a.length2 - b.length2)\n .slice(0, MAX_PLANES)\n .map(({ g }) => ({ g, offset: dot(g, g) / 2 }));\n\n // Candidate BZ corners: intersections of three planes inside all planes\n const tolerance = 1e-10;\n const corners: Vector[] = [];\n const n = planes.length;\n for (let i = 0; i < n; i++) {\n for (let j = i + 1; j < n; j++) {\n for (let k = j + 1; k < n; k++) {\n const v = solve3(\n [planes[i].g, planes[j].g, planes[k].g],\n [planes[i].offset, planes[j].offset, planes[k].offset],\n tolerance,\n );\n if (!v) continue;\n let inside = true;\n for (const p of planes) {\n if (dot(p.g, v) > p.offset + tolerance) {\n inside = false;\n break;\n }\n }\n if (inside) corners.push(v);\n }\n }\n }\n\n // Deduplicate the corners\n const cornerMap: Map<string, Vector> = new Map();\n for (const v of corners) {\n const key = vertexKey(v);\n if (!cornerMap.has(key)) cornerMap.set(key, v);\n }\n const vertices = [...cornerMap.values()];\n\n // Group the corners that lie on each face plane; the face of the BZ is a\n // convex polygon of these coplanar vertices\n const faces: Vector[][] = [];\n const triangles: number[][] = [];\n const trianglesVertices: Vector[] = [];\n const vertexIndex: Map<string, number> = new Map();\n\n const addVertex = (v: Vector): number => {\n const key = vertexKey(v);\n let idx = vertexIndex.get(key);\n if (idx === undefined) {\n idx = trianglesVertices.length;\n vertexIndex.set(key, idx);\n trianglesVertices.push(v);\n }\n return idx;\n };\n\n for (const p of planes) {\n const on = vertices.filter(\n (v) => Math.abs(dot(p.g, v) - p.offset) < 1e-6,\n );\n if (on.length < 3) continue;\n\n // Sort the coplanar vertices angularly around the face centroid\n const centroid = [\n on.reduce((s, v) => s + v[0], 0) / on.length,\n on.reduce((s, v) => s + v[1], 0) / on.length,\n on.reduce((s, v) => s + v[2], 0) / on.length,\n ];\n const ref = Math.abs(p.g[0]) < 0.9 ? new Float64Array([1, 0, 0]) : new Float64Array([0, 1, 0]);\n let e1 = cross(p.g, ref);\n const e1Norm = norm(e1);\n e1 = new Float64Array([e1[0] / e1Norm, e1[1] / e1Norm, e1[2] / e1Norm]);\n const e2 = cross(p.g, e1);\n\n const ordered = [...on].sort((a, b) => {\n const da = new Float64Array([\n a[0] - centroid[0],\n a[1] - centroid[1],\n a[2] - centroid[2],\n ]);\n const db = new Float64Array([\n b[0] - centroid[0],\n b[1] - centroid[1],\n b[2] - centroid[2],\n ]);\n const angleA = Math.atan2(dot(da, e2), dot(da, e1));\n const angleB = Math.atan2(dot(db, e2), dot(db, e1));\n return angleA - angleB;\n });\n\n faces.push(ordered);\n\n // Fan triangulation of the face\n const first = addVertex(ordered[0]);\n for (let m = 1; m < ordered.length - 1; m++) {\n triangles.push([first, addVertex(ordered[m]), addVertex(ordered[m + 1])]);\n }\n }\n\n return {\n triangles_vertices: trianglesVertices.map((v) => Array.from(v)),\n triangles,\n faces: faces.map((face) => face.map((v) => Array.from(v))),\n };\n}\n","// prettier-ignore\n/** Space group data array indexed by space group number: [bravais_letter, centering, chiral]. */\nexport const spgroup_data: ([string, string, boolean] | null)[] = [\n null, // unused (SG = 0)\n [\"a\",\"P\", false], [\"a\",\"P\", true], [\"m\",\"P\", false], [\"m\",\"P\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", false], [\"m\",\"P\", false], [\"m\",\"C\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], \n [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], \n [\"o\",\"C\", false], [\"o\",\"F\", false], [\"o\",\"I\", false], [\"o\",\"I\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false],\n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], [\"o\",\"C\", false],\n [\"o\",\"C\", false], [\"o\",\"A\", false], [\"o\",\"A\", false], [\"o\",\"A\", false],\n [\"o\",\"A\", false], [\"o\",\"F\", false], [\"o\",\"F\", false], [\"o\",\"I\", false],\n [\"o\",\"I\", false], [\"o\",\"I\", false], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"F\", true], [\"o\",\"F\", true], [\"o\",\"I\", true], [\"o\",\"I\", true],\n [\"o\",\"I\", true], [\"o\",\"I\", true], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true],\n [\"t\",\"I\", true], [\"t\",\"I\", true], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"R\", true],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], \n [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", true], [\"h\",\"R\", true], [\"h\",\"R\", true], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true],\n [\"h\",\"P\", true], [\"h\",\"P\", true], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", true],\n [\"c\",\"P\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"I\", true], \n [\"c\",\"P\", true], [\"c\",\"I\", true], [\"c\",\"P\", false], [\"c\",\"P\", false], \n [\"c\",\"F\", false], [\"c\",\"F\", false], [\"c\",\"I\", false], [\"c\",\"P\", false],\n [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false], [\"c\",\"I\", false],\n [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true],\n [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], \n [\"c\",\"I\", true], [\"c\",\"I\", true]];\n\n// prettier-ignore\n/** Centering symbols for each space group (1-indexed). */\nexport const centering: string[] = [\n \"P\",\"P\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"P\",\n \"P\",\"C\",\"C\",\"F\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\n \"C\",\"A\",\"A\",\"A\",\"A\",\"F\",\"F\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\"C\",\"C\",\"C\",\"C\",\"F\",\"F\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"R\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\n \"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"F\",\"I\",\"P\",\n \"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"P\",\"I\",\"P\",\"F\",\n \"I\",\"P\",\"F\",\"I\",\"P\",\"P\",\"P\",\"P\",\"F\",\"F\",\"F\",\"F\",\"I\",\"I\"];\n","import { Matrix, createMatrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { scale } from \"@/core/matrix/operations/scale\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\n\nconst TWO_PI = 2 * Math.PI;\n\n/** Build a 3x3 Matrix from 9 row-major values. */\nexport function matrixFromRowMajor(data: ArrayLike<number>): Matrix {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return createMatrix(3, 3, Array.from(data));\n}\n\n/**\n * Return [a, b, c, cosalpha, cosbeta, cosgamma] for a 3x3 lattice whose\n * rows are the lattice vectors.\n */\nexport function cellParams(\n lattice: Matrix,\n): [number, number, number, number, number, number] {\n const d = lattice.data;\n const v1 = [d[0], d[1], d[2]];\n const v2 = [d[3], d[4], d[5]];\n const v3 = [d[6], d[7], d[8]];\n const a = Math.hypot(v1[0], v1[1], v1[2]);\n const b = Math.hypot(v2[0], v2[1], v2[2]);\n const c = Math.hypot(v3[0], v3[1], v3[2]);\n const dot = (u: number[], v: number[]) =>\n u[0] * v[0] + u[1] * v[1] + u[2] * v[2];\n const cosalpha = dot(v2, v3) / b / c;\n const cosbeta = dot(v1, v3) / a / c;\n const cosgamma = dot(v1, v2) / a / b;\n return [a, b, c, cosalpha, cosbeta, cosgamma];\n}\n\n/** Reciprocal-space cell rows, such that dot(real, recip.T) = 2π I. */\nexport function getReciprocalCellRows(real: Matrix): Matrix {\n return transpose(scale(gjInverse(real), TWO_PI));\n}\n\n/** Real-space cell rows given reciprocal rows, such that dot(recip, real.T) = 2π I. */\nexport function getRealCellFromReciprocalRows(recip: Matrix): Matrix {\n return transpose(scale(gjInverse(recip), TWO_PI));\n}\n\n/**\n * Return the (P, invP) transformation matrices from the crystallographic\n * conventional cell to the primitive cell, as in Table 3 of the HPKOT paper:\n * (a_P, b_P, c_P) = (a, b, c) P and (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T.\n */\nexport function getPmatrix(\n bravaisLattice: string,\n): { P: number[][]; invP: number[][] } {\n if ([\"cP\", \"tP\", \"hP\", \"oP\", \"mP\"].includes(bravaisLattice)) {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if ([\"cF\", \"oF\"].includes(bravaisLattice)) {\n return {\n P: [\n [0, 0.5, 0.5],\n [0.5, 0, 0.5],\n [0.5, 0.5, 0],\n ],\n invP: [\n [-1, 1, 1],\n [1, -1, 1],\n [1, 1, -1],\n ],\n };\n }\n if ([\"cI\", \"tI\", \"oI\"].includes(bravaisLattice)) {\n return {\n P: [\n [-0.5, 0.5, 0.5],\n [0.5, -0.5, 0.5],\n [0.5, 0.5, -0.5],\n ],\n invP: [\n [0, 1, 1],\n [1, 0, 1],\n [1, 1, 0],\n ],\n };\n }\n if (bravaisLattice === \"hR\") {\n return {\n P: [\n [2 / 3, -1 / 3, -1 / 3],\n [1 / 3, 1 / 3, -2 / 3],\n [1 / 3, 1 / 3, 1 / 3],\n ],\n invP: [\n [1, 0, 1],\n [-1, 1, 1],\n [0, -1, 1],\n ],\n };\n }\n if (bravaisLattice === \"oC\") {\n return {\n P: [\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, -1, 0],\n [1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"oA\") {\n return {\n P: [\n [0, 0, 1],\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n ],\n invP: [\n [0, 1, -1],\n [0, 1, 1],\n [1, 0, 0],\n ],\n };\n }\n if (bravaisLattice === \"mC\") {\n return {\n P: [\n [0.5, -0.5, 0],\n [0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 1, 0],\n [-1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"aP\") {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n throw new Error(`Invalid bravais_lattice ${bravaisLattice}`);\n}\n\nexport interface PrimitiveCellResult {\n lattice: number[][];\n positions: number[][];\n types: number[];\n mapping: number[];\n}\n\n/**\n * Build the crystallographic primitive cell from a standardized conventional\n * cell using the HPKOT P matrices, deduplicating atoms that coincide modulo 1.\n */\nexport function getPrimitive(\n lattice: number[][],\n positions: number[][],\n types: number[],\n bravaisLattice: string,\n threshold = 1e-6,\n): PrimitiveCellResult {\n const { P, invP } = getPmatrix(bravaisLattice);\n\n const volumeRatio = Math.round(Math.abs(det3(invP)));\n\n // (a_P, b_P, c_P) = (a, b, c) P => prim vector j = sum_k P[k][j] * a_k,\n // i.e. prim_lattice = P^T @ lattice\n const primLattice = matmul3(transpose3(P), lattice);\n // (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T => row-vector form: positions @ invP.T\n const primPositions = matmul3(positions, transpose3(invP));\n\n const n = positions.length;\n\n // Mark equivalent atoms (same position modulo 1, shifted so that ±0.5 wrap)\n const match = (u: number, v: number) => {\n const diff = Math.abs(((u - v + 0.5) % 1 + 1) % 1 - 0.5);\n return diff < threshold;\n };\n\n const groups: number[][] = [];\n const assigned = new Array<boolean>(n).fill(false);\n\n for (let i = 0; i < n; i++) {\n if (assigned[i]) continue;\n const group: number[] = [];\n for (let j = i; j < n; j++) {\n if (\n match(primPositions[j][0], primPositions[i][0]) &&\n match(primPositions[j][1], primPositions[i][1]) &&\n match(primPositions[j][2], primPositions[i][2])\n ) {\n group.push(j);\n assigned[j] = true;\n }\n }\n groups.push(group);\n }\n\n for (const group of groups) {\n if (group.length !== volumeRatio) {\n throw new Error(\n `Problem creating primitive cell, found group of atoms with length ${group.length} != ${volumeRatio}`,\n );\n }\n const typeSet = new Set(group.map((idx) => types[idx]));\n if (typeSet.size !== 1) {\n throw new Error(\n \"The following atoms go on top of each other, but they are of different type!\",\n );\n }\n }\n\n groups.sort((a, b) => a[0] - b[0]);\n\n const mapping = new Array<number>(n).fill(-1);\n for (let primIdx = 0; primIdx < groups.length; primIdx++) {\n for (const atIdx of groups[primIdx]) mapping[atIdx] = primIdx;\n }\n\n return {\n lattice: primLattice,\n positions: groups.map((g) => primPositions[g[0]]),\n types: groups.map((g) => types[g[0]]),\n mapping,\n };\n}\n\nfunction transpose3(m: number[][]): number[][] {\n return [\n [m[0][0], m[1][0], m[2][0]],\n [m[0][1], m[1][1], m[2][1]],\n [m[0][2], m[1][2], m[2][2]],\n ];\n}\n\nfunction matmul3(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] * b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nfunction det3(m: number[][]): number {\n return (\n m[0][0] * (m[1][1] * m[2][2] - m[1][2] * m[2][1]) -\n m[0][1] * (m[1][0] * m[2][2] - m[1][2] * m[2][0]) +\n m[0][2] * (m[1][0] * m[2][1] - m[1][1] * m[2][0])\n );\n}\n\n/** Evaluate an expression that only requires precomputed k-parameters. */\nexport function evalExprSimple(expr: string, kparam: Record<string, number>): number {\n switch (expr) {\n case \"0\":\n return 0;\n case \"1/2\":\n return 0.5;\n case \"1\":\n return 1;\n case \"-1/2\":\n return -0.5;\n case \"1/4\":\n return 0.25;\n case \"3/8\":\n return 0.375;\n case \"3/4\":\n return 0.75;\n case \"5/8\":\n return 0.625;\n case \"1/3\":\n return 1 / 3;\n default: {\n const val = kparam[expr];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${expr}' in eval_expr_simple but this has not been defined or not yet computed`,\n );\n }\n return val;\n }\n }\n}\n\n/** Extend kparam with derived expressions (1-x, -x, 1/2-x, ...). */\nexport function extendKparam(kparam: Record<string, number>): Record<string, number> {\n const extended: Record<string, number> = {};\n for (const [key, val] of Object.entries(kparam)) {\n extended[key] = val;\n extended[`-${key}`] = -val;\n extended[`1-${key}`] = 1 - val;\n extended[`-1+${key}`] = -1 + val;\n extended[`1/2-${key}`] = 0.5 - val;\n extended[`1/2+${key}`] = 0.5 + val;\n }\n return extended;\n}\n\n/**\n * Evaluate a k-parameter expression as a function of the cell parameters and\n * previously computed k-parameters. Mirrors the hardcoded table in seekpath.\n */\nexport function evalExpr(\n expr: string,\n a: number,\n b: number,\n c: number,\n cosalpha: number,\n cosbeta: number,\n cosgamma: number,\n kparam: Record<string, number>,\n): number {\n const sinbeta = Math.sqrt(1 - cosbeta * cosbeta);\n\n const k = (name: string): number => {\n const val = kparam[name];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${name}' but this has not been defined or not yet computed`,\n );\n }\n return val;\n };\n const Z = () => k(\"Z\");\n const E = () => k(\"E\");\n const F = () => k(\"F\");\n const U = () => k(\"U\");\n const W = () => k(\"W\");\n const S = () => k(\"S\");\n const M = () => k(\"M\");\n const X = () => k(\"X\");\n const D = () => k(\"D\");\n const Y = () => k(\"Y\");\n\n switch (expr) {\n case \"(a*a/b/b+(1+a/c*cosbeta)/sinbeta/sinbeta)/4\":\n return (a * a / b / b + (1 + a / c * cosbeta) / sinbeta / sinbeta) / 4;\n case \"1-Z*b*b/a/a\":\n return 1 - Z() * b * b / a / a;\n case \"1/2-2*Z*c*cosbeta/a\":\n return 0.5 - 2 * Z() * c * cosbeta / a;\n case \"E/2+a*a/4/b/b+a*c*cosbeta/2/b/b\":\n return E() / 2 + a * a / 4 / b / b + a * c * cosbeta / 2 / b / b;\n case \"2*F-Z\":\n return 2 * F() - Z();\n case \"c/2/a/cosbeta*(1-4*U+a*a*sinbeta*sinbeta/b/b)\":\n return (\n c / 2 / a / cosbeta * (1 - 4 * U() + a * a * sinbeta * sinbeta / b / b)\n );\n case \"-1/4+W/2-Z*c*cosbeta/a\":\n return -0.25 + W() / 2 - Z() * c * cosbeta / a;\n case \"(2+a/c*cosbeta)/4/sinbeta/sinbeta\":\n return (2 + a / c * cosbeta) / 4 / sinbeta / sinbeta;\n case \"3/4-b*b/4/a/a/sinbeta/sinbeta\":\n return 3 / 4 - b * b / 4 / a / a / sinbeta / sinbeta;\n case \"S-(3/4-S)*a*cosbeta/c\":\n return S() - (3 / 4 - S()) * a * cosbeta / c;\n case \"(1+a*a/b/b)/4\":\n return (1 + a * a / b / b) / 4;\n case \"-a*c*cosbeta/2/b/b\":\n return -a * c * cosbeta / 2 / b / b;\n case \"1+Z-2*M\":\n return 1 + Z() - 2 * M();\n case \"X-2*D\":\n return X() - 2 * D();\n case \"(1+a/c*cosbeta)/2/sinbeta/sinbeta\":\n return (1 + a / c * cosbeta) / 2 / sinbeta / sinbeta;\n case \"1/2+Y*c*cosbeta/a\":\n return 0.5 + Y() * c * cosbeta / a;\n case \"a*a/4/c/c\":\n return a * a / 4 / c / c;\n case \"5/6-2*D\":\n return 5 / 6 - 2 * D();\n case \"1/3+D\":\n return 1 / 3 + D();\n case \"1/6-c*c/9/a/a\":\n return 1 / 6 - c * c / 9 / a / a;\n case \"1/2-2*Z\":\n return 0.5 - 2 * Z();\n case \"1/2+Z\":\n return 0.5 + Z();\n case \"(1+b*b/c/c)/4\":\n return (1 + b * b / c / c) / 4;\n case \"(1+c*c/b/b)/4\":\n return (1 + c * c / b / b) / 4;\n case \"(1+b*b/a/a)/4\":\n return (1 + b * b / a / a) / 4;\n case \"(1+a*a/b/b-a*a/c/c)/4\":\n return (1 + a * a / b / b - a * a / c / c) / 4;\n case \"(1+a*a/b/b+a*a/c/c)/4\":\n return (1 + a * a / b / b + a * a / c / c) / 4;\n case \"(1+c*c/a/a-c*c/b/b)/4\":\n return (1 + c * c / a / a - c * c / b / b) / 4;\n case \"(1+c*c/a/a+c*c/b/b)/4\":\n return (1 + c * c / a / a + c * c / b / b) / 4;\n case \"(1+b*b/a/a-b*b/c/c)/4\":\n return (1 + b * b / a / a - b * b / c / c) / 4;\n case \"(1+c*c/b/b-c*c/a/a)/4\":\n return (1 + c * c / b / b - c * c / a / a) / 4;\n case \"(1+a*a/c/c)/4\":\n return (1 + a * a / c / c) / 4;\n case \"(b*b-a*a)/4/c/c\":\n return (b * b - a * a) / 4 / c / c;\n case \"(a*a+b*b)/4/c/c\":\n return (a * a + b * b) / 4 / c / c;\n case \"(1+c*c/a/a)/4\":\n return (1 + c * c / a / a) / 4;\n case \"(c*c-b*b)/4/a/a\":\n return (c * c - b * b) / 4 / a / a;\n case \"(b*b+c*c)/4/a/a\":\n return (b * b + c * c) / 4 / a / a;\n case \"(a*a-c*c)/4/b/b\":\n return (a * a - c * c) / 4 / b / b;\n case \"(c*c+a*a)/4/b/b\":\n return (c * c + a * a) / 4 / b / b;\n case \"a*a/2/c/c\":\n return a * a / 2 / c / c;\n default:\n throw new Error(\n `Unknown expression, define a new case: '${expr}'`,\n );\n }\n}\n\n/** Wrap a cell in a Matrix to use matrix helpers. */\nexport function toMatrix(rows: number[][]): Matrix {\n return createMatrix(3, 3, rows.flat());\n}\n\n/** Row-vector times matrix: x_abs[i] = v . col_i(m). */\nexport function vecMulMat(v: number[], m: number[][]): number[] {\n return [\n v[0] * m[0][0] + v[1] * m[1][0] + v[2] * m[2][0],\n v[0] * m[0][1] + v[1] * m[1][1] + v[2] * m[2][1],\n v[0] * m[0][2] + v[1] * m[1][2] + v[2] * m[2][2],\n ];\n}\n","import { Matrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\nimport { niggli_reduce } from \"../spglib-wasm\";\nimport {\n cellParams,\n getReciprocalCellRows,\n getRealCellFromReciprocalRows,\n matrixFromRowMajor,\n} from \"./seekpathTools\";\n\nconst M2_MATRICES = [\n [\n [0, 0, 1],\n [1, 0, 0],\n [0, 1, 0],\n ],\n [\n [0, 1, 0],\n [0, 0, 1],\n [1, 0, 0],\n ],\n [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n];\n\n/** Determine the aP label (aP2 all-obtuse / aP3 all-acute) as in HPKOT. */\nconst M3_I = [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n];\nconst M3_XX = [\n [1, 0, 0],\n [0, -1, 0],\n [0, 0, -1],\n];\nconst M3_YY = [\n [-1, 0, 0],\n [0, 1, 0],\n [0, 0, -1],\n];\nconst M3_ZZ = [\n [-1, 0, 0],\n [0, -1, 0],\n [0, 0, 1],\n];\n\nfunction mulRows(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] * b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nexport interface APTransform {\n lattice: number[][];\n positions: number[][];\n extBravais: string;\n}\n\n/**\n * Apply the Niggli reduction plus the M2/M3 vector transforms of the HPKOT\n * paper to bring a triclinic conventional cell into the all-obtuse (aP2) or\n * all-acute (aP3) setting.\n */\nexport async function transformAP(\n lattice: number[][],\n positions: number[][],\n): Promise<APTransform> {\n const convLattice = matrixFromRowMajor(lattice.flat());\n\n const reciprocalCellOrig = getReciprocalCellRows(convLattice);\n const reduced = await niggli_reduce(Array.from(reciprocalCellOrig.data));\n if (!reduced) throw new Error(\"Niggli reduction failed for aP lattice\");\n const reciprocalCell2 = matrixFromRowMajor(reduced);\n const realCell2 = getRealCellFromReciprocalRows(reciprocalCell2);\n\n const [ka2, kb2, kc2, coskalpha2, coskbeta2, coskgamma2] =\n cellParams(reciprocalCell2);\n const conditions = [\n Math.abs(kb2 * kc2 * coskalpha2),\n Math.abs(kc2 * ka2 * coskbeta2),\n Math.abs(ka2 * kb2 * coskgamma2),\n ];\n\n let smallest = 0;\n if (conditions[1] < conditions[smallest]) smallest = 1;\n if (conditions[2] < conditions[smallest]) smallest = 2;\n const M2 = matrixFromRowMajor(M2_MATRICES[smallest].flat());\n const realCell3 = mul(transpose(M2), realCell2);\n\n const reciprocalCell3 = getReciprocalCellRows(realCell3);\n const [, , , ca3, cb3, cg3] = cellParams(reciprocalCell3);\n\n let M3: number[][];\n if ((ca3 > 0 && cb3 > 0 && cg3 > 0) || (ca3 <= 0 && cb3 <= 0 && cg3 <= 0))\n M3 = M3_I;\n else if (\n (ca3 > 0 && cb3 <= 0 && cg3 <= 0) ||\n (ca3 <= 0 && cb3 > 0 && cg3 > 0)\n )\n M3 = M3_XX;\n else if (\n (ca3 <= 0 && cb3 > 0 && cg3 <= 0) ||\n (ca3 > 0 && cb3 <= 0 && cg3 > 0)\n )\n M3 = M3_YY;\n else if (\n (ca3 <= 0 && cb3 <= 0 && cg3 > 0) ||\n (ca3 > 0 && cb3 > 0 && cg3 <= 0)\n )\n M3 = M3_ZZ;\n else\n throw new Error(\n \"Problem identifying M3 matrix in aP lattice: sign pattern of cosines ambiguous\",\n );\n\n const M3mat = matrixFromRowMajor(M3.flat());\n const realCellFinal = mul(transpose(M3mat), realCell3);\n const reciprocalCellFinal = getReciprocalCellRows(realCellFinal);\n const [, , , ca, cb, cg] = cellParams(reciprocalCellFinal);\n\n let extBravais: string;\n if (ca <= 0 && cb <= 0 && cg <= 0) extBravais = \"aP2\";\n else if (ca >= 0 && cb >= 0 && cg >= 0) extBravais = \"aP3\";\n else\n throw new Error(\n \"Unexpected aP lattice, neither all-obtuse nor all-acute in reciprocal space\",\n );\n\n // Express the (absolute) atomic positions in the new real cell basis\n const finalRows = Array.from(realCellFinal.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const absPositions = mulRows(positions, lattice);\n const invFinal = gjInverse(matrixFromRowMajor(finalRows.flat()));\n const newPositions = absPositions.map((p) => {\n const v = createVector(p);\n const res = mul(invFinal, v).data;\n return [res[0], res[1], res[2]];\n });\n\n return {\n lattice: finalRows,\n positions: newPositions,\n extBravais,\n };\n}\n\nfunction createVector(v: number[]): Matrix {\n return { rows: 3, cols: 1, data: new Float64Array(v) };\n}\n\n/** Determine the aP label (aP2 / aP3) for a triclinic conventional lattice. */\nexport async function determineAP(convLattice: Matrix): Promise<string> {\n const rows = Array.from(convLattice.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const { extBravais } = await transformAP(rows, []);\n return extBravais;\n}\n\n/** Determine the Seekpath extended Bravais lattice from a conventional cell. */\nexport function determineExtBravais(\n bL: string,\n spgN: number,\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n): string {\n const threshold = 1e-7;\n\n switch (bL) {\n case \"cP\":\n if (spgN < 195 || spgN > 230)\n throw new Error(\"cP requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cP1\" : \"cP2\";\n\n case \"cF\":\n if (spgN < 195 || spgN > 230)\n throw new Error(\"cF requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cF1\" : \"cF2\";\n\n case \"cI\":\n return \"cI1\";\n\n case \"tP\":\n return \"tP1\";\n\n case \"tI\":\n if (c - a < threshold) {\n console.warn(\"tI lattice, a ≈ c\");\n }\n return c <= a ? \"tI1\" : \"tI2\";\n\n case \"oP\":\n return \"oP1\";\n\n case \"oF\": {\n const A = 1.0 / a ** 2;\n const B = 1.0 / b ** 2;\n const C = 1.0 / c ** 2;\n\n if (A > B + C) {\n return \"oF1\";\n }\n\n if (C > A + B) {\n return \"oF2\";\n } else return \"oF3\";\n }\n\n case \"oI\": {\n const sorted = [\n { v: c, id: 1 },\n { v: b, id: 3 },\n { v: a, id: 2 },\n ]\n .sort((x, y) => x.v - y.v || x.id - y.id)\n .reverse();\n\n if (Math.abs(sorted[0].v - sorted[1].v) < threshold) {\n console.warn(\"oI near-degeneracy\");\n }\n\n return `${bL}${sorted[0].id}`;\n }\n\n case \"oC\":\n return a <= b ? \"oC1\" : \"oC2\";\n\n case \"oA\":\n return b <= c ? \"oA1\" : \"oA2\";\n\n case \"hP\":\n return [\n 143, 144, 145, 146, 147, 148, 149, 151, 153, 157, 159, 160, 161, 162,\n 163,\n ].includes(spgN)\n ? \"hP1\"\n : \"hP2\";\n\n case \"hR\":\n return Math.sqrt(3) * a <= Math.sqrt(2) * c ? \"hR1\" : \"hR2\";\n\n case \"mP\":\n return \"mP1\";\n\n case \"mC\": {\n const rad = Math.PI / 180;\n const cosbeta = Math.cos(beta * rad);\n const sinbeta = Math.sin(beta * rad);\n\n const term1 = b - a * Math.sqrt(1 - cosbeta ** 2);\n\n if (Math.abs(term1) < threshold) {\n console.warn(\"mC near-degeneracy\");\n }\n\n if (b < a * sinbeta) return \"mC1\";\n\n const expr = (-a * cosbeta) / c + (a ** 2 * (1 - cosbeta ** 2)) / b ** 2;\n if (Math.abs(expr - 1.0) < threshold) {\n console.warn(\"mC second degeneracy\");\n }\n\n return expr <= 1 ? \"mC2\" : \"mC3\";\n }\n\n case \"aP\":\n throw new Error(\"aP must be handled by determineAP\");\n\n default:\n throw new Error(`Unknown bravais lattice: ${bL}`);\n }\n}\n","// AUTO-GENERATED FILE — DO NOT EDIT\n// Source: https://github.com/materialscloud-org/seekpath (HPKOT band path data)\n\nexport interface BandPathData {\n kparam: [string, string][];\n points: Record<string, [string, string, string]>;\n path: [string, string][];\n}\n\nexport const bandPathData: Record<string, BandPathData> = {\n \"aP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V\": [\"1/2\", \"1/2\", \"0\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"U\", \"GAMMA\"],\n [\"GAMMA\", \"V\"]\n ],\n },\n \"aP3\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"Y_2\": [\"0\", \"-1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"1/2\", \"-1/2\", \"0\"],\n \"U_2\": [\"-1/2\", \"0\", \"1/2\"],\n \"T_2\": [\"0\", \"-1/2\", \"1/2\"],\n \"R_2\": [\"-1/2\", \"-1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R_2\", \"GAMMA\"],\n [\"GAMMA\", \"T_2\"],\n [\"U_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"cF1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"],\n [\"X\", \"W_2\"]\n ],\n },\n \"cF2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"]\n ],\n },\n \"cI1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"H\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"H\"],\n [\"H\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"P\"],\n [\"P\", \"H\"],\n [\"P\", \"N\"]\n ],\n },\n \"cP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"],\n [\"M\", \"X_1\"]\n ],\n },\n \"cP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"]\n ],\n },\n \"hP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"],\n [\"K\", \"H_2\"]\n ],\n },\n \"hP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"]\n ],\n },\n \"hR1\": {\n kparam: [\n [\"D\", \"a*a/4/c/c\"],\n [\"Y\", \"5/6-2*D\"],\n [\"N\", \"1/3+D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"L_2\": [\"0\", \"-1/2\", \"0\"],\n \"L_4\": [\"0\", \"0\", \"-1/2\"],\n \"F\": [\"1/2\", \"0\", \"1/2\"],\n \"F_2\": [\"1/2\", \"1/2\", \"0\"],\n \"S_0\": [\"N\", \"-N\", \"0\"],\n \"S_2\": [\"1-N\", \"0\", \"N\"],\n \"S_4\": [\"N\", \"0\", \"-N\"],\n \"S_6\": [\"1-N\", \"N\", \"0\"],\n \"H_0\": [\"1/2\", \"-1+Y\", \"1-Y\"],\n \"H_2\": [\"Y\", \"1-Y\", \"1/2\"],\n \"H_4\": [\"Y\", \"1/2\", \"1-Y\"],\n \"H_6\": [\"1/2\", \"1-Y\", \"-1+Y\"],\n \"M_0\": [\"N\", \"-1+Y\", \"N\"],\n \"M_2\": [\"1-N\", \"1-Y\", \"1-N\"],\n \"M_4\": [\"Y\", \"N\", \"N\"],\n \"M_6\": [\"1-N\", \"1-N\", \"1-Y\"],\n \"M_8\": [\"N\", \"N\", \"-1+Y\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"H_2\"],\n [\"H_0\", \"L\"],\n [\"L\", \"GAMMA\"],\n [\"GAMMA\", \"S_0\"],\n [\"S_2\", \"F\"],\n [\"F\", \"GAMMA\"]\n ],\n },\n \"hR2\": {\n kparam: [\n [\"Z\", \"1/6-c*c/9/a/a\"],\n [\"H\", \"1/2-2*Z\"],\n [\"N\", \"1/2+Z\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P_0\": [\"H\", \"-1+H\", \"H\"],\n \"P_2\": [\"H\", \"H\", \"H\"],\n \"R_0\": [\"1-H\", \"-H\", \"-H\"],\n \"M\": [\"1-N\", \"-N\", \"1-N\"],\n \"M_2\": [\"N\", \"-1+N\", \"-1+N\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"F\": [\"1/2\", \"-1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"L\"],\n [\"L\", \"T\"],\n [\"T\", \"P_0\"],\n [\"P_2\", \"GAMMA\"],\n [\"GAMMA\", \"F\"]\n ],\n },\n \"mC1\": {\n kparam: [\n [\"Z\", \"(2+a/c*cosbeta)/4/sinbeta/sinbeta\"],\n [\"H\", \"1/2-2*Z*c*cosbeta/a\"],\n [\"S\", \"3/4-b*b/4/a/a/sinbeta/sinbeta\"],\n [\"P\", \"S-(3/4-S)*a*cosbeta/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y_2\": [\"-1/2\", \"1/2\", \"0\"],\n \"Y_4\": [\"1/2\", \"-1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"C\": [\"1-S\", \"1-S\", \"0\"],\n \"C_2\": [\"-1+S\", \"S\", \"0\"],\n \"C_4\": [\"S\", \"-1+S\", \"0\"],\n \"D\": [\"-1+P\", \"P\", \"1/2\"],\n \"D_2\": [\"1-P\", \"1-P\", \"1/2\"],\n \"E\": [\"-1+Z\", \"1-Z\", \"1-H\"],\n \"E_2\": [\"-Z\", \"Z\", \"H\"],\n \"E_4\": [\"Z\", \"-Z\", \"1-H\"]\n },\n path: [\n [\"GAMMA\", \"C\"],\n [\"C_2\", \"Y_2\"],\n [\"Y_2\", \"GAMMA\"],\n [\"GAMMA\", \"M_2\"],\n [\"M_2\", \"D\"],\n [\"D_2\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC2\": {\n kparam: [\n [\"Z\", \"(a*a/b/b+(1+a/c*cosbeta)/sinbeta/sinbeta)/4\"],\n [\"M\", \"(1+a*a/b/b)/4\"],\n [\"D\", \"-a*c*cosbeta/2/b/b\"],\n [\"X\", \"1/2-2*Z*c*cosbeta/a\"],\n [\"P\", \"1+Z-2*M\"],\n [\"S\", \"X-2*D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"1/2\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"F\": [\"-1+P\", \"1-P\", \"1-S\"],\n \"F_2\": [\"1-P\", \"P\", \"S\"],\n \"F_4\": [\"P\", \"1-P\", \"1-S\"],\n \"H\": [\"-Z\", \"Z\", \"X\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-X\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-X\"],\n \"G\": [\"-M\", \"M\", \"D\"],\n \"G_2\": [\"M\", \"1-M\", \"-D\"],\n \"G_4\": [\"M\", \"-M\", \"-D\"],\n \"G_6\": [\"1-M\", \"M\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"M\"],\n [\"M\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC3\": {\n kparam: [\n [\"Z\", \"(a*a/b/b+(1+a/c*cosbeta)/sinbeta/sinbeta)/4\"],\n [\"R\", \"1-Z*b*b/a/a\"],\n [\"E\", \"1/2-2*Z*c*cosbeta/a\"],\n [\"F\", \"E/2+a*a/4/b/b+a*c*cosbeta/2/b/b\"],\n [\"U\", \"2*F-Z\"],\n [\"W\", \"c/2/a/cosbeta*(1-4*U+a*a*sinbeta*sinbeta/b/b)\"],\n [\"D\", \"-1/4+W/2-Z*c*cosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"I\": [\"-1+R\", \"R\", \"1/2\"],\n \"I_2\": [\"1-R\", \"1-R\", \"1/2\"],\n \"K\": [\"-U\", \"U\", \"W\"],\n \"K_2\": [\"-1+U\", \"1-U\", \"1-W\"],\n \"K_4\": [\"1-U\", \"U\", \"W\"],\n \"H\": [\"-Z\", \"Z\", \"E\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-E\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-E\"],\n \"N\": [\"-F\", \"F\", \"D\"],\n \"N_2\": [\"F\", \"1-F\", \"-D\"],\n \"N_4\": [\"F\", \"-F\", \"-D\"],\n \"N_6\": [\"1-F\", \"F\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"A\"],\n [\"A\", \"I_2\"],\n [\"I\", \"M_2\"],\n [\"M_2\", \"GAMMA\"],\n [\"GAMMA\", \"Y\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mP1\": {\n kparam: [\n [\"Y\", \"(1+a/c*cosbeta)/2/sinbeta/sinbeta\"],\n [\"N\", \"1/2+Y*c*cosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"1/2\", \"0\"],\n \"B\": [\"0\", \"0\", \"1/2\"],\n \"B_2\": [\"0\", \"0\", \"-1/2\"],\n \"Y\": [\"1/2\", \"0\", \"0\"],\n \"Y_2\": [\"-1/2\", \"0\", \"0\"],\n \"C\": [\"1/2\", \"1/2\", \"0\"],\n \"C_2\": [\"-1/2\", \"1/2\", \"0\"],\n \"D\": [\"0\", \"1/2\", \"1/2\"],\n \"D_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"A\": [\"-1/2\", \"0\", \"1/2\"],\n \"E\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"H\": [\"-Y\", \"0\", \"1-N\"],\n \"H_2\": [\"-1+Y\", \"0\", \"N\"],\n \"H_4\": [\"-Y\", \"0\", \"-N\"],\n \"M\": [\"-Y\", \"1/2\", \"1-N\"],\n \"M_2\": [\"-1+Y\", \"1/2\", \"N\"],\n \"M_4\": [\"-Y\", \"1/2\", \"-N\"]\n },\n path: [\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"D\"],\n [\"D\", \"B\"],\n [\"B\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"E\"],\n [\"E\", \"Z\"],\n [\"Z\", \"C_2\"],\n [\"C_2\", \"Y_2\"],\n [\"Y_2\", \"GAMMA\"]\n ],\n },\n \"oA1\": {\n kparam: [\n [\"X\", \"(1+b*b/c/c)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"-1/2\", \"1/2\", \"0\"],\n \"T\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oA2\": {\n kparam: [\n [\"X\", \"(1+c*c/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC1\": {\n kparam: [\n [\"X\", \"(1+a*a/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"-1/2\", \"1/2\", \"0\"],\n \"T\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC2\": {\n kparam: [\n [\"X\", \"(1+b*b/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oF1\": {\n kparam: [\n [\"J\", \"(1+a*a/b/b-a*a/c/c)/4\"],\n [\"H\", \"(1+a*a/b/b+a*a/c/c)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"SIGMA_0\": [\"0\", \"H\", \"H\"],\n \"U_0\": [\"1\", \"1-H\", \"1-H\"],\n \"A_0\": [\"1/2\", \"1/2+J\", \"J\"],\n \"C_0\": [\"1/2\", \"1/2-J\", \"1-J\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"GAMMA\"],\n [\"GAMMA\", \"SIGMA_0\"],\n [\"U_0\", \"T\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF2\": {\n kparam: [\n [\"J\", \"(1+c*c/a/a-c*c/b/b)/4\"],\n [\"K\", \"(1+c*c/a/a+c*c/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"1\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"LAMBDA_0\": [\"K\", \"K\", \"0\"],\n \"Q_0\": [\"1-K\", \"1-K\", \"1\"],\n \"G_0\": [\"1/2-J\", \"1-J\", \"1/2\"],\n \"H_0\": [\"1/2+J\", \"J\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"Q_0\", \"Z\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF3\": {\n kparam: [\n [\"H\", \"(1+a*a/b/b-a*a/c/c)/4\"],\n [\"K\", \"(1+b*b/a/a-b*b/c/c)/4\"],\n [\"P\", \"(1+c*c/b/b-c*c/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"A_0\": [\"1/2\", \"1/2+H\", \"H\"],\n \"C_0\": [\"1/2\", \"1/2-H\", \"1-H\"],\n \"B_0\": [\"1/2+K\", \"1/2\", \"K\"],\n \"D_0\": [\"1/2-K\", \"1/2\", \"1-K\"],\n \"G_0\": [\"P\", \"1/2+P\", \"1/2\"],\n \"H_0\": [\"1-P\", \"1/2-P\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"D_0\", \"T\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"T\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oI1\": {\n kparam: [\n [\"Z\", \"(1+a*a/c/c)/4\"],\n [\"H\", \"(1+b*b/c/c)/4\"],\n [\"D\", \"(b*b-a*a)/4/c/c\"],\n [\"N\", \"(a*a+b*b)/4/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Z\", \"Z\", \"Z\"],\n \"F_2\": [\"Z\", \"1-Z\", \"-Z\"],\n \"Y_0\": [\"H\", \"-H\", \"H\"],\n \"U_0\": [\"1-H\", \"H\", \"-H\"],\n \"L_0\": [\"-N\", \"N\", \"1/2-D\"],\n \"M_0\": [\"N\", \"-N\", \"1/2+D\"],\n \"J_0\": [\"1/2-D\", \"1/2+D\", \"-N\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_2\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Y_0\"],\n [\"U_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI2\": {\n kparam: [\n [\"Z\", \"(1+b*b/a/a)/4\"],\n [\"H\", \"(1+c*c/a/a)/4\"],\n [\"D\", \"(c*c-b*b)/4/a/a\"],\n [\"N\", \"(b*b+c*c)/4/a/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Y_0\": [\"Z\", \"-Z\", \"Z\"],\n \"U_2\": [\"-Z\", \"Z\", \"1-Z\"],\n \"LAMBDA_0\": [\"H\", \"H\", \"-H\"],\n \"G_2\": [\"-H\", \"1-H\", \"H\"],\n \"K\": [\"1/2-D\", \"-N\", \"N\"],\n \"K_2\": [\"1/2+D\", \"N\", \"-N\"],\n \"K_4\": [\"-N\", \"1/2-D\", \"1/2+D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U_2\"],\n [\"Y_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_2\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI3\": {\n kparam: [\n [\"Z\", \"(1+c*c/b/b)/4\"],\n [\"Y\", \"(1+a*a/b/b)/4\"],\n [\"D\", \"(a*a-c*c)/4/b/b\"],\n [\"M\", \"(c*c+a*a)/4/b/b\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Y\", \"Y\", \"Y\"],\n \"F_0\": [\"Y\", \"-Y\", \"1-Y\"],\n \"LAMBDA_0\": [\"Z\", \"Z\", \"-Z\"],\n \"G_0\": [\"1-Z\", \"-Z\", \"Z\"],\n \"V_0\": [\"M\", \"1/2-D\", \"-M\"],\n \"H_0\": [\"-M\", \"1/2+D\", \"M\"],\n \"H_2\": [\"1/2+D\", \"-M\", \"1/2-D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"S\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"S\"],\n [\"S\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"U\"],\n [\"U\", \"R\"],\n [\"R\", \"T\"],\n [\"T\", \"Z\"],\n [\"X\", \"U\"],\n [\"Y\", \"T\"],\n [\"S\", \"R\"]\n ],\n },\n \"tI1\": {\n kparam: [\n [\"H\", \"(1+c*c/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Z\": [\"H\", \"H\", \"-H\"],\n \"Z_0\": [\"-H\", \"1-H\", \"H\"],\n \"N\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z_0\", \"M\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"]\n ],\n },\n \"tI2\": {\n kparam: [\n [\"H\", \"(1+a*a/c/c)/4\"],\n [\"Z\", \"a*a/2/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"1/2\", \"0\"],\n \"S_0\": [\"-H\", \"H\", \"H\"],\n \"S\": [\"H\", \"1-H\", \"-H\"],\n \"R\": [\"-Z\", \"Z\", \"1/2\"],\n \"G\": [\"1/2\", \"1/2\", \"-Z\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"M\"],\n [\"M\", \"S\"],\n [\"S_0\", \"GAMMA\"],\n [\"X\", \"R\"],\n [\"G\", \"M\"]\n ],\n },\n \"tP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"1/2\", \"1/2\", \"1/2\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"R\"],\n [\"R\", \"A\"],\n [\"A\", \"Z\"],\n [\"X\", \"R\"],\n [\"M\", \"A\"]\n ],\n },\n};\n\nexport const extBravaisLattices = Object.keys(bandPathData);\n","import { Structure } from \"../../../structure\";\nimport { getSymmetry } from \"../spglib\";\nimport { MoyoDataset } from \"../spglib-wasm\";\nimport { spgroup_data } from \"../spgData\";\n\nimport { parameters } from \"../../../../lattice/parameters\";\n\nimport { determinant } from \"@/core/matrix/operations/determinant\";\n\nimport { transformAP, determineExtBravais, determineAP } from \"./bravais\";\nimport {\n cellParams,\n evalExpr,\n evalExprSimple,\n extendKparam,\n getPmatrix,\n getPrimitive,\n getReciprocalCellRows,\n matrixFromRowMajor,\n vecMulMat,\n} from \"./seekpathTools\";\nimport { bandPathData } from \"./bandPathData\";\n\nconst RAD2DEG = 180 / Math.PI;\n\nfunction rowsFromFlat(data: ArrayLike<number>): number[][] {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return [\n [data[0], data[1], data[2]],\n [data[3], data[4], data[5]],\n [data[6], data[7], data[8]],\n ];\n}\n\n/** Compute [a, b, c, alphaDeg, betaDeg, gammaDeg] from a row-major 3x3 lattice. */\nfunction cellParamsDegrees(data: ArrayLike<number>): number[] {\n const [a, b, c, cosalpha, cosbeta, cosgamma] = cellParams(\n matrixFromRowMajor(data),\n );\n const acos = (x: number) => Math.acos(Math.max(-1, Math.min(1, x))) * RAD2DEG;\n return [a, b, c, acos(cosalpha), acos(cosbeta), acos(cosgamma)];\n}\n\n/** Determine the Seekpath extended Bravais lattice from symmetry data. */\nexport async function getSeekPathHighSymPath(\n structure: Structure,\n symTol = 1e-6,\n): Promise<string> {\n const symData = await getSymmetry(structure, symTol);\n\n const conventionalLattice = symData.conventional.lattice;\n const [a, b, c, alpha, beta, gamma] = parameters(conventionalLattice);\n const spgN = symData.calculationResults.number;\n\n const props = spgroup_data[spgN];\n if (!props) throw new Error(`No space group data for SG ${spgN}`);\n const bL = `${props[0]}${props[1]}`;\n\n if (bL === \"aP\") {\n return determineAP(conventionalLattice.basis);\n }\n\n return determineExtBravais(bL, spgN, a, b, c, alpha, beta, gamma);\n}\n\nexport interface GetPathOptions {\n withTimeReversal?: boolean;\n threshold?: number;\n symprec?: number;\n}\n\nexport interface SeekPathResult {\n point_coords: Record<string, [number, number, number]>;\n path: [string, string][];\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n bravais_lattice: string;\n bravais_lattice_extended: string;\n conv_lattice: number[][];\n conv_positions: number[][];\n conv_types: number[];\n primitive_lattice: number[][];\n primitive_positions: number[][];\n primitive_types: number[];\n reciprocal_primitive_lattice: number[][];\n inverse_primitive_transformation_matrix: number[][];\n primitive_transformation_matrix: number[][];\n volume_original_wrt_conv: number;\n volume_original_wrt_prim: number;\n spacegroup_number: number;\n spacegroup_international: string;\n rotation_matrix: number[][];\n}\n\n/**\n * Return the k-point path information for a band structure, following the\n * HPKOT recipe. Mirrors `seekpath.get_path`.\n */\nexport async function getPath(\n structure: Structure,\n opts: GetPathOptions = {},\n): Promise<SeekPathResult> {\n const {\n withTimeReversal = true,\n threshold = 1e-7,\n symprec = 1e-5,\n } = opts;\n\n const symData = await getSymmetry(structure, symprec);\n const calcResults: MoyoDataset = symData.calculationResults;\n\n const stdCell = calcResults.std_cell;\n const convLatticeFlat = stdCell.lattice.basis;\n const convPositions = stdCell.positions.map((p) => Array.from(p));\n const convTypes = Array.from(stdCell.numbers);\n\n const spgrpNum = calcResults.number;\n const properties = spgroup_data[spgrpNum];\n if (!properties) {\n throw new Error(`No space group data for SG ${spgrpNum}`);\n }\n const bravaisLattice = `${properties[0]}${properties[1]}`;\n const hasInv = properties[2];\n\n const [a, b, c, alphaDeg, betaDeg, gammaDeg] = cellParamsDegrees(\n convLatticeFlat,\n );\n\n // Implement all different extended Bravais lattices\n let extBravais: string;\n let convLattice: number[][];\n let convPositionsFinal: number[][];\n\n if (bravaisLattice === \"aP\") {\n const ap = await transformAP(rowsFromFlat(convLatticeFlat), convPositions);\n extBravais = ap.extBravais;\n convLattice = ap.lattice;\n convPositionsFinal = ap.positions;\n } else {\n extBravais = determineExtBravais(\n bravaisLattice,\n spgrpNum,\n a,\n b,\n c,\n alphaDeg,\n betaDeg,\n gammaDeg,\n );\n convLattice = rowsFromFlat(convLatticeFlat);\n convPositionsFinal = convPositions;\n }\n\n // Primitive cell from the conventional cell via the HPKOT P matrix\n const primitive = getPrimitive(\n convLattice,\n convPositionsFinal,\n convTypes,\n bravaisLattice,\n );\n const { P, invP } = getPmatrix(bravaisLattice);\n\n // Get the path data (k-parameters definitions, point definitions, path)\n const data = bandPathData[extBravais];\n if (!data) throw new Error(`No band path data for extended Bravais ${extBravais}`);\n\n const [kparamDef, pointsDef, basePath] = [\n data.kparam,\n data.points,\n data.path,\n ];\n\n const cosalpha = Math.cos(alphaDeg * Math.PI / 180);\n const cosbeta = Math.cos(betaDeg * Math.PI / 180);\n const cosgamma = Math.cos(gammaDeg * Math.PI / 180);\n\n const kparam: Record<string, number> = {};\n for (const [kparamName, kparamExpr] of kparamDef) {\n kparam[kparamName] = evalExpr(\n kparamExpr,\n a,\n b,\n c,\n cosalpha,\n cosbeta,\n cosgamma,\n kparam,\n );\n }\n const kparamExtended = extendKparam(kparam);\n\n const points: Record<string, [number, number, number]> = {};\n for (const [pointName, coordsDef] of Object.entries(pointsDef)) {\n points[pointName] = coordsDef.map((e) =>\n evalExprSimple(e, kparamExtended),\n ) as [number, number, number];\n }\n\n // If there is no inversion symmetry nor time-reversal symmetry, add\n // additional -k points\n const augmentedPath = !hasInv && !withTimeReversal;\n\n let path: [string, string][] = basePath;\n if (augmentedPath) {\n const negPoints: Record<string, [number, number, number]> = {};\n for (const [pointName, coords] of Object.entries(points)) {\n if (pointName === \"GAMMA\") continue;\n negPoints[`${pointName}'`] = [-coords[0], -coords[1], -coords[2]];\n }\n Object.assign(points, negPoints);\n\n const oldPath = basePath;\n const newSegments: [string, string][] = [];\n for (const [startP, endP] of oldPath) {\n newSegments.push([\n startP === \"GAMMA\" ? startP : `${startP}'`,\n endP === \"GAMMA\" ? endP : `${endP}'`,\n ]);\n }\n path = [...basePath, ...newSegments];\n }\n\n const primitiveMatrix = matrixFromRowMajor(primitive.lattice.flat());\n const reciprocalPrimitive = getReciprocalCellRows(primitiveMatrix);\n\n const origDet = Math.abs(\n determinant(matrixFromRowMajor(Array.from(structure.lattice.basis.data))),\n );\n const convDet = Math.abs(determinant(matrixFromRowMajor(convLattice.flat())));\n const primDet = Math.abs(determinant(primitiveMatrix));\n\n return {\n point_coords: points,\n path,\n has_inversion_symmetry: hasInv,\n augmented_path: augmentedPath,\n bravais_lattice: bravaisLattice,\n bravais_lattice_extended: extBravais,\n conv_lattice: convLattice,\n conv_positions: convPositionsFinal,\n conv_types: convTypes,\n primitive_lattice: primitive.lattice,\n primitive_positions: primitive.positions,\n primitive_types: primitive.types,\n reciprocal_primitive_lattice: Array.from(reciprocalPrimitive.data).reduce<\n number[][]\n >(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n ),\n inverse_primitive_transformation_matrix: invP,\n primitive_transformation_matrix: P,\n volume_original_wrt_conv: origDet / convDet,\n volume_original_wrt_prim: origDet / primDet,\n spacegroup_number: spgrpNum,\n spacegroup_international: calcResults.hm_symbol,\n rotation_matrix: rowsFromFlat(calcResults.std_rotation_matrix),\n };\n}\n\nexport interface ExplicitKPathResult extends SeekPathResult {\n explicit_kpoints_abs: number[][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_labels: string[];\n explicit_kpoints_linearcoord: number[];\n explicit_segments: [number, number][];\n}\n\nfunction vecAdd(a: number[], b: number[]): number[] {\n return [a[0] + b[0], a[1] + b[1], a[2] + b[2]];\n}\n\nfunction vecSub(a: number[], b: number[]): number[] {\n return [a[0] - b[0], a[1] - b[1], a[2] - b[2]];\n}\n\nfunction vecScale(a: number[], k: number): number[] {\n return [a[0] * k, a[1] * k, a[2] * k];\n}\n\nfunction vecNorm(a: number[]): number {\n return Math.hypot(a[0], a[1], a[2]);\n}\n\n/**\n * Given the output of `getPath`, compute an \"explicit\" path, i.e. a full list\n * of k-points along each segment. Mirrors `seekpath.get_explicit_from_implicit`.\n */\nexport function getExplicitFromImplicit(\n result: Pick<\n SeekPathResult,\n \"path\" | \"point_coords\" | \"reciprocal_primitive_lattice\"\n >,\n referenceDistance = 0.025,\n): {\n kpoints_rel: number[][];\n kpoints_abs: number[][];\n kpoints_labels: string[];\n kpoints_linearcoord: number[];\n segments: [number, number][];\n} {\n const recip = result.reciprocal_primitive_lattice;\n\n const kpointsRel: number[][] = [];\n const kpointsLabels: string[] = [];\n const kpointsLinearcoord: number[] = [];\n const segments: [number, number][] = [];\n let previousLinearcoord = 0;\n\n for (const [startLabel, stopLabel] of result.path) {\n const startCoord = result.point_coords[startLabel];\n const stopCoord = result.point_coords[stopLabel];\n const startCoordAbs = vecMulMat(startCoord, recip);\n const stopCoordAbs = vecMulMat(stopCoord, recip);\n const segmentLength = vecNorm(vecSub(stopCoordAbs, startCoordAbs));\n const numPoints = Math.max(2, Math.floor(segmentLength / referenceDistance));\n\n let segmentStart = kpointsLabels.length;\n for (let i = 0; i < numPoints; i++) {\n // Skip the first point if it's the same as the last one of the\n // previous segment\n if (i === 0) {\n if (\n kpointsLabels.length &&\n kpointsLabels[kpointsLabels.length - 1] === startLabel\n ) {\n segmentStart -= 1;\n continue;\n }\n }\n\n kpointsRel.push(\n vecAdd(startCoord, vecScale(vecSub(stopCoord, startCoord), i / (numPoints - 1))),\n );\n if (i === 0) kpointsLabels.push(startLabel);\n else if (i === numPoints - 1) kpointsLabels.push(stopLabel);\n else kpointsLabels.push(\"\");\n kpointsLinearcoord.push(\n previousLinearcoord + (segmentLength * i) / (numPoints - 1),\n );\n }\n previousLinearcoord += segmentLength;\n segments.push([segmentStart, kpointsLabels.length]);\n }\n\n return {\n kpoints_rel: kpointsRel,\n kpoints_abs: kpointsRel.map((p) => vecMulMat(p, recip)),\n kpoints_labels: kpointsLabels,\n kpoints_linearcoord: kpointsLinearcoord,\n segments,\n };\n}\n\n/**\n * Return the k-point path for a band structure in scaled and absolute\n * coordinates, following the HPKOT recipe. Mirrors\n * `seekpath.get_explicit_k_path`.\n */\nexport async function getExplicitKPath(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<ExplicitKPathResult> {\n const { referenceDistance = 0.025, ...rest } = opts;\n const res = await getPath(structure, rest);\n const explicit = getExplicitFromImplicit(res, referenceDistance);\n\n return {\n ...res,\n explicit_kpoints_abs: explicit.kpoints_abs,\n explicit_kpoints_rel: explicit.kpoints_rel,\n explicit_kpoints_labels: explicit.kpoints_labels,\n explicit_kpoints_linearcoord: explicit.kpoints_linearcoord,\n explicit_segments: explicit.segments,\n };\n}\n\n// re-export for convenience\nexport { bandPathData } from \"./bandPathData\";\n","import { Structure } from \"../../../structure\";\n\nimport { getExplicitKPath } from \"./seekpath\";\nimport type { GetPathOptions } from \"./seekpath\";\nimport { getBZPolyhedron } from \"./bzPolyhedron\";\nimport { vecMulMat } from \"./seekpathTools\";\n\n/** Data object compatible with the `brillouinzone-visualizer` widget. */\nexport interface BZVisualizerData {\n b1: number[];\n b2: number[];\n b3: number[];\n faces_data: {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n };\n kpoints: Record<string, number[]>;\n kpoints_rel: Record<string, number[]>;\n path: [string, string][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_linearcoord: number[];\n explicit_kpoints_labels: string[];\n explicit_kpoints_abs: number[][];\n explicit_segments: [number, number][];\n bravais_lattice: string;\n bravais_lattice_extended: string;\n spacegroup_number: number;\n spacegroup_international: string;\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n}\n\n/**\n * Run the HPKOT high-symmetry path computation and assemble the data object\n * consumed by the `brillouinzone-visualizer` web widget, mirroring the\n * seekpath example-data generator.\n */\nexport async function getBrillouinZoneData(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<BZVisualizerData> {\n const res = await getExplicitKPath(structure, opts);\n\n const [b1, b2, b3] = res.reciprocal_primitive_lattice;\n const faces_data = getBZPolyhedron(b1, b2, b3);\n\n const kpoints: Record<string, number[]> = {};\n const kpoints_rel: Record<string, number[]> = res.point_coords;\n for (const [label, rel] of Object.entries(kpoints_rel)) {\n kpoints[label] = vecMulMat(rel, res.reciprocal_primitive_lattice);\n }\n\n return {\n b1,\n b2,\n b3,\n faces_data,\n kpoints,\n kpoints_rel,\n path: res.path,\n explicit_kpoints_rel: res.explicit_kpoints_rel,\n explicit_kpoints_linearcoord: res.explicit_kpoints_linearcoord,\n explicit_kpoints_labels: res.explicit_kpoints_labels,\n explicit_kpoints_abs: res.explicit_kpoints_abs,\n explicit_segments: res.explicit_segments,\n bravais_lattice: res.bravais_lattice,\n bravais_lattice_extended: res.bravais_lattice_extended,\n spacegroup_number: res.spacegroup_number,\n spacegroup_international: res.spacegroup_international,\n has_inversion_symmetry: res.has_inversion_symmetry,\n augmented_path: res.augmented_path,\n };\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/** Minimum-image distance between two sites. */\nexport function getDistance(\n structure: Structure,\n idx1: number,\n idx2: number,\n): number {\n const displacement = getDisplacement(structure, idx1, idx2);\n\n const G = metricTensor(structure.lattice).data;\n\n return Math.sqrt(distanceSquared(displacement, G));\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/** Distances from site `idx` to every other site. */\nexport function getDistances(structure: Structure, idx: number): Float64Array {\n const n = structure.sites.length;\n const out = new Float64Array(n);\n\n const G = metricTensor(structure.lattice).data;\n\n for (let j = 0; j < n; j++) {\n if (j === idx) {\n out[j] = 0;\n continue;\n }\n\n const disp = getDisplacement(structure, idx, j);\n\n out[j] = Math.sqrt(distanceSquared(disp, G));\n }\n\n return out;\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/** Pairwise distance matrix for all sites, stored as an array of Float64Array rows. */\nexport function getDistancesMatrix(structure: Structure): Float64Array[] {\n const n = structure.sites.length;\n\n const matrix: Float64Array[] = Array.from(\n { length: n },\n () => new Float64Array(n),\n );\n\n const G = metricTensor(structure.lattice).data;\n\n for (let i = 0; i < n; i++) {\n matrix[i][i] = 0;\n\n for (let j = i + 1; j < n; j++) {\n const disp = getDisplacement(structure, i, j);\n\n const d = Math.sqrt(distanceSquared(disp, G));\n\n matrix[i][j] = d;\n matrix[j][i] = d;\n }\n }\n\n return matrix;\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n// generic method for finding sites on a given condition.\n\n/** Find site indices matching a predicate. */\nexport function findSites(\n structure: Structure,\n predicate: (site: Site, index: number) => boolean,\n): number[] {\n const indices: number[] = [];\n\n for (let i = 0; i < structure.sites.length; i++) {\n if (predicate(structure.sites[i], i)) {\n indices.push(i);\n }\n }\n\n return indices;\n}\n","import { Species } from \"../../../species/species\";\nimport { Structure } from \"../../structure\";\nimport { findSites } from \"./findSites\";\n\n// matches species.symbol only.\n\n/** Find site indices whose species symbol matches the given species or string. */\nexport function findSitesBySpecies(\n structure: Structure,\n species: Species | string,\n): number[] {\n const symbol = typeof species === \"string\" ? species : species.symbol;\n\n return findSites(structure, (site) => site.species.symbol === symbol);\n}\n","import { determinant } from \"../matrix/operations/determinant\";\nimport { Lattice } from \"./lattice\";\n\n/** Compute the unit cell volume as the absolute determinant of the basis. */\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\n/**\n * Compute the volume of a structure's lattice cell.\n * @param structure - Structure to evaluate.\n * @returns Volume in Ang^3.\n */\nexport function volume(structure: Structure): number {\n return latticeVolume(structure.lattice);\n}\n","import { Structure } from \"../structure\";\nimport { gcd } from \"../../math/numeric\";\n\n/**\n * Count each element's occurrences in the structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to counts.\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\n/**\n * Return the Hill-ordered chemical formula of a structure.\n * @param structure - Structure to evaluate.\n * @returns Hill-formula string.\n */\nexport function hillFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), hillOrder);\n}\n\n/**\n * Return the reduced Hill-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced formula string.\n */\nexport function reducedFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n );\n}\n","/** Element metadata from the periodic table. */\nexport interface ElementInfo {\n atomicNumber: number;\n symbol: string;\n name: string;\n mass: number;\n [key: string]: unknown;\n}\n\n/** Atomic-number-keyed periodic table of all known elements. */\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\n/** Symbol-keyed element lookup, derived from PeriodicTable. */\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\n/** Look up an element by its chemical symbol.\n * @param symbol - Element symbol (e.g. \"Fe\")\n * @returns The matching ElementInfo, or undefined if not found. */\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\n/** Atomic-number-to-symbol lookup map. */\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 return 0;\n }\n\n return element.mass;\n}\n\n/**\n * Sum the masses of all sites in the structure.\n * @param structure - Structure to evaluate.\n * @returns Total mass in atomic mass units.\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/**\n * Compute the density of a structure.\n * @param structure - Structure to evaluate.\n * @returns Density in amu/Ang^3.\n */\nexport function density(structure: Structure): number {\n const vol = volume(structure);\n\n if (vol < 1e-300) {\n throw new Error(\"Degenerate cell has no volume\");\n }\n\n return cellMass(structure) / vol;\n}\n","import { Structure } from \"../structure\";\nimport { Species } from \"../../species/species\";\n\n/**\n * Collect unique Species from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of unique Species.\n */\nexport function getSpecies(structure: Structure): Species[] {\n const species = new Map<string, Species>();\n\n for (const site of structure.sites) {\n const key = site.species.symbol;\n\n if (!species.has(key)) {\n species.set(key, site.species);\n }\n }\n\n return Array.from(species.values());\n}\n\n/**\n * Collect unique element symbols from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of element symbols.\n */\nexport function getElements(structure: Structure): string[] {\n return getSpecies(structure).map((s) => s.symbol);\n}\n\n/**\n * Count occurrences of each species symbol in a structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to occurrence counts.\n */\nexport function getSpeciesCounts(structure: Structure): Map<string, number> {\n const counts = new Map<string, number>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n counts.set(symbol, (counts.get(symbol) ?? 0) + 1);\n }\n\n return counts;\n}\n","import { Species } from \"../species/species\";\n\n/** Generic site properties map. */\nexport type SiteProperties = Record<string, any>;\n\n/** A 3D vector type. */\nexport type Vec3 = [number, number, number] | Float64Array | number[];\n\n/** A site with a species, fractional coordinates, and optional properties. */\nexport type Site<P extends SiteProperties = SiteProperties> = {\n species: Species;\n frac: Vec3;\n properties?: P;\n};\n\n/** Create a new Site object.\n * @param species - The species at the site.\n * @param frac - Fractional coordinates.\n * @param properties - Optional properties.\n * @returns A new Site. */\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 { Lattice } from \"../lattice/lattice\";\nimport { Site } from \"./site\";\nimport { cartesian } from \"./cartesian\";\n\nimport { norm } from \"../matrix/operations/vector/norm\";\n\n/** Compute the minimum image distance between two sites.\n * @param lattice - The lattice.\n * @param a - First site.\n * @param b - Second site.\n * @returns Minimum image distance. */\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\n/** Wrap a site's fractional coordinates into [0, 1).\n * @param site - The site to wrap.\n * @returns A new site with wrapped coordinates. */\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","/** A chemical species with a symbol and optional properties. */\nexport type Species<P extends Record<string, any> = Record<string, any>> = {\n symbol: string;\n properties?: P;\n};\n\n/** Create a new Species.\n * @param symbol - Element symbol.\n * @param properties - Optional properties.\n * @returns A new Species. */\nexport function createSpecies<P extends Record<string, any>>(\n symbol: string,\n properties?: P,\n): Species<P> {\n return { symbol, properties };\n}\n","import { Matrix } from \"../matrix\";\nimport { identity } from \"../matrix\";\n\n/** Scalar or multi-channel volumetric grid data. */\nexport interface VolumetricData {\n readonly data: Float64Array;\n readonly shape: [number, number, number];\n readonly channels: number;\n readonly basis?: Matrix;\n readonly origin: [number, number, number];\n readonly field?: string;\n readonly metadata?: Record<string, unknown>;\n}\n\ntype ReduceAxis = \"all\" | \"channels\";\n\n/** Reduction axis configuration. */\nexport interface ReduceOptions {\n axis?: ReduceAxis;\n}\n\n/** Create a VolumetricData from shape and optional data buffer. */\nexport function createVolumetricData(params: {\n shape: [number, number, number];\n channels?: number;\n\n /**\n * Flat voxel-major buffer.\n *\n * Layout:\n * [v000c0, v000c1, ..., v001c0, v001c1, ...]\n */\n data?: Float64Array | Iterable<number>;\n\n basis?: Matrix;\n origin?: [number, number, number];\n\n field?: string;\n metadata?: Record<string, unknown>;\n}): VolumetricData {\n const {\n shape,\n channels = 1,\n data,\n basis,\n origin = [0, 0, 0],\n field,\n metadata,\n } = params;\n\n const [D, H, W] = shape;\n const size = D * H * W * channels;\n\n const buffer =\n data instanceof Float64Array\n ? data\n : data\n ? Float64Array.from(data)\n : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(\n `VolumetricData mismatch: expected ${size}, got ${buffer.length}`,\n );\n }\n\n return {\n data: buffer,\n shape,\n channels,\n basis: basis ?? identity(3),\n origin,\n field,\n metadata,\n };\n}\n\n/** Compute the flat buffer index for a voxel coordinate and channel. */\n/** @param vol - Volumetric data. */\n/** @param x - Column index. */\n/** @param y - Row index. */\n/** @param z - Depth index. */\n/** @param c - Channel index. */\n/** @returns Linear index into the data buffer. */\nexport function index(\n vol: VolumetricData,\n x: number,\n y: number,\n z: number,\n c: number,\n) {\n const [D, H, W] = vol.shape;\n const { channels } = vol;\n\n return ((z * H + y) * W + x) * channels + c;\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Create a volumetric grid filled with a constant value. */\n/** @param shape - Grid dimensions [depth, height, width]. */\n/** @param value - Fill value. */\n/** @param channels - Number of channels (default 1). */\n/** @returns A new VolumetricData filled with value. */\nexport function fill(\n shape: [number, number, number],\n value: number,\n channels = 1,\n) {\n const size = shape[0] * shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size).fill(value),\n });\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Generate volumetric data by evaluating a function over every voxel and channel. */\n/** @param shape - Grid dimensions [depth, height, width]. */\n/** @param fn - Callback receiving (x, y, z, c) returning the value at that voxel. */\n/** @param channels - Number of channels (default 1). */\n/** @returns A new VolumetricData populated by fn. */\nexport function fromFunction(\n shape: [number, number, number],\n fn: (x: number, y: number, z: number, c: number) => number,\n channels = 1,\n) {\n const [D, H, W] = shape;\n const data = new Float64Array(D * H * W * channels);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n for (let y = 0; y < H; y++) {\n for (let x = 0; x < W; x++) {\n for (let c = 0; c < channels; c++) {\n data[i++] = fn(x, y, z, c);\n }\n }\n }\n }\n\n return createVolumetricData({\n shape,\n channels,\n data,\n });\n}\n","import { Matrix } from \"../../matrix\";\nimport { createVolumetricData } from \"../volumetric\";\n\n/** Stack a list of 2-D Matrix slices into a 3-D volumetric grid. */\n/** @param slices - Array of matrices (depth dimension). */\n/** @returns A new VolumetricData with shape [slices.length, H, W]. */\nexport function fromMatrixSlices(slices: Matrix[]) {\n if (slices.length === 0) {\n throw new Error(\"No slices provided\");\n }\n\n const H = slices[0].rows;\n const W = slices[0].cols;\n const D = slices.length;\n\n const data = new Float64Array(D * H * W);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n const m = slices[z];\n\n if (m.rows !== H || m.cols !== W) {\n throw new Error(\"Inconsistent matrix slice dimensions\");\n }\n\n data.set(m.data, i);\n i += m.data.length;\n }\n\n return createVolumetricData({\n shape: [D, H, W],\n data,\n });\n}\n","import { fill } from \"./fill\";\n\n/** Create a volumetric grid filled with ones. */\n/** @param shape - Grid dimensions [depth, height, width]. */\n/** @param channels - Number of channels (default 1). */\n/** @returns A new VolumetricData with all values set to 1. */\nexport function ones(shape: [number, number, number], channels = 1) {\n return fill(shape, 1, channels);\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Create a volumetric grid filled with zeros. */\n/** @param shape - Grid dimensions [depth, height, width]. */\n/** @param channels - Number of channels (default 1). */\n/** @returns A new VolumetricData with all values set to 0. */\nexport function zeros(shape: [number, number, number], channels = 1) {\n const size = shape[0] * shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size),\n });\n}\n","export interface SymmetryOperation {\n matrix: number[][];\n translation: number[];\n}\n\nfunction parseFraction(s: string): number {\n const trimmed = s.trim();\n\n if (trimmed.includes(\"/\")) {\n const [num, den] = trimmed.split(\"/\").map(Number);\n return num / den;\n }\n\n return Number(trimmed);\n}\n\nfunction parseComponent(expr: string): { coeffs: number[]; offset: number } {\n const cleaned = expr.replace(/\\s+/g, \"\");\n let offset = 0;\n const coeffs = [0, 0, 0];\n\n const terms = cleaned.match(/[+-]?[^+-]+/g) ?? [];\n\n const VAR_INDEX: Record<string, number> = { x: 0, y: 1, z: 2 };\n\n for (const term of terms) {\n const t = term.trim();\n\n if (t.length > 0 && VAR_INDEX[t.at(-1)!] !== undefined) {\n const idx = VAR_INDEX[t.at(-1)!];\n const sign = t.startsWith(\"-\") ? -1 : 1;\n\n coeffs[idx] += sign;\n } else {\n const frac = t.match(/([+-]?\\d+\\s*\\/\\s*\\d+)/);\n\n if (frac) {\n offset += parseFraction(frac[1].replace(/\\s/g, \"\"));\n } else {\n const val = Number(t);\n\n if (!isNaN(val)) {\n offset += val;\n }\n }\n }\n }\n\n return { coeffs, offset };\n}\n\n/** Parse a single symmetry operation string like '-y, x, z+1/2' into a matrix + translation.\n * @param op - The operation string (e.g. '-y, x, z+1/2').\n * @returns A SymmetryOperation with 3x3 matrix and translation vector. */\nexport function parseOperation(op: string): SymmetryOperation {\n const components = op.split(\",\").map((s) => parseComponent(s));\n\n return {\n matrix: components.map((c) => c.coeffs),\n translation: components.map((c) => c.offset),\n };\n}\n\n/** Parse all symmetry operation strings from a CIF _symmetry_equiv_pos_as_xyz loop.\n * @param ops - Array of operation strings (e.g. [\"x, y, z\", \"-x, -y, z\"]).\n * @returns Array of SymmetryOperation objects. */\nexport function parseOperations(ops: string[]): SymmetryOperation[] {\n return ops.map(parseOperation);\n}\n\n/** Apply a symmetry operation to fractional coordinates.\n * @param op - The symmetry operation.\n * @param frac - Fractional coordinates [x, y, z].\n * * @returns New fractional coordinates after applying the operation. */\nexport function applyOperation(\n op: SymmetryOperation,\n frac: number[],\n): number[] {\n const result = [0, 0, 0];\n\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n result[i] += op.matrix[i][j] * frac[j];\n }\n\n result[i] += op.translation[i];\n }\n\n return result;\n}\n","/**\n * Reads lines from a string one at a time, without pre-splitting into an array.\n */\nexport class LineReader {\n private pos = 0;\n /** Number of lines returned so far (including blank lines). */\n count = 0;\n\n constructor(private readonly text: string) {}\n\n /** Return the next line (without the newline character), or `null` at EOF. */\n next(): string | null {\n if (this.pos >= this.text.length) return null;\n const end = this.text.indexOf(\"\\n\", this.pos);\n const line = end === -1 ? this.text.slice(this.pos) : this.text.slice(this.pos, end);\n this.pos = end === -1 ? this.text.length : end + 1;\n this.count++;\n return line;\n }\n\n /** Return a trimmed line, or throw on unexpected EOF. */\n nextTrimmed(): string {\n const line = this.next();\n if (line === null) throw new Error(\"Unexpected EOF\");\n return line.trim();\n }\n}\n","import { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { parameters } from \"../../lattice/parameters\";\nimport { Structure } from \"../../structure/structure\";\nimport {\n parseOperations,\n applyOperation,\n} from \"./symmetryOperations\";\nimport { LineReader } from \"../helpers\";\n\nfunction cleanValue(value: string | undefined): number {\n if (value === undefined) return NaN;\n\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\n/** Parses a CIF (Crystallographic Information File) string into a Structure. */\nexport function fromCIF(text: string): Structure {\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 atomHeaders: string[] = [];\n const atomRows: string[][] = [];\n\n let inLoop = false;\n let currentHeaders: string[] = [];\n let collectingAtoms = false;\n let collectingSymOps = false;\n const symOpStrings: string[] = [];\n\n const r = new LineReader(text);\n let rawLine: string | null;\n while ((rawLine = r.next()) !== null) {\n const line = rawLine.trim();\n if (!line) continue;\n\n 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 collectingSymOps = 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 collectingSymOps = false;\n } else if (line.includes(\"_symmetry_equiv_pos_as_xyz\")) {\n collectingSymOps = true;\n collectingAtoms = false;\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 if (inLoop && collectingSymOps) {\n const tokens = tokenize(line);\n\n for (const t of tokens) {\n const cleaned = t.replace(/['\"]/g, \"\").trim();\n\n if (cleaned.includes(\",\")) {\n symOpStrings.push(cleaned);\n }\n }\n }\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 maxCol = Math.max(ix, iy, iz, ispecies);\n\n const asymSites = atomRows.map((row) => {\n if (row.length <= maxCol) {\n throw new Error(\"Incomplete atom site data row\");\n }\n\n return {\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\n if (symOpStrings.length === 0) {\n return { lattice, sites: asymSites };\n }\n\n const symOps = parseOperations(symOpStrings);\n\n const EPS = 1e-3;\n\n function wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n }\n\n function cleanNearZero(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n }\n\n function posKey(species: string, frac: number[]): string {\n const w = frac.map((v) => {\n const c = cleanNearZero(wrapValue(v));\n return Math.round(c * 1000) / 1000;\n });\n\n return `${species}:${w[0]},${w[1]},${w[2]}`;\n }\n\n const seen = new Set<string>();\n const sites: { species: { symbol: string }; frac: Float64Array }[] = [];\n\n for (const site of asymSites) {\n for (const op of symOps) {\n const operated = applyOperation(op, Array.from(site.frac));\n\n const frac = [\n cleanNearZero(wrapValue(operated[0])),\n cleanNearZero(wrapValue(operated[1])),\n cleanNearZero(wrapValue(operated[2])),\n ];\n\n const key = posKey(site.species.symbol, frac);\n\n if (!seen.has(key)) {\n seen.add(key);\n\n sites.push({\n species: { symbol: site.species.symbol },\n frac: new Float64Array(frac),\n });\n }\n }\n }\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a CIF string. */\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 { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { cartesian, fractional } from \"../site\";\nimport { LineReader } from \"./helpers\";\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/** Parses a POSCAR/CONTCAR string into a Structure. */\nexport function fromPOSCAR(text: string): Structure {\n const r = new LineReader(text);\n\n // comment/title\n r.next();\n\n // scale factor\n const scale = Number(r.nextTrimmed());\n\n // lattice vectors (row-major)\n const latticeData: number[] = [];\n\n for (let i = 0; i < 3; i++) {\n const v = r.nextTrimmed().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 = r.nextTrimmed().split(/\\s+/);\n\n // atom counts\n const counts = r.nextTrimmed().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 let selective = false;\n\n let line = r.nextTrimmed();\n if (isSelective(line)) {\n selective = true;\n line = r.nextTrimmed();\n }\n\n // direct is true unless cartesian is.\n let direct = true;\n direct = !isCartesian(line);\n\n const sites: Site[] = [];\n\n let speciesIndex = 0;\n let remaining = counts[0];\n\n const totalAtoms = counts.reduce((a, b) => a + b, 0);\n\n for (let i = 0; i < totalAtoms; i++) {\n const tokens = r.nextTrimmed().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 const props: Record<string, unknown> = {};\n\n if (selective) {\n const sd = tokens.slice(3, 6).map((t) => t.toLowerCase() === \"t\");\n\n if (sd.length === 3) {\n props.selectiveDynamics = sd as [boolean, boolean, boolean];\n }\n }\n\n sites.push({\n species: {\n symbol: symbols[speciesIndex],\n },\n frac,\n ...(Object.keys(props).length > 0 ? { properties: props } : {}),\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 selectiveDynamics: selective || undefined,\n _cursorEnd: r.count,\n };\n}\n\n/** Serializes a Structure to a POSCAR string. */\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]} ${m[8]}`);\n\n // preserve order of first appearance\n const grouped = new Map<string, typeof structure.sites>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n const group = grouped.get(symbol);\n\n if (group) {\n group.push(site);\n } else {\n grouped.set(symbol, [site]);\n }\n }\n\n\n const species = [...grouped.keys()];\n const sites = [...grouped.values()].flat();\n\n lines.push(species.join(\" \"));\n lines.push(species.map((s) => (grouped.get(s) ?? []).length).join(\" \"));\n\n const hasSelective = structure.selectiveDynamics ?? sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n lines.push(\"Selective Dynamics\");\n }\n\n lines.push(direct ? \"Direct\" : \"Cartesian\");\n\n for (const site of sites) {\n const coords = direct ? site.frac : cartesian(structure.lattice, site);\n\n let line = `${coords[0]} ${coords[1]} ${coords[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\n/** AiiDA-compatible site representation. */\nexport interface AiiDASite {\n position: [number, number, number];\n kind_name: string[];\n}\n\n/** AiiDA-compatible structure data format. */\nexport interface StructureData {\n cell: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ];\n kinds: [];\n sites: AiiDASite[];\n}\n\n/** Parses an AiiDA StructureData object into a Structure. */\nexport function fromStructureData(data: StructureData): Structure {\n const lattice = createLattice([\n ...data.cell[0],\n ...data.cell[1],\n ...data.cell[2],\n ]);\n\n const kindMap = new Map(data.kinds.map((kind: any) => [kind.name, kind]));\n\n const sites = data.sites.map((site: any) => {\n const kind = kindMap.get(site.kind_name);\n\n if (!kind) {\n throw new Error(`Unknown kind \"${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\n/** Serializes a Structure to an AiiDA StructureData-compatible object. */\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 { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site/cartesian\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\nfunction nextSectionLine(r: LineReader, section: string): void {\n let line: string | null;\n while ((line = r.next()) !== null) {\n if (line.trim().toUpperCase() === section) return;\n }\n throw new Error(`Missing ${section}`);\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\n/** Parses an XSF (XCrySDen Structure Format) string into a Structure. */\nexport function fromXSF(text: string): Structure {\n const r = new LineReader(text);\n\n nextSectionLine(r, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ]);\n\n nextSectionLine(r, \"PRIMCOORD\");\n\n const countLine = r.nextTrimmed();\n const [nAtoms] = countLine.split(/\\s+/).map(Number);\n\n if (!Number.isInteger(nAtoms) || nAtoms < 0) {\n throw new Error(\"Invalid atom count in PRIMCOORD\");\n }\n\n const invData = inverse(lattice).data;\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = r.nextTrimmed().split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n sites.push({\n species: { symbol },\n // inlined frac conv for perf.\n frac: new Float64Array([\n invData[0] * x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\n/** Serializes a Structure to an XSF string. */\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n 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 { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\ntype PropDef = {\n name: string;\n type: string;\n count: number;\n offset: number;\n};\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\nfunction parseProperties(propStr: string): PropDef[] {\n const parts = propStr.split(\":\");\n const props: PropDef[] = [];\n let offset = 0;\n\n for (let i = 0; i < parts.length; i += 3) {\n const count = Number(parts[i + 2]);\n props.push({\n name: parts[i],\n type: parts[i + 1],\n count,\n offset,\n });\n offset += count;\n }\n\n return props;\n}\n\n/** Parses an extended XYZ string into a Structure. */\nexport function fromXYZ(text: string): Structure {\n const r = new LineReader(text);\n\n // skip leading blank lines\n let line: string | null;\n do {\n line = r.next();\n } while (line !== null && line.trim().length === 0);\n\n if (line === null) throw new Error(\"XYZ file is too short\");\n\n const n = Number(line.trim());\n\n if (!Number.isInteger(n) || n < 0) {\n throw new Error(\"Invalid atom count in XYZ file\");\n }\n\n const comment = r.next();\n if (comment === null) throw new Error(\"XYZ file is too short\");\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const propDefs = info.Properties\n ? parseProperties(info.Properties)\n : [\n { name: \"species\", type: \"S\", count: 1, offset: 0 },\n { name: \"pos\", type: \"R\", count: 3, offset: 1 },\n ];\n\n const sites: Site[] = [];\n\n let hasSelective = false;\n\n const invData = inverse(lattice).data;\n\n for (let i = 0; i < n; i++) {\n const atomLine = r.next();\n if (atomLine === null)\n throw new Error(\"Atom count exceeds available lines in XYZ file\");\n\n const tokens = atomLine.trim().split(/\\s+/);\n\n let symbol = \"\";\n let x = 0,\n y = 0,\n z = 0;\n const props: Record<string, unknown> = {};\n\n for (const def of propDefs) {\n const values = tokens.slice(def.offset, def.offset + def.count);\n\n if (def.name === \"species\") {\n symbol = values[0];\n } else if (def.name === \"pos\") {\n x = Number(values[0]);\n y = Number(values[1]);\n z = Number(values[2]);\n } else if (def.name === \"selectiveDynamics\") {\n const sd = values.map((v: string) => v.toLowerCase() === \"t\") as [\n boolean,\n boolean,\n boolean,\n ];\n props.selectiveDynamics = sd;\n hasSelective = true;\n } else {\n if (def.type === \"L\") {\n props[def.name] = values.map((v: string) => v.toLowerCase() === \"t\");\n } else if (def.type === \"R\" || def.type === \"I\") {\n props[def.name] = values.map(Number);\n } else {\n props[def.name] = values.length === 1 ? values[0] : values;\n }\n }\n }\n\n if (!symbol) throw new Error(\"Missing species in XYZ\");\n if (!z && z !== 0) throw new Error(\"Invalid coordinates in XYZ\");\n\n const site: Site = {\n species: { symbol },\n // inlined site conv for perf.\n frac: new Float64Array([\n invData[0] * x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n };\n\n if (Object.keys(props).length > 0) {\n site.properties = props;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n selectiveDynamics: hasSelective || undefined,\n };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\n/** Serializes a Structure to an extended XYZ string. */\nexport function toXYZ(structure: Structure): string {\n const lines: string[] = [];\n\n const sites = structure.sites;\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n const propParts: string[] = [\"species\", \"S\", \"1\", \"pos\", \"R\", \"3\"];\n const hasSelective =\n structure.selectiveDynamics ??\n sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n propParts.push(\"selectiveDynamics\", \"L\", \"3\");\n }\n\n lines.push(`Lattice=\"${latticeStr}\" Properties=${propParts.join(\":\")}`);\n\n for (const site of sites) {\n const cart = cartesian(structure.lattice, site);\n let line = `${site.species.symbol} ${cart[0]} ${cart[1]} ${cart[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice\";\n\nimport { fractional, cartesian } from \"../site\";\nimport { Structure } from \"../structure\";\n\n/** Parses an OPTIMADE structure data object into a Structure. */\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\n/** Serializes a Structure to an OPTIMADE-compatible data object. */\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","/**\n * Convert a single measurement between units.\n * @param value - Numeric value to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Converted value.\n */\nexport 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\n/**\n * Convert an array of measurements between units.\n * @param arr - Array of numeric values to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Array of converted values.\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\n/** Supported length unit identifiers. */\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\n/** Unit system for length conversions with angstrom as base. */\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","// derived from https://manual.gromacs.org/current/reference-manual/file-formats.html#gro\n\n// NOTE: GROMACS stores all lengths (coordinates and box vectors) in nm.\n// Internally matsci-parse uses Å.\n\n// Its common convention for GROMACs to use Hw or Ow for water, we dont try to fix this at-all\n// therefore cross format parsing (to a software that needs elemental indication) will probably fail.\n\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LengthUnitSystem } from \"../units/length\";\n\nfunction pad5(str: string) {\n return str.length > 5 ? str.slice(0, 5) : str.padStart(5);\n}\n\nfunction formatCoord(x: number) {\n return x.toFixed(3).padStart(8);\n}\n\n/** Parses a GROMACS GRO string into a Structure. */\nexport function fromGRO(text: string): Structure {\n const lines = text.split(/\\r?\\n/).filter((l) => l.length > 0);\n\n let cursor = 0;\n\n const title = lines[cursor++];\n\n const timeMatch = title.match(/t=\\s*([-+]?[0-9]*\\.?[0-9]+)/i);\n const time = timeMatch ? Number(timeMatch[1]) : undefined;\n\n const nAtoms = Number(lines[cursor++]);\n\n if (!Number.isFinite(nAtoms)) {\n throw new Error(\"Invalid GRO atom count\");\n }\n\n type Atom = {\n symbol: string;\n cart: Float64Array;\n };\n\n const atoms: Atom[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const line = lines[cursor++];\n\n const x = Number(line.slice(20, 28));\n const y = Number(line.slice(28, 36));\n const z = Number(line.slice(36, 44));\n\n let atomName = line.slice(10, 15).trim();\n\n let symbol = atomName.replace(/[0-9]/g, \"\");\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n\n atoms.push({\n symbol,\n cart: new Float64Array(\n LengthUnitSystem.convertArray([x, y, z], \"nm\", \"angstrom\"),\n ),\n });\n }\n\n let lattice = null;\n\n const boxLine = lines[cursor];\n\n if (boxLine) {\n const vals = boxLine.trim().split(/\\s+/).map(Number);\n\n const matrix = LengthUnitSystem.convertArray(\n [\n vals[0] ?? 0,\n vals[3] ?? 0,\n vals[4] ?? 0,\n vals[5] ?? 0,\n vals[1] ?? 0,\n vals[6] ?? 0,\n vals[7] ?? 0,\n vals[8] ?? 0,\n vals[2] ?? 0,\n ],\n \"nm\",\n \"angstrom\",\n );\n\n const hasOffDiagonal =\n matrix[1] !== 0 ||\n matrix[2] !== 0 ||\n matrix[3] !== 0 ||\n matrix[5] !== 0 ||\n matrix[6] !== 0 ||\n matrix[7] !== 0;\n\n lattice = hasOffDiagonal\n ? createLattice(matrix)\n : createLattice([matrix[0], matrix[4], matrix[8]]);\n }\n\n const sites: Site[] = atoms.map((atom) => ({\n species: { symbol: atom.symbol },\n frac: lattice\n ? fractional(lattice, atom.cart)\n : new Float64Array([NaN, NaN, NaN]),\n }));\n\n return {\n lattice,\n sites,\n time,\n };\n}\n\n/** Serializes a Structure to a GROMACS GRO string. */\nexport function toGRO(\n structure: Structure,\n options?: {\n title?: string;\n time?: number;\n },\n): string {\n const title =\n options?.title ??\n (options?.time !== undefined\n ? `Generated structure, t=${options.time}`\n : \"Generated by matsci-parse\");\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(structure.sites.length));\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n\n const [x, y, z] = LengthUnitSystem.convertArray(\n Array.from(cart),\n \"angstrom\",\n \"nm\",\n );\n\n lines.push(\n pad5(\"1\") +\n pad5(\"RES\") +\n pad5(site.species.symbol) +\n pad5(String(i + 1)) +\n formatCoord(x) +\n formatCoord(y) +\n formatCoord(z),\n );\n }\n\n const m = structure.lattice.basis.data;\n\n const [a, b, c] = LengthUnitSystem.convertArray(\n [m[0], m[4], m[8]],\n \"angstrom\",\n \"nm\",\n );\n\n lines.push([a, b, c].map((v) => v.toFixed(5)).join(\" \"));\n\n return lines.join(\"\\n\");\n}\n","import { fromParameters } from \"../lattice\";\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nconst DEFAULT_PADDING = 10.0;\n\nfunction parseCRYST1(line: string) {\n const a = Number(line.slice(6, 15));\n const b = Number(line.slice(15, 24));\n const c = Number(line.slice(24, 33));\n\n const alpha = Number(line.slice(33, 40));\n const beta = Number(line.slice(40, 47));\n const gamma = Number(line.slice(47, 54));\n\n return { a, b, c, alpha, beta, gamma };\n}\n\nfunction isCRYST1Sane(\n a: number,\n b: number,\n c: number,\n extentX: number,\n extentY: number,\n extentZ: number,\n): boolean {\n // reject degenerate or identity cells\n if (a <= 1e-3 || b <= 1e-3 || c <= 1e-3) return false;\n\n // reject clearly too small cells\n const margin = 1.2; // allow small packing inefficiency\n\n if (a < extentX * margin) return false;\n if (b < extentY * margin) return false;\n if (c < extentZ * margin) return false;\n\n // also reject ridiculous huge identity placeholders\n if (a === 1 && b === 1 && c === 1) return false;\n\n return true;\n}\n\n/** Parses a PDB (Protein Data Bank) string into a Structure. */\nexport function fromPDB(text: string): Structure {\n const lines = text.split(/\\r?\\n/);\n\n let crystal: {\n a: number;\n b: number;\n c: number;\n alpha: number;\n beta: number;\n gamma: number;\n } | null = null;\n\n type ParsedAtom = {\n symbol: string;\n x: number;\n y: number;\n z: number;\n };\n\n const atoms: ParsedAtom[] = [];\n\n let xmin = Infinity;\n let ymin = Infinity;\n let zmin = Infinity;\n\n let xmax = -Infinity;\n let ymax = -Infinity;\n let zmax = -Infinity;\n\n for (const line of lines) {\n if (line.startsWith(\"CRYST1\")) {\n crystal = parseCRYST1(line);\n continue;\n }\n\n if (!line.startsWith(\"ATOM \") && !line.startsWith(\"HETATM\")) {\n continue;\n }\n\n const x = Number(line.slice(30, 38));\n const y = Number(line.slice(38, 46));\n const z = Number(line.slice(46, 54));\n\n let symbol = line.slice(76, 78).trim();\n\n if (!symbol) {\n symbol = line.slice(12, 16).replace(/[0-9]/g, \"\").trim();\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n }\n\n atoms.push({ symbol, x, y, z });\n\n xmin = Math.min(xmin, x);\n ymin = Math.min(ymin, y);\n zmin = Math.min(zmin, z);\n\n xmax = Math.max(xmax, x);\n ymax = Math.max(ymax, y);\n zmax = Math.max(zmax, z);\n }\n\n if (atoms.length === 0) {\n throw new Error(\"No ATOM/HETATM records found.\");\n }\n\n const extentX = xmax - xmin;\n const extentY = ymax - ymin;\n const extentZ = zmax - zmin;\n\n let lattice = createLattice([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n\n let originX = xmin - DEFAULT_PADDING;\n let originY = ymin - DEFAULT_PADDING;\n let originZ = zmin - DEFAULT_PADDING;\n\n const useCrystal =\n crystal !== null &&\n isCRYST1Sane(crystal.a, crystal.b, crystal.c, extentX, extentY, extentZ);\n\n if (useCrystal) {\n lattice = fromParameters(\n crystal.a,\n crystal.b,\n crystal.c,\n crystal.alpha,\n crystal.beta,\n crystal.gamma,\n );\n\n originX = 0;\n originY = 0;\n originZ = 0;\n } else {\n const a = Math.max(extentX + 2 * DEFAULT_PADDING, 1.0);\n const b = Math.max(extentY + 2 * DEFAULT_PADDING, 1.0);\n const c = Math.max(extentZ + 2 * DEFAULT_PADDING, 1.0);\n\n lattice = createLattice([a, 0, 0, 0, b, 0, 0, 0, c]);\n }\n\n const sites: Site[] = atoms.map(({ symbol, x, y, z }) => ({\n species: { symbol },\n frac: fractional(\n lattice,\n new Float64Array([x - originX, y - originY, z - originZ]),\n ),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a PDB string. */\nexport function toPDB(\n structure: Structure,\n options?: {\n title?: string;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n\n const lines: string[] = [];\n\n lines.push(`HEADER ${title}`);\n\n let index = 1;\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n const symbol = site.species.symbol;\n\n lines.push(\n [\n \"ATOM \",\n index.toString().padStart(5),\n \" \",\n symbol.padEnd(4),\n \" MOL \",\n \"A\",\n \" 1 \",\n c[0].toFixed(3).padStart(8),\n c[1].toFixed(3).padStart(8),\n c[2].toFixed(3).padStart(8),\n \" 1.00\",\n \" 0.00\",\n \" \",\n symbol.padStart(2),\n ].join(\"\"),\n );\n\n index++;\n }\n\n lines.push(\"END\");\n\n return lines.join(\"\\n\");\n}\n","/**\n * QE ibrav → Lattice vector mapping.\n *\n * Implements all 29 QE ibrav values (-14 to +14, excluding 0).\n * Maps the ibrav index + celldm or A,B,C parameters to a 3x3 lattice basis.\n *\n * @see https://www.quantum-espresso.org/Doc/INPUT_PW.html\n */\n\nimport { createLattice } from \"../../lattice\";\nimport type { Lattice } from \"../../lattice\";\nimport { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { clean } from \"../../math/numeric\";\n\nconst SQRT3 = Math.sqrt(3);\nconst SQRT2 = Math.sqrt(2);\n\n/**\n * Construct a Lattice from QE ibrav index and crystal parameters.\n *\n * **Output units: Bohr.** The caller must convert to Angstrom if needed.\n *\n * @param ibrav Bravais lattice index (-14 to +14, excluding 0)\n * @param celldm celldm(1..6): celldm(1) in Bohr, others unitless ratios/cosines\n * @param ABC Optional alternative: [A, B, C, cosAB, cosAC, cosBC] with A,B,C in Angstrom\n */\nexport function ibravToLattice(\n ibrav: number,\n celldm: number[],\n ABC?: [number, number, number, number, number, number],\n): Lattice {\n if (ibrav === 0) {\n throw new Error(\"ibrav=0 requires explicit CELL_PARAMETERS\");\n }\n\n // resolve lattice parameter a in Bohr\n let a: number;\n let b: number;\n let c: number;\n let cosab: number;\n let cosac: number;\n let cosbc: number;\n\n if (ABC) {\n // A,B,C in Angstrom → convert to Bohr\n const [Av, Bv, Cv, cosAB, cosAC, cosBC] = ABC;\n a = Av * BOHR_PER_ANGSTROM;\n b = Bv * BOHR_PER_ANGSTROM;\n c = Cv * BOHR_PER_ANGSTROM;\n cosab = cosAB;\n cosac = cosAC;\n cosbc = cosBC;\n } else {\n a = celldm[0] ?? 0;\n b = a * (celldm[1] ?? 0);\n c = a * (celldm[2] ?? 0);\n\n // meaning of celldm(4..6) depends on ibrav\n // defaults set per-case below\n cosab = 0;\n cosac = 0;\n cosbc = 0;\n }\n\n const v: number[] = new Array(9);\n\n switch (ibrav) {\n case 1: {\n // Cubic P (sc): v1 = a(1,0,0), v2 = a(0,1,0), v3 = a(0,0,1)\n const pp = fromParameters(a, a, a, 90, 90, 90);\n return pp;\n }\n\n case 2: {\n // Cubic F (fcc): v1 = (a/2)(-1,0,1), v2 = (a/2)(0,1,1), v3 = (a/2)(-1,1,0)\n const h = a / 2;\n v[0] = -h; v[1] = 0; v[2] = h;\n v[3] = 0; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = h; v[8] = 0;\n break;\n }\n\n case 3: {\n // Cubic I (bcc): v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1)\n const h = a / 2;\n v[0] = h; v[1] = h; v[2] = h;\n v[3] = -h; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = -h; v[8] = h;\n break;\n }\n\n case -3: {\n // Cubic I (bcc), more symmetric: v1 = (a/2)(-1,1,1), v2 = (a/2)(1,-1,1), v3 = (a/2)(1,1,-1)\n const h = a / 2;\n v[0] = -h; v[1] = h; v[2] = h;\n v[3] = h; v[4] = -h; v[5] = h;\n v[6] = h; v[7] = h; v[8] = -h;\n break;\n }\n\n case 4: {\n // Hexagonal and Trigonal P: celldm(3) = c/a\n // v1 = a(1,0,0), v2 = a(-1/2, sqrt(3)/2, 0), v3 = a(0,0,c/a)\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 120);\n }\n\n case 5: {\n // Trigonal R, 3fold axis c: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n v[0] = a * tx; v[1] = -a * ty; v[2] = a * tz;\n v[3] = 0; v[4] = a * 2 * ty; v[5] = a * tz;\n v[6] = -a * tx; v[7] = -a * ty; v[8] = a * tz;\n break;\n }\n\n case -5: {\n // Trigonal R, 3fold axis <111>: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n const u = tz - 2 * SQRT2 * ty;\n const vv = tz + SQRT2 * ty;\n const ap = a / SQRT3;\n v[0] = ap * u; v[1] = ap * vv; v[2] = ap * vv;\n v[3] = ap * vv; v[4] = ap * u; v[5] = ap * vv;\n v[6] = ap * vv; v[7] = ap * vv; v[8] = ap * u;\n break;\n }\n\n case 6: {\n // Tetragonal P (st): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 90);\n }\n\n case 7: {\n // Tetragonal I (bct): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const h = a / 2;\n const hh = h * ca;\n v[0] = h; v[1] = -h; v[2] = hh;\n v[3] = h; v[4] = h; v[5] = hh;\n v[6] = -h; v[7] = -h; v[8] = hh;\n break;\n }\n\n case 8: {\n // Orthorhombic P: celldm(2) = b/a, celldm(3) = c/a\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a * ba, a * ca, 90, 90, 90);\n }\n\n case 9: {\n // Orthorhombic base-centered (bco): celldm(2) = b/a, celldm(3) = c/a\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case -9: {\n // Orthorhombic BC, alternate: v1 = (a/2, -b/2, 0), v2 = (a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = -bb / 2; v[2] = 0;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case 91: {\n // Orthorhombic one-face base-centered A-type\n // v1 = (a, 0, 0), v2 = (0, b/2, -c/2), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a; v[1] = 0; v[2] = 0;\n v[3] = 0; v[4] = bb / 2; v[5] = -cc / 2;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 10: {\n // Orthorhombic face-centered\n // v1 = (a/2, 0, c/2), v2 = (a/2, b/2, 0), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = cc / 2;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 11: {\n // Orthorhombic body-centered\n // v1 = (a/2, b/2, c/2), v2 = (-a/2, b/2, c/2), v3 = (-a/2, -b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = cc / 2;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = cc / 2;\n v[6] = -a / 2; v[7] = -bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 12: {\n // Monoclinic P, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const gamma = Math.acos(cg) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, 90, gamma);\n }\n\n case -12: {\n // Monoclinic P, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const beta = Math.acos(cb) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, beta, 90);\n }\n\n case 13: {\n // Monoclinic base-centered, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n // v1 = (a/2, 0, -c/2), v2 = (b*cos(gamma), b*sin(gamma), 0), v3 = (a/2, 0, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const sg = Math.sqrt(Math.max(0, 1 - cg * cg));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = -cc / 2;\n v[3] = bb * cg; v[4] = bb * sg; v[5] = 0;\n v[6] = a / 2; v[7] = 0; v[8] = cc / 2;\n break;\n }\n\n case -13: {\n // Monoclinic base-centered, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (c*cos(beta), 0, c*sin(beta))\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const sb = Math.sqrt(Math.max(0, 1 - cb * cb));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = cc * cb; v[7] = 0; v[8] = cc * sb;\n break;\n }\n\n case 14: {\n // Triclinic: celldm(2..6)\n // Same as fromParameters with explicit angles\n if (ABC) {\n return fromParameters(a, b, c,\n Math.acos(cosbc) * (180 / Math.PI),\n Math.acos(cosac) * (180 / Math.PI),\n Math.acos(cosab) * (180 / Math.PI),\n );\n }\n const ba = celldm[1] ?? 1;\n const ca = celldm[2] ?? 1;\n const cbc = celldm[3] ?? 0; // cos(alpha) between b and c\n const cac = celldm[4] ?? 0; // cos(beta) between a and c\n const cab = celldm[5] ?? 0; // cos(gamma) between a and b\n const bb = a * ba;\n const cc = a * ca;\n return fromParameters(a, bb, cc,\n Math.acos(cbc) * (180 / Math.PI),\n Math.acos(cac) * (180 / Math.PI),\n Math.acos(cab) * (180 / Math.PI),\n );\n }\n\n default:\n throw new Error(`Unsupported ibrav value: ${ibrav}`);\n }\n\n return createLattice(v.map(clean));\n}\n","/**\n * Quantum ESPRESSO Fortran namelist parser.\n *\n * Parses QE-style namelists (`&NAME ... /`) from input text.\n * Supports strings, reals (including Fortran D notation),\n * logicals, integers, and array syntax `key(i) = value`.\n */\n\nexport interface QeNamelist {\n /** Namelist block name (uppercase). */\n name: string;\n /** Key → raw string value (keys stored lowercase). */\n values: Map<string, string>;\n}\n\nfunction convertFortranReal(s: string): string {\n const v = s.replace(/[dD]/g, \"e\");\n return String(Number.parseFloat(v));\n}\n\nfunction convertValue(raw: string): string {\n const trimmed = raw.trim();\n\n // quoted string\n if (\n (trimmed.startsWith(\"'\") && trimmed.endsWith(\"'\")) ||\n (trimmed.startsWith('\"') && trimmed.endsWith('\"'))\n ) {\n return trimmed.slice(1, -1);\n }\n\n // logical\n if (/^\\.(?:true|false)\\.$/i.test(trimmed)) {\n return trimmed.toLowerCase() === \".true.\" ? \"true\" : \"false\";\n }\n\n // Fortran D-notation real\n if (/[dD]/.test(trimmed)) {\n return convertFortranReal(trimmed);\n }\n\n return trimmed;\n}\n\n/**\n * Parse a single QE namelist block from lines.\n * Returns the namelist and the index after the closing `/`.\n */\nfunction parseOne(\n lines: string[],\n start: number,\n): { namelist: QeNamelist; end: number } | null {\n const openLine = lines[start].trim();\n\n const openMatch = openLine.match(/^&(\\w+)/i);\n if (!openMatch) return null;\n\n const name = openMatch[1].toUpperCase();\n const values = new Map<string, string>();\n\n for (let i = start + 1; i < lines.length; i++) {\n let line = lines[i];\n\n // strip inline comments\n const commentIdx = line.indexOf(\"!\");\n if (commentIdx >= 0) line = line.slice(0, commentIdx);\n\n // closing slash\n if (/^\\//.test(line.trim())) {\n return { namelist: { name, values }, end: i };\n }\n\n // key = value pairs (commas optional)\n const pairs = line.split(\",\");\n for (const pair of pairs) {\n const eqIdx = pair.indexOf(\"=\");\n if (eqIdx < 0) continue;\n\n const key = pair.slice(0, eqIdx).trim().toLowerCase();\n const raw = pair.slice(eqIdx + 1);\n\n if (!key) continue;\n\n // check for array syntax: key(i)\n const arrMatch = key.match(/^(\\w+)\\((\\d+)\\)$/);\n const storeKey = arrMatch ? `${arrMatch[1]}(${arrMatch[2]})` : key;\n\n values.set(storeKey, convertValue(raw));\n }\n }\n\n // unterminated namelist\n return { namelist: { name, values }, end: lines.length };\n}\n\n/**\n * Parse all QE namelists from input text.\n * Returns namelists in order of appearance.\n */\nexport function parseQeNamelist(text: string): QeNamelist[] {\n const lines = text.split(\"\\n\");\n const result: QeNamelist[] = [];\n\n for (let i = 0; i < lines.length; i++) {\n if (/^\\s*&\\w+/.test(lines[i])) {\n const parsed = parseOne(lines, i);\n if (parsed) {\n result.push(parsed.namelist);\n i = parsed.end;\n }\n }\n }\n\n return result;\n}\n\n/** Find a namelist block by name. */\nfunction findBlock(\n namelists: QeNamelist[],\n block: string,\n): QeNamelist | undefined {\n const upper = block.toUpperCase();\n return namelists.find((n) => n.name === upper);\n}\n\n/** Get a raw string value from a namelist block. */\nexport function getString(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): string | undefined {\n return findBlock(namelists, block)?.values.get(key.toLowerCase());\n}\n\n/** Get a numeric value from a namelist block. */\nexport function getNumber(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): number | undefined {\n const raw = getString(namelists, block, key);\n if (raw === undefined) return undefined;\n const n = Number.parseFloat(raw);\n return Number.isNaN(n) ? undefined : n;\n}\n\n/** Get an array value (e.g. celldm(1)..celldm(6)) from a namelist block. */\nexport function getArray(\n namelists: QeNamelist[],\n block: string,\n key: string,\n size: number,\n): number[] {\n const lower = key.toLowerCase();\n const result: number[] = [];\n for (let i = 1; i <= size; i++) {\n const raw = getString(namelists, block, `${lower}(${i})`);\n if (raw !== undefined) {\n result.push(Number.parseFloat(raw));\n } else {\n result.push(0);\n }\n }\n return result;\n}\n","import { createLattice } from \"../../lattice/lattice\";\nimport { kspacingToGrid } from \"../../lattice/kspacingToGrid\";\nimport { ibravToLattice } from \"./ibrav\";\nimport { fractional } from \"../../site\";\nimport { getElement } from \"../../data/periodictable/atomicData\";\nimport type { Site } from \"../../site/site\";\nimport type { Structure } from \"../../structure/structure\";\nimport { parseQeNamelist, getNumber, getString, getArray } from \"./namelist\";\nimport type {\n AtomicSpeciesEntry,\n AtomicPositionEntry,\n CellParameterEntry,\n KPointsCard,\n} from \"./schema/cards\";\nimport type { QeControlOptions } from \"./schema/control\";\nimport type { QeSystemOptions } from \"./schema/system\";\nimport type { QeElectronsOptions } from \"./schema/electrons\";\n\nconst BOHR_TO_ANGSTROM = 0.529177;\n\ntype AtomCoordMode = \"crystal\" | \"angstrom\" | \"bohr\" | \"alat\";\n\n// ──────────────────────────────────────────────────────────────────────\n// Options — composed from schema types\n// ──────────────────────────────────────────────────────────────────────\n\n/** User-facing options for {@link toPW}. Composed from schema types. */\nexport interface QEOptions {\n control?: QeControlOptions;\n system?: QeSystemOptions;\n electrons?: QeElectronsOptions;\n kpoints?:\n | { grid: [number, number, number]; shift?: [number, number, number] }\n | { kspacing: number };\n pseudo?: { pseudos?: Record<string, string> };\n}\n\nconst QE_DEFAULTS: Required<\n Pick<QEOptions, \"control\" | \"system\" | \"electrons\" | \"kpoints\" | \"pseudo\">\n> = {\n control: {\n title: \"Generated by matsci-parse\",\n calculation: \"scf\",\n pseudo_dir: \"./\",\n },\n system: {\n ecutwfc: 30,\n },\n electrons: {\n conv_thr: 1e-6,\n },\n kpoints: { kspacing: 0.22 },\n pseudo: { pseudos: {} },\n};\n\n// ──────────────────────────────────────────────────────────────────────\n// fromPW — unchanged\n// ──────────────────────────────────────────────────────────────────────\n\n/** Parses a Quantum ESPRESSO PW input string into a Structure. */\nexport function fromPW(text: string): Structure {\n const namelists = parseQeNamelist(text);\n const lines = text.split(\"\\n\");\n\n // --- extract &SYSTEM parameters ---\n const ibrav = getNumber(namelists, \"SYSTEM\", \"ibrav\") ?? 0;\n const nat = getNumber(namelists, \"SYSTEM\", \"nat\");\n const celldm = getArray(namelists, \"SYSTEM\", \"celldm\", 6);\n\n // --- build lattice ---\n let lattice: ReturnType<typeof createLattice>;\n\n if (ibrav !== 0) {\n // ibravToLattice returns lattice vectors in Bohr → convert to angstrom\n const bohr = ibravToLattice(ibrav, celldm);\n const m = bohr.basis.data;\n lattice = createLattice([\n m[0] * BOHR_TO_ANGSTROM,\n m[1] * BOHR_TO_ANGSTROM,\n m[2] * BOHR_TO_ANGSTROM,\n m[3] * BOHR_TO_ANGSTROM,\n m[4] * BOHR_TO_ANGSTROM,\n m[5] * BOHR_TO_ANGSTROM,\n m[6] * BOHR_TO_ANGSTROM,\n m[7] * BOHR_TO_ANGSTROM,\n m[8] * BOHR_TO_ANGSTROM,\n ]);\n } else {\n // ibrav=0: lattice must come from CELL_PARAMETERS block\n const { lattice: cellLattice, units: cellUnits } =\n parseCellParameters(lines);\n\n if (cellUnits === \"alat\") {\n if (celldm[0] === 0) {\n throw new Error(\"CELL_PARAMETERS alat requires celldm(1) in &SYSTEM\");\n }\n // lattice vectors are in units of celldm(1) Bohr → convert to angstrom\n const factor = celldm[0] / BOHR_TO_ANGSTROM;\n const m = cellLattice.basis.data;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else if (cellUnits === \"bohr\") {\n // lattice vectors in Bohr → convert to angstrom\n const m = cellLattice.basis.data;\n const factor = 1 / BOHR_TO_ANGSTROM;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else {\n // angstrom — use directly\n lattice = cellLattice;\n }\n }\n\n // --- parse atomic positions ---\n const {\n lines: atomLines,\n units,\n selectiveDynamics,\n } = parseAtomicPositions(lines);\n\n if (atomLines.length === 0) {\n throw new Error(\"ATOMIC_POSITIONS block not found\");\n }\n\n if (nat !== undefined && atomLines.length !== nat) {\n throw new Error(\n `Expected ${nat} atoms (from &SYSTEM nat), got ${atomLines.length}`,\n );\n }\n\n const sites: Site[] = [];\n\n for (const line of atomLines) {\n const parts = line.split(/\\s+/);\n const symbol = parts[0];\n const x = +parts[1];\n const y = +parts[2];\n const z = +parts[3];\n\n let frac: Float64Array;\n\n switch (units) {\n case \"crystal\":\n frac = new Float64Array([x, y, z]);\n break;\n\n case \"angstrom\":\n frac = fractional(lattice, new Float64Array([x, y, z]));\n break;\n\n case \"bohr\": {\n // Bohr → angstrom → fractional\n const angstrom = new Float64Array([\n x * BOHR_TO_ANGSTROM,\n y * BOHR_TO_ANGSTROM,\n z * BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n\n case \"alat\": {\n // alat = celldm(1) Bohr → Bohr → angstrom → fractional\n if (celldm[0] === 0) {\n throw new Error(\n \"ATOMIC_POSITIONS alat requires celldm(1) in &SYSTEM\",\n );\n }\n const bohr = new Float64Array([\n x * celldm[0],\n y * celldm[0],\n z * celldm[0],\n ]);\n const angstrom = new Float64Array([\n bohr[0] / BOHR_TO_ANGSTROM,\n bohr[1] / BOHR_TO_ANGSTROM,\n bohr[2] / BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n }\n\n const site: Site = { species: { symbol }, frac };\n\n if (selectiveDynamics && parts.length >= 7) {\n const ifPos = [+parts[4], +parts[5], +parts[6]];\n (site.properties ??= {}).ifPos = ifPos;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n ...(selectiveDynamics ? { selectiveDynamics: true } : {}),\n };\n}\n\n// ---------- internal parsing helpers ----------\n\ninterface CellParamsResult {\n lattice: ReturnType<typeof createLattice>;\n units: string;\n}\n\nfunction parseCellParameters(lines: string[]): CellParamsResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^CELL_PARAMETERS/i.test(line)) {\n const unitMatch = line.match(\n /^CELL_PARAMETERS\\s*(?:\\{|\\()?(\\w+)(?:\\}|\\))?/i,\n );\n const units = unitMatch?.[1]?.toLowerCase() ?? \"angstrom\";\n\n const rows: number[][] = [];\n for (let j = 1; j <= 3; j++) {\n if (i + j >= lines.length) {\n throw new Error(\"Incomplete CELL_PARAMETERS block\");\n }\n rows.push(lines[i + j].trim().split(/\\s+/).map(Number));\n }\n\n return {\n lattice: createLattice([...rows[0], ...rows[1], ...rows[2]]),\n units,\n };\n }\n }\n\n throw new Error(\"CELL_PARAMETERS block not found\");\n}\n\ninterface AtomBlockResult {\n lines: string[];\n units: AtomCoordMode;\n selectiveDynamics: boolean;\n}\n\nfunction parseAtomicPositions(lines: string[]): AtomBlockResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^ATOMIC_POSITIONS/i.test(line)) {\n const unitMatch = line.match(\n /^ATOMIC_POSITIONS\\s*(?:\\{|\\()?(\\w+)(?:\\}|\\))?/i,\n );\n const units = (unitMatch?.[1]?.toLowerCase() ??\n \"angstrom\") as AtomCoordMode;\n\n const atomLines: string[] = [];\n\n // check for \"Selective dynamics\" on the NEXT line\n let selectiveDynamics = false;\n let j = i + 1;\n if (j < lines.length && /^selective\\s+dynamics/i.test(lines[j].trim())) {\n selectiveDynamics = true;\n j++;\n }\n\n for (; j < lines.length; j++) {\n const l = lines[j].trim();\n if (!l) break;\n\n const parts = l.split(/\\s+/);\n if (\n parts.length < 4 ||\n !/^[A-Za-z]/.test(parts[0]) ||\n parts.slice(1, 4).some((x) => Number.isNaN(+x))\n ) {\n break;\n }\n\n atomLines.push(l);\n }\n\n return { lines: atomLines, units, selectiveDynamics };\n }\n }\n\n return { lines: [], units: \"angstrom\", selectiveDynamics: false };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// toPW — data-driven\n// ──────────────────────────────────────────────────────────────────────\n\nconst RESERVED: Record<string, string[]> = {\n CONTROL: [\"title\"],\n};\n\n/** Serializes a Structure to a Quantum ESPRESSO PW input string. */\nexport function toPW(structure: Structure, options?: QEOptions): string {\n const ctrl = { ...QE_DEFAULTS.control, ...options?.control };\n const sys = { ...QE_DEFAULTS.system, ...options?.system };\n const { nat: _nat, ntyp: _ntyp, ibrav: _ibrav, ...sysOpts } = sys;\n const elec = { ...QE_DEFAULTS.electrons, ...options?.electrons };\n\n // --- derive card data from Structure ---\n const speciesOrder = collectSpecies(structure.sites);\n const species = buildAtomicSpecies(speciesOrder, options?.pseudo?.pseudos);\n const positions = buildAtomicPositions(structure);\n const cell = buildCellParameters(structure.lattice);\n const kpoints = buildKPoints(structure, options?.kpoints);\n\n // --- serialize ---\n const lines: string[] = [];\n\n lines.push(`title = '${ctrl.title}'`);\n lines.push(\"\");\n writeNamelist(lines, \"CONTROL\", { ...ctrl, title: undefined });\n lines.push(\"\");\n writeNamelist(lines, \"SYSTEM\", {\n ...sysOpts,\n nat: structure.sites.length,\n ntyp: speciesOrder.length,\n ibrav: 0,\n });\n lines.push(\"\");\n writeNamelist(lines, \"ELECTRONS\", elec);\n lines.push(\"\");\n\n lines.push(...serializeAtomicSpecies(species));\n lines.push(\"\");\n lines.push(...serializeKPoints(kpoints));\n lines.push(\"\");\n lines.push(...serializeCellParameters(cell));\n lines.push(\"\");\n lines.push(\n ...serializeAtomicPositions(positions, structure.selectiveDynamics),\n );\n\n return lines.join(\"\\n\");\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card builders — Structure + options → typed card data\n// ──────────────────────────────────────────────────────────────────────\n\n/** Collect unique species in first-appearance order. */\nfunction collectSpecies(sites: Site[]): string[] {\n const seen = new Set<string>();\n const order: string[] = [];\n for (const site of sites) {\n const sym = site.species.symbol;\n if (!seen.has(sym)) {\n seen.add(sym);\n order.push(sym);\n }\n }\n return order;\n}\n\n/** Build ATOMIC_SPECIES rows from species order + pseudopotential map. */\nfunction buildAtomicSpecies(\n speciesOrder: string[],\n pseudos?: Record<string, string>,\n): AtomicSpeciesEntry[] {\n return speciesOrder.map((symbol) => {\n const el = getElement(symbol);\n return {\n symbol,\n mass: el?.mass ?? 0,\n pseudo: pseudos?.[symbol] ?? `${symbol}.UPF`,\n };\n });\n}\n\n/** Build ATOMIC_POSITIONS rows from Structure sites. */\nfunction buildAtomicPositions(structure: Structure): AtomicPositionEntry[] {\n // group sites by species in first-appearance order\n const grouped = new Map<string, Site[]>();\n for (const site of structure.sites) {\n const sym = site.species.symbol;\n const group = grouped.get(sym);\n if (group) {\n group.push(site);\n } else {\n grouped.set(sym, [site]);\n }\n }\n\n const speciesOrder = collectSpecies(structure.sites);\n const entries: AtomicPositionEntry[] = [];\n\n for (const sym of speciesOrder) {\n const group = grouped.get(sym) ?? [];\n for (const site of group) {\n const entry: AtomicPositionEntry = {\n symbol: sym,\n x: site.frac[0],\n y: site.frac[1],\n z: site.frac[2],\n };\n if (site.properties?.ifPos) {\n entry.ifPos = [\n site.properties.ifPos[0],\n site.properties.ifPos[1],\n site.properties.ifPos[2],\n ];\n }\n entries.push(entry);\n }\n }\n\n return entries;\n}\n\n/** Build CELL_PARAMETERS rows from Lattice. */\nfunction buildCellParameters(\n lattice: Structure[\"lattice\"],\n): CellParameterEntry[] {\n const m = lattice.basis.data;\n return [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ];\n}\n\n/** Build K_POINTS card from options (with kspacing default). */\nfunction buildKPoints(\n structure: Structure,\n kpoints?: QEOptions[\"kpoints\"],\n): KPointsCard {\n if (kpoints) {\n if (\"grid\" in kpoints) {\n return {\n mode: \"automatic\",\n grid: kpoints.grid,\n shift: kpoints.shift ?? [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, kpoints.kspacing),\n shift: [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, QE_DEFAULTS.kpoints.kspacing),\n shift: [0, 0, 0],\n };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card serializers — typed card data → string lines\n// ──────────────────────────────────────────────────────────────────────\n\nfunction serializeAtomicSpecies(entries: AtomicSpeciesEntry[]): string[] {\n const lines = [\"ATOMIC_SPECIES\"];\n for (const e of entries) {\n lines.push(`${e.symbol} ${e.mass} ${e.pseudo}`);\n }\n return lines;\n}\n\nfunction serializeKPoints(card: KPointsCard): string[] {\n switch (card.mode) {\n case \"gamma\":\n return [\"K_POINTS gamma\"];\n case \"automatic\":\n return [\n \"K_POINTS automatic\",\n `${card.grid[0]} ${card.grid[1]} ${card.grid[2]} ${card.shift[0]} ${card.shift[1]} ${card.shift[2]}`,\n ];\n default:\n // list / bands / covering — not used by toPW but handled for completeness\n throw new Error(`K_POINTS mode '${card.mode}' not yet supported in toPW`);\n }\n}\n\nfunction serializeCellParameters(\n entries: CellParameterEntry[],\n unit: \"angstrom\" | \"bohr\" | \"alat\" = \"angstrom\",\n): string[] {\n const lines = [`CELL_PARAMETERS ${unit}`];\n for (const [a, b, c] of entries) {\n lines.push(`${a} ${b} ${c}`);\n }\n return lines;\n}\n\nfunction serializeAtomicPositions(\n entries: AtomicPositionEntry[],\n selectiveDynamics?: boolean,\n unit: \"crystal\" | \"angstrom\" | \"bohr\" | \"alat\" = \"crystal\",\n): string[] {\n const lines = [`ATOMIC_POSITIONS ${unit}`];\n if (selectiveDynamics) {\n lines.push(\"Selective dynamics\");\n }\n for (const e of entries) {\n let suffix = \"\";\n if (e.ifPos) {\n suffix = ` ${e.ifPos[0]} ${e.ifPos[1]} ${e.ifPos[2]}`;\n }\n lines.push(`${e.symbol} ${e.x} ${e.y} ${e.z}${suffix}`);\n }\n return lines;\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Namelist serializer — generic key → value\n// ──────────────────────────────────────────────────────────────────────\n\nfunction writeNamelist(\n lines: string[],\n name: string,\n params: Record<string, unknown>,\n): void {\n const reserved = new Set(RESERVED[name] ?? []);\n const entries = Object.entries(params).filter(\n ([k, v]) => !reserved.has(k) && v !== undefined,\n );\n if (entries.length === 0) {\n lines.push(`&${name}`);\n lines.push(\"/\");\n return;\n }\n lines.push(`&${name}`);\n for (const [key, value] of entries) {\n if (typeof value === \"string\") {\n lines.push(` ${key} = '${value}'`);\n } else if (typeof value === \"boolean\") {\n lines.push(` ${key} = .${value ? \"TRUE\" : \"FALSE\"}.`);\n } else if (typeof value === \"number\" && !Number.isFinite(value)) {\n continue;\n } else {\n lines.push(` ${key} = ${value}`);\n }\n }\n lines.push(\"/\");\n}\n","'use strict';\n\nconst nameStartChar = ':A-Za-z_\\\\u00C0-\\\\u00D6\\\\u00D8-\\\\u00F6\\\\u00F8-\\\\u02FF\\\\u0370-\\\\u037D\\\\u037F-\\\\u1FFF\\\\u200C-\\\\u200D\\\\u2070-\\\\u218F\\\\u2C00-\\\\u2FEF\\\\u3001-\\\\uD7FF\\\\uF900-\\\\uFDCF\\\\uFDF0-\\\\uFFFD';\nconst nameChar = nameStartChar + '\\\\-.\\\\d\\\\u00B7\\\\u0300-\\\\u036F\\\\u203F-\\\\u2040';\nexport const nameRegexp = '[' + nameStartChar + '][' + nameChar + ']*';\nconst regexName = new RegExp('^' + nameRegexp + '$');\n\nexport function getAllMatches(string, regex) {\n const matches = [];\n let match = regex.exec(string);\n while (match) {\n const allmatches = [];\n allmatches.startIndex = regex.lastIndex - match[0].length;\n const len = match.length;\n for (let index = 0; index < len; index++) {\n allmatches.push(match[index]);\n }\n matches.push(allmatches);\n match = regex.exec(string);\n }\n return matches;\n}\n\nexport const isName = function (string) {\n const match = regexName.exec(string);\n return !(match === null || typeof match === 'undefined');\n}\n\nexport function isExist(v) {\n return typeof v !== 'undefined';\n}\n\nexport function isEmptyObject(obj) {\n return Object.keys(obj).length === 0;\n}\n\nexport function getValue(v) {\n if (exports.isExist(v)) {\n return v;\n } else {\n return '';\n }\n}\n\n/**\n * Dangerous property names that could lead to prototype pollution or security issues\n */\nexport const DANGEROUS_PROPERTY_NAMES = [\n // '__proto__',\n // 'constructor',\n // 'prototype',\n 'hasOwnProperty',\n 'toString',\n 'valueOf',\n '__defineGetter__',\n '__defineSetter__',\n '__lookupGetter__',\n '__lookupSetter__'\n];\n\nexport const criticalProperties = [\"__proto__\", \"constructor\", \"prototype\"];","'use strict';\n\nimport { getAllMatches, isName } from './util.js';\n\nconst defaultOptions = {\n allowBooleanAttributes: false, //A tag can have attributes without any value\n unpairedTags: []\n};\n\n//const tagsPattern = new RegExp(\"<\\\\/?([\\\\w:\\\\-_\\.]+)\\\\s*\\/?>\",\"g\");\nexport function validate(xmlData, options) {\n options = Object.assign({}, defaultOptions, options);\n\n //xmlData = xmlData.replace(/(\\r\\n|\\n|\\r)/gm,\"\");//make it single line\n //xmlData = xmlData.replace(/(^\\s*<\\?xml.*?\\?>)/g,\"\");//Remove XML starting tag\n //xmlData = xmlData.replace(/(<!DOCTYPE[\\s\\w\\\"\\.\\/\\-\\:]+(\\[.*\\])*\\s*>)/g,\"\");//Remove DOCTYPE\n const tags = [];\n let tagFound = false;\n\n //indicates that the root tag has been closed (aka. depth 0 has been reached)\n let reachedRoot = false;\n\n if (xmlData[0] === '\\ufeff') {\n // check for byte order mark (BOM)\n xmlData = xmlData.substr(1);\n }\n\n for (let i = 0; i < xmlData.length; i++) {\n\n if (xmlData[i] === '<' && xmlData[i + 1] === '?') {\n i += 2;\n i = readPI(xmlData, i);\n if (i.err) return i;\n } else if (xmlData[i] === '<') {\n //starting of tag\n //read until you reach to '>' avoiding any '>' in attribute value\n let tagStartPos = i;\n i++;\n\n if (xmlData[i] === '!') {\n i = readCommentAndCDATA(xmlData, i);\n continue;\n } else {\n let closingTag = false;\n if (xmlData[i] === '/') {\n //closing tag\n closingTag = true;\n i++;\n }\n //read tagname\n let tagName = '';\n for (; i < xmlData.length &&\n xmlData[i] !== '>' &&\n xmlData[i] !== ' ' &&\n xmlData[i] !== '\\t' &&\n xmlData[i] !== '\\n' &&\n xmlData[i] !== '\\r'; i++\n ) {\n tagName += xmlData[i];\n }\n tagName = tagName.trim();\n //console.log(tagName);\n\n if (tagName[tagName.length - 1] === '/') {\n //self closing tag without attributes\n tagName = tagName.substring(0, tagName.length - 1);\n //continue;\n i--;\n }\n if (!validateTagName(tagName)) {\n let msg;\n if (tagName.trim().length === 0) {\n msg = \"Invalid space after '<'.\";\n } else {\n msg = \"Tag '\" + tagName + \"' is an invalid name.\";\n }\n return getErrorObject('InvalidTag', msg, getLineNumberForPosition(xmlData, i));\n }\n\n const result = readAttributeStr(xmlData, i);\n if (result === false) {\n return getErrorObject('InvalidAttr', \"Attributes for '\" + tagName + \"' have open quote.\", getLineNumberForPosition(xmlData, i));\n }\n let attrStr = result.value;\n i = result.index;\n\n if (attrStr[attrStr.length - 1] === '/') {\n //self closing tag\n const attrStrStart = i - attrStr.length;\n attrStr = attrStr.substring(0, attrStr.length - 1);\n const isValid = validateAttributeString(attrStr, options);\n if (isValid === true) {\n tagFound = true;\n //continue; //text may presents after self closing tag\n } else {\n //the result from the nested function returns the position of the error within the attribute\n //in order to get the 'true' error line, we need to calculate the position where the attribute begins (i - attrStr.length) and then add the position within the attribute\n //this gives us the absolute index in the entire xml, which we can use to find the line at last\n return getErrorObject(isValid.err.code, isValid.err.msg, getLineNumberForPosition(xmlData, attrStrStart + isValid.err.line));\n }\n } else if (closingTag) {\n if (!result.tagClosed) {\n return getErrorObject('InvalidTag', \"Closing tag '\" + tagName + \"' doesn't have proper closing.\", getLineNumberForPosition(xmlData, i));\n } else if (attrStr.trim().length > 0) {\n return getErrorObject('InvalidTag', \"Closing tag '\" + tagName + \"' can't have attributes or invalid starting.\", getLineNumberForPosition(xmlData, tagStartPos));\n } else if (tags.length === 0) {\n return getErrorObject('InvalidTag', \"Closing tag '\" + tagName + \"' has not been opened.\", getLineNumberForPosition(xmlData, tagStartPos));\n } else {\n const otg = tags.pop();\n if (tagName !== otg.tagName) {\n let openPos = getLineNumberForPosition(xmlData, otg.tagStartPos);\n return getErrorObject('InvalidTag',\n \"Expected closing tag '\" + otg.tagName + \"' (opened in line \" + openPos.line + \", col \" + openPos.col + \") instead of closing tag '\" + tagName + \"'.\",\n getLineNumberForPosition(xmlData, tagStartPos));\n }\n\n //when there are no more tags, we reached the root level.\n if (tags.length == 0) {\n reachedRoot = true;\n }\n }\n } else {\n const isValid = validateAttributeString(attrStr, options);\n if (isValid !== true) {\n //the result from the nested function returns the position of the error within the attribute\n //in order to get the 'true' error line, we need to calculate the position where the attribute begins (i - attrStr.length) and then add the position within the attribute\n //this gives us the absolute index in the entire xml, which we can use to find the line at last\n return getErrorObject(isValid.err.code, isValid.err.msg, getLineNumberForPosition(xmlData, i - attrStr.length + isValid.err.line));\n }\n\n //if the root level has been reached before ...\n if (reachedRoot === true) {\n return getErrorObject('InvalidXml', 'Multiple possible root nodes found.', getLineNumberForPosition(xmlData, i));\n } else if (options.unpairedTags.indexOf(tagName) !== -1) {\n //don't push into stack\n } else {\n tags.push({ tagName, tagStartPos });\n }\n tagFound = true;\n }\n\n //skip tag text value\n //It may include comments and CDATA value\n for (i++; i < xmlData.length; i++) {\n if (xmlData[i] === '<') {\n if (xmlData[i + 1] === '!') {\n //comment or CADATA\n i++;\n i = readCommentAndCDATA(xmlData, i);\n continue;\n } else if (xmlData[i + 1] === '?') {\n i = readPI(xmlData, ++i);\n if (i.err) return i;\n } else {\n break;\n }\n } else if (xmlData[i] === '&') {\n const afterAmp = validateAmpersand(xmlData, i);\n if (afterAmp == -1)\n return getErrorObject('InvalidChar', \"char '&' is not expected.\", getLineNumberForPosition(xmlData, i));\n i = afterAmp;\n } else {\n if (reachedRoot === true && !isWhiteSpace(xmlData[i])) {\n return getErrorObject('InvalidXml', \"Extra text at the end\", getLineNumberForPosition(xmlData, i));\n }\n }\n } //end of reading tag text value\n if (xmlData[i] === '<') {\n i--;\n }\n }\n } else {\n if (isWhiteSpace(xmlData[i])) {\n continue;\n }\n return getErrorObject('InvalidChar', \"char '\" + xmlData[i] + \"' is not expected.\", getLineNumberForPosition(xmlData, i));\n }\n }\n\n if (!tagFound) {\n return getErrorObject('InvalidXml', 'Start tag expected.', 1);\n } else if (tags.length == 1) {\n return getErrorObject('InvalidTag', \"Unclosed tag '\" + tags[0].tagName + \"'.\", getLineNumberForPosition(xmlData, tags[0].tagStartPos));\n } else if (tags.length > 0) {\n return getErrorObject('InvalidXml', \"Invalid '\" +\n JSON.stringify(tags.map(t => t.tagName), null, 4).replace(/\\r?\\n/g, '') +\n \"' found.\", { line: 1, col: 1 });\n }\n\n return true;\n};\n\nfunction isWhiteSpace(char) {\n return char === ' ' || char === '\\t' || char === '\\n' || char === '\\r';\n}\n/**\n * Read Processing insstructions and skip\n * @param {*} xmlData\n * @param {*} i\n */\nfunction readPI(xmlData, i) {\n const start = i;\n for (; i < xmlData.length; i++) {\n if (xmlData[i] == '?' || xmlData[i] == ' ') {\n //tagname\n const tagname = xmlData.substr(start, i - start);\n if (i > 5 && tagname === 'xml') {\n return getErrorObject('InvalidXml', 'XML declaration allowed only at the start of the document.', getLineNumberForPosition(xmlData, i));\n } else if (xmlData[i] == '?' && xmlData[i + 1] == '>') {\n //check if valid attribut string\n i++;\n break;\n } else {\n continue;\n }\n }\n }\n return i;\n}\n\nfunction readCommentAndCDATA(xmlData, i) {\n if (xmlData.length > i + 5 && xmlData[i + 1] === '-' && xmlData[i + 2] === '-') {\n //comment\n for (i += 3; i < xmlData.length; i++) {\n if (xmlData[i] === '-' && xmlData[i + 1] === '-' && xmlData[i + 2] === '>') {\n i += 2;\n break;\n }\n }\n } else if (\n xmlData.length > i + 8 &&\n xmlData[i + 1] === 'D' &&\n xmlData[i + 2] === 'O' &&\n xmlData[i + 3] === 'C' &&\n xmlData[i + 4] === 'T' &&\n xmlData[i + 5] === 'Y' &&\n xmlData[i + 6] === 'P' &&\n xmlData[i + 7] === 'E'\n ) {\n let angleBracketsCount = 1;\n for (i += 8; i < xmlData.length; i++) {\n if (xmlData[i] === '<') {\n angleBracketsCount++;\n } else if (xmlData[i] === '>') {\n angleBracketsCount--;\n if (angleBracketsCount === 0) {\n break;\n }\n }\n }\n } else if (\n xmlData.length > i + 9 &&\n xmlData[i + 1] === '[' &&\n xmlData[i + 2] === 'C' &&\n xmlData[i + 3] === 'D' &&\n xmlData[i + 4] === 'A' &&\n xmlData[i + 5] === 'T' &&\n xmlData[i + 6] === 'A' &&\n xmlData[i + 7] === '['\n ) {\n for (i += 8; i < xmlData.length; i++) {\n if (xmlData[i] === ']' && xmlData[i + 1] === ']' && xmlData[i + 2] === '>') {\n i += 2;\n break;\n }\n }\n }\n\n return i;\n}\n\nconst doubleQuote = '\"';\nconst singleQuote = \"'\";\n\n/**\n * Keep reading xmlData until '<' is found outside the attribute value.\n * @param {string} xmlData\n * @param {number} i\n */\nfunction readAttributeStr(xmlData, i) {\n let attrStr = '';\n let startChar = '';\n let tagClosed = false;\n for (; i < xmlData.length; i++) {\n if (xmlData[i] === doubleQuote || xmlData[i] === singleQuote) {\n if (startChar === '') {\n startChar = xmlData[i];\n } else if (startChar !== xmlData[i]) {\n //if vaue is enclosed with double quote then single quotes are allowed inside the value and vice versa\n } else {\n startChar = '';\n }\n } else if (xmlData[i] === '>') {\n if (startChar === '') {\n tagClosed = true;\n break;\n }\n }\n attrStr += xmlData[i];\n }\n if (startChar !== '') {\n return false;\n }\n\n return {\n value: attrStr,\n index: i,\n tagClosed: tagClosed\n };\n}\n\n/**\n * Select all the attributes whether valid or invalid.\n */\nconst validAttrStrRegxp = new RegExp('(\\\\s*)([^\\\\s=]+)(\\\\s*=)?(\\\\s*([\\'\"])(([\\\\s\\\\S])*?)\\\\5)?', 'g');\n\n//attr, =\"sd\", a=\"amit's\", a=\"sd\"b=\"saf\", ab cd=\"\"\n\nfunction validateAttributeString(attrStr, options) {\n //console.log(\"start:\"+attrStr+\":end\");\n\n //if(attrStr.trim().length === 0) return true; //empty string\n\n const matches = getAllMatches(attrStr, validAttrStrRegxp);\n const attrNames = {};\n\n for (let i = 0; i < matches.length; i++) {\n if (matches[i][1].length === 0) {\n //nospace before attribute name: a=\"sd\"b=\"saf\"\n return getErrorObject('InvalidAttr', \"Attribute '\" + matches[i][2] + \"' has no space in starting.\", getPositionFromMatch(matches[i]))\n } else if (matches[i][3] !== undefined && matches[i][4] === undefined) {\n return getErrorObject('InvalidAttr', \"Attribute '\" + matches[i][2] + \"' is without value.\", getPositionFromMatch(matches[i]));\n } else if (matches[i][3] === undefined && !options.allowBooleanAttributes) {\n //independent attribute: ab\n return getErrorObject('InvalidAttr', \"boolean attribute '\" + matches[i][2] + \"' is not allowed.\", getPositionFromMatch(matches[i]));\n }\n /* else if(matches[i][6] === undefined){//attribute without value: ab=\n return { err: { code:\"InvalidAttr\",msg:\"attribute \" + matches[i][2] + \" has no value assigned.\"}};\n } */\n const attrName = matches[i][2];\n if (!validateAttrName(attrName)) {\n return getErrorObject('InvalidAttr', \"Attribute '\" + attrName + \"' is an invalid name.\", getPositionFromMatch(matches[i]));\n }\n if (!Object.prototype.hasOwnProperty.call(attrNames, attrName)) {\n //check for duplicate attribute.\n attrNames[attrName] = 1;\n } else {\n return getErrorObject('InvalidAttr', \"Attribute '\" + attrName + \"' is repeated.\", getPositionFromMatch(matches[i]));\n }\n }\n\n return true;\n}\n\nfunction validateNumberAmpersand(xmlData, i) {\n let re = /\\d/;\n if (xmlData[i] === 'x') {\n i++;\n re = /[\\da-fA-F]/;\n }\n for (; i < xmlData.length; i++) {\n if (xmlData[i] === ';')\n return i;\n if (!xmlData[i].match(re))\n break;\n }\n return -1;\n}\n\nfunction validateAmpersand(xmlData, i) {\n // https://www.w3.org/TR/xml/#dt-charref\n i++;\n if (xmlData[i] === ';')\n return -1;\n if (xmlData[i] === '#') {\n i++;\n return validateNumberAmpersand(xmlData, i);\n }\n let count = 0;\n for (; i < xmlData.length; i++, count++) {\n if (xmlData[i].match(/\\w/) && count < 20)\n continue;\n if (xmlData[i] === ';')\n break;\n return -1;\n }\n return i;\n}\n\nfunction getErrorObject(code, message, lineNumber) {\n return {\n err: {\n code: code,\n msg: message,\n line: lineNumber.line || lineNumber,\n col: lineNumber.col,\n },\n };\n}\n\nfunction validateAttrName(attrName) {\n return isName(attrName);\n}\n\n// const startsWithXML = /^xml/i;\n\nfunction validateTagName(tagname) {\n return isName(tagname) /* && !tagname.match(startsWithXML) */;\n}\n\n//this function returns the line number for the character at the given index\nfunction getLineNumberForPosition(xmlData, index) {\n const lines = xmlData.substring(0, index).split(/\\r?\\n/);\n return {\n line: lines.length,\n\n // column number is last line's length + 1, because column numbering starts at 1:\n col: lines[lines.length - 1].length + 1\n };\n}\n\n//this function returns the position of the first character of match within attrStr\nfunction getPositionFromMatch(match) {\n return match.startIndex + match[1].length;\n}\n","// ---------------------------------------------------------------------------\n// Complete HTML5 named entity reference\n// Organized by logical categories for easy maintenance and selective importing\n// ---------------------------------------------------------------------------\n\n/**\n * Basic Latin & Special Characters\n * @type {Record<string, string>}\n */\nexport const BASIC_LATIN = {\n amp: '&',\n AMP: '&',\n lt: '<',\n LT: '<',\n gt: '>',\n GT: '>',\n quot: '\"',\n QUOT: '\"',\n apos: \"'\",\n lsquo: '‘',\n rsquo: '’',\n ldquo: '“',\n rdquo: '”',\n lsquor: '‚',\n rsquor: '’',\n ldquor: '„',\n bdquo: '„',\n comma: ',',\n period: '.',\n colon: ':',\n semi: ';',\n excl: '!',\n quest: '?',\n num: '#',\n dollar: '$',\n percent: '%',\n ast: '*',\n commat: '@',\n lowbar: '_',\n verbar: '|',\n vert: '|',\n sol: '/',\n bsol: '\\\\',\n lbrace: '{',\n rbrace: '}',\n lbrack: '[',\n rbrack: ']',\n lpar: '(',\n rpar: ')',\n nbsp: '\\u00a0',\n iexcl: '¡',\n cent: '¢',\n pound: '£',\n curren: '¤',\n yen: '¥',\n brvbar: '¦',\n sect: '§',\n uml: '¨',\n copy: '©',\n COPY: '©',\n ordf: 'ª',\n laquo: '«',\n not: '¬',\n shy: '\\u00ad',\n reg: '®',\n REG: '®',\n macr: '¯',\n deg: '°',\n plusmn: '±',\n sup2: '²',\n sup3: '³',\n acute: '´',\n micro: 'µ',\n para: '¶',\n middot: '·',\n cedil: '¸',\n sup1: '¹',\n ordm: 'º',\n raquo: '»',\n frac14: '¼',\n frac12: '½',\n half: '½',\n frac34: '¾',\n iquest: '¿',\n times: '×',\n div: '÷',\n divide: '÷',\n};\n\n/**\n * Latin Extended & Accented Letters (A-Z)\n * @type {Record<string, string>}\n */\nexport const LATIN_ACCENTS = {\n Agrave: 'À',\n agrave: 'à',\n Aacute: 'Á',\n aacute: 'á',\n Acirc: 'Â',\n acirc: 'â',\n Atilde: 'Ã',\n atilde: 'ã',\n Auml: 'Ä',\n auml: 'ä',\n Aring: 'Å',\n aring: 'å',\n AElig: 'Æ',\n aelig: 'æ',\n Ccedil: 'Ç',\n ccedil: 'ç',\n Egrave: 'È',\n egrave: 'è',\n Eacute: 'É',\n eacute: 'é',\n Ecirc: 'Ê',\n ecirc: 'ê',\n Euml: 'Ë',\n euml: 'ë',\n Igrave: 'Ì',\n igrave: 'ì',\n Iacute: 'Í',\n iacute: 'í',\n Icirc: 'Î',\n icirc: 'î',\n Iuml: 'Ï',\n iuml: 'ï',\n ETH: 'Ð',\n eth: 'ð',\n Ntilde: 'Ñ',\n ntilde: 'ñ',\n Ograve: 'Ò',\n ograve: 'ò',\n Oacute: 'Ó',\n oacute: 'ó',\n Ocirc: 'Ô',\n ocirc: 'ô',\n Otilde: 'Õ',\n otilde: 'õ',\n Ouml: 'Ö',\n ouml: 'ö',\n Oslash: 'Ø',\n oslash: 'ø',\n Ugrave: 'Ù',\n ugrave: 'ù',\n Uacute: 'Ú',\n uacute: 'ú',\n Ucirc: 'Û',\n ucirc: 'û',\n Uuml: 'Ü',\n uuml: 'ü',\n Yacute: 'Ý',\n yacute: 'ý',\n THORN: 'Þ',\n thorn: 'þ',\n szlig: 'ß',\n yuml: 'ÿ',\n Yuml: 'Ÿ',\n};\n\n/**\n * Latin Extended (Letters with diacritics)\n * @type {Record<string, string>}\n */\nexport const LATIN_EXTENDED = {\n Amacr: 'Ā',\n amacr: 'ā',\n Abreve: 'Ă',\n abreve: 'ă',\n Aogon: 'Ą',\n aogon: 'ą',\n Cacute: 'Ć',\n cacute: 'ć',\n Ccirc: 'Ĉ',\n ccirc: 'ĉ',\n Cdot: 'Ċ',\n cdot: 'ċ',\n Ccaron: 'Č',\n ccaron: 'č',\n Dcaron: 'Ď',\n dcaron: 'ď',\n Dstrok: 'Đ',\n dstrok: 'đ',\n Emacr: 'Ē',\n emacr: 'ē',\n Ecaron: 'Ě',\n ecaron: 'ě',\n Edot: 'Ė',\n edot: 'ė',\n Eogon: 'Ę',\n eogon: 'ę',\n Gcirc: 'Ĝ',\n gcirc: 'ĝ',\n Gbreve: 'Ğ',\n gbreve: 'ğ',\n Gdot: 'Ġ',\n gdot: 'ġ',\n Gcedil: 'Ģ',\n Hcirc: 'Ĥ',\n hcirc: 'ĥ',\n Hstrok: 'Ħ',\n hstrok: 'ħ',\n Itilde: 'Ĩ',\n itilde: 'ĩ',\n Imacr: 'Ī',\n imacr: 'ī',\n Iogon: 'Į',\n iogon: 'į',\n Idot: 'İ',\n IJlig: 'IJ',\n ijlig: 'ij',\n Jcirc: 'Ĵ',\n jcirc: 'ĵ',\n Kcedil: 'Ķ',\n kcedil: 'ķ',\n kgreen: 'ĸ',\n Lacute: 'Ĺ',\n lacute: 'ĺ',\n Lcedil: 'Ļ',\n lcedil: 'ļ',\n Lcaron: 'Ľ',\n lcaron: 'ľ',\n Lmidot: 'Ŀ',\n lmidot: 'ŀ',\n Lstrok: 'Ł',\n lstrok: 'ł',\n Nacute: 'Ń',\n nacute: 'ń',\n Ncaron: 'Ň',\n ncaron: 'ň',\n Ncedil: 'Ņ',\n ncedil: 'ņ',\n ENG: 'Ŋ',\n eng: 'ŋ',\n Omacr: 'Ō',\n omacr: 'ō',\n Odblac: 'Ő',\n odblac: 'ő',\n OElig: 'Œ',\n oelig: 'œ',\n Racute: 'Ŕ',\n racute: 'ŕ',\n Rcaron: 'Ř',\n rcaron: 'ř',\n Rcedil: 'Ŗ',\n rcedil: 'ŗ',\n Sacute: 'Ś',\n sacute: 'ś',\n Scirc: 'Ŝ',\n scirc: 'ŝ',\n Scedil: 'Ş',\n scedil: 'ş',\n Scaron: 'Š',\n scaron: 'š',\n Tcedil: 'Ţ',\n tcedil: 'ţ',\n Tcaron: 'Ť',\n tcaron: 'ť',\n Tstrok: 'Ŧ',\n tstrok: 'ŧ',\n Utilde: 'Ũ',\n utilde: 'ũ',\n Umacr: 'Ū',\n umacr: 'ū',\n Ubreve: 'Ŭ',\n ubreve: 'ŭ',\n Uring: 'Ů',\n uring: 'ů',\n Udblac: 'Ű',\n udblac: 'ű',\n Uogon: 'Ų',\n uogon: 'ų',\n Wcirc: 'Ŵ',\n wcirc: 'ŵ',\n Ycirc: 'Ŷ',\n ycirc: 'ŷ',\n Zacute: 'Ź',\n zacute: 'ź',\n Zdot: 'Ż',\n zdot: 'ż',\n Zcaron: 'Ž',\n zcaron: 'ž',\n};\n\n/**\n * Greek Letters\n * @type {Record<string, string>}\n */\nexport const GREEK = {\n Alpha: 'Α',\n alpha: 'α',\n Beta: 'Β',\n beta: 'β',\n Gamma: 'Γ',\n gamma: 'γ',\n Delta: 'Δ',\n delta: 'δ',\n Epsilon: 'Ε',\n epsilon: 'ε',\n epsiv: 'ϵ',\n varepsilon: 'ϵ',\n Zeta: 'Ζ',\n zeta: 'ζ',\n Eta: 'Η',\n eta: 'η',\n Theta: 'Θ',\n theta: 'θ',\n thetasym: 'ϑ',\n vartheta: 'ϑ',\n Iota: 'Ι',\n iota: 'ι',\n Kappa: 'Κ',\n kappa: 'κ',\n kappav: 'ϰ',\n varkappa: 'ϰ',\n Lambda: 'Λ',\n lambda: 'λ',\n Mu: 'Μ',\n mu: 'μ',\n Nu: 'Ν',\n nu: 'ν',\n Xi: 'Ξ',\n xi: 'ξ',\n Omicron: 'Ο',\n omicron: 'ο',\n Pi: 'Π',\n pi: 'π',\n piv: 'ϖ',\n varpi: 'ϖ',\n Rho: 'Ρ',\n rho: 'ρ',\n rhov: 'ϱ',\n varrho: 'ϱ',\n Sigma: 'Σ',\n sigma: 'σ',\n sigmaf: 'ς',\n sigmav: 'ς',\n varsigma: 'ς',\n Tau: 'Τ',\n tau: 'τ',\n Upsilon: 'Υ',\n upsilon: 'υ',\n upsi: 'υ',\n Upsi: 'ϒ',\n upsih: 'ϒ',\n Phi: 'Φ',\n phi: 'φ',\n phiv: 'ϕ',\n varphi: 'ϕ',\n Chi: 'Χ',\n chi: 'χ',\n Psi: 'Ψ',\n psi: 'ψ',\n Omega: 'Ω',\n omega: 'ω',\n ohm: 'Ω',\n Gammad: 'Ϝ',\n gammad: 'ϝ',\n digamma: 'ϝ',\n};\n\n/**\n * Cyrillic Letters\n * @type {Record<string, string>}\n */\nexport const CYRILLIC = {\n Afr: '𝔄',\n afr: '𝔞',\n Acy: 'А',\n acy: 'а',\n Bcy: 'Б',\n bcy: 'б',\n Vcy: 'В',\n vcy: 'в',\n Gcy: 'Г',\n gcy: 'г',\n Dcy: 'Д',\n dcy: 'д',\n IEcy: 'Е',\n iecy: 'е',\n IOcy: 'Ё',\n iocy: 'ё',\n ZHcy: 'Ж',\n zhcy: 'ж',\n Zcy: 'З',\n zcy: 'з',\n Icy: 'И',\n icy: 'и',\n Jcy: 'Й',\n jcy: 'й',\n Kcy: 'К',\n kcy: 'к',\n Lcy: 'Л',\n lcy: 'л',\n Mcy: 'М',\n mcy: 'м',\n Ncy: 'Н',\n ncy: 'н',\n Ocy: 'О',\n ocy: 'о',\n Pcy: 'П',\n pcy: 'п',\n Rcy: 'Р',\n rcy: 'р',\n Scy: 'С',\n scy: 'с',\n Tcy: 'Т',\n tcy: 'т',\n Ucy: 'У',\n ucy: 'у',\n Fcy: 'Ф',\n fcy: 'ф',\n KHcy: 'Х',\n khcy: 'х',\n TScy: 'Ц',\n tscy: 'ц',\n CHcy: 'Ч',\n chcy: 'ч',\n SHcy: 'Ш',\n shcy: 'ш',\n SHCHcy: 'Щ',\n shchcy: 'щ',\n HARDcy: 'Ъ',\n hardcy: 'ъ',\n Ycy: 'Ы',\n ycy: 'ы',\n SOFTcy: 'Ь',\n softcy: 'ь',\n Ecy: 'Э',\n ecy: 'э',\n YUcy: 'Ю',\n yucy: 'ю',\n YAcy: 'Я',\n yacy: 'я',\n DJcy: 'Ђ',\n djcy: 'ђ',\n GJcy: 'Ѓ',\n gjcy: 'ѓ',\n Jukcy: 'Є',\n jukcy: 'є',\n DScy: 'Ѕ',\n dscy: 'ѕ',\n Iukcy: 'І',\n iukcy: 'і',\n YIcy: 'Ї',\n yicy: 'ї',\n Jsercy: 'Ј',\n jsercy: 'ј',\n LJcy: 'Љ',\n ljcy: 'љ',\n NJcy: 'Њ',\n njcy: 'њ',\n TSHcy: 'Ћ',\n tshcy: 'ћ',\n KJcy: 'Ќ',\n kjcy: 'ќ',\n Ubrcy: 'Ў',\n ubrcy: 'ў',\n DZcy: 'Џ',\n dzcy: 'џ',\n};\n\n/**\n * Mathematical Operators & Relations\n * @type {Record<string, string>}\n */\nexport const MATH = {\n plus: '+',\n pm: '±',\n times: '×',\n div: '÷',\n divide: '÷',\n sdot: '⋅',\n star: '☆',\n starf: '★',\n bigstar: '★',\n lowast: '∗',\n ast: '*',\n midast: '*',\n compfn: '∘',\n smallcircle: '∘',\n bullet: '•',\n bull: '•',\n nbsp: '\\u00a0',\n hellip: '…',\n mldr: '…',\n prime: '′',\n Prime: '″',\n tprime: '‴',\n bprime: '‵',\n backprime: '‵',\n minus: '−',\n minusd: '∸',\n dotminus: '∸',\n plusdo: '∔',\n dotplus: '∔',\n plusmn: '±',\n minusplus: '∓',\n mnplus: '∓',\n mp: '∓',\n setminus: '∖',\n smallsetminus: '∖',\n Backslash: '∖',\n setmn: '∖',\n ssetmn: '∖',\n lowbar: '_',\n verbar: '|',\n vert: '|',\n VerticalLine: '|',\n colon: ':',\n Colon: '∷',\n Proportion: '∷',\n ratio: '∶',\n equals: '=',\n ne: '≠',\n nequiv: '≢',\n equiv: '≡',\n Congruent: '≡',\n sim: '∼',\n thicksim: '∼',\n thksim: '∼',\n sime: '≃',\n simeq: '≃',\n TildeEqual: '≃',\n asymp: '≈',\n approx: '≈',\n thickapprox: '≈',\n thkap: '≈',\n TildeTilde: '≈',\n ncong: '≇',\n cong: '≅',\n TildeFullEqual: '≅',\n asympeq: '≍',\n CupCap: '≍',\n bump: '≎',\n Bumpeq: '≎',\n HumpDownHump: '≎',\n bumpe: '≏',\n bumpeq: '≏',\n HumpEqual: '≏',\n le: '≤',\n LessEqual: '≤',\n ge: '≥',\n GreaterEqual: '≥',\n lesseqgtr: '⋚',\n lesseqqgtr: '⪋',\n greater: '>',\n less: '<',\n};\n\n/**\n * Mathematical Operators (Advanced)\n * @type {Record<string, string>}\n */\nexport const MATH_ADVANCED = {\n alefsym: 'ℵ',\n aleph: 'ℵ',\n beth: 'ℶ',\n gimel: 'ℷ',\n daleth: 'ℸ',\n forall: '∀',\n ForAll: '∀',\n part: '∂',\n PartialD: '∂',\n exist: '∃',\n Exists: '∃',\n nexist: '∄',\n nexists: '∄',\n empty: '∅',\n emptyset: '∅',\n emptyv: '∅',\n varnothing: '∅',\n nabla: '∇',\n Del: '∇',\n isin: '∈',\n isinv: '∈',\n in: '∈',\n Element: '∈',\n notin: '∉',\n notinva: '∉',\n ni: '∋',\n niv: '∋',\n SuchThat: '∋',\n ReverseElement: '∋',\n notni: '∌',\n notniva: '∌',\n prod: '∏',\n Product: '∏',\n coprod: '∐',\n Coproduct: '∐',\n sum: '∑',\n Sum: '∑',\n minus: '−',\n mp: '∓',\n plusdo: '∔',\n dotplus: '∔',\n setminus: '∖',\n lowast: '∗',\n radic: '√',\n Sqrt: '√',\n prop: '∝',\n propto: '∝',\n Proportional: '∝',\n varpropto: '∝',\n infin: '∞',\n infintie: '⧝',\n ang: '∠',\n angle: '∠',\n angmsd: '∡',\n measuredangle: '∡',\n angsph: '∢',\n mid: '∣',\n VerticalBar: '∣',\n nmid: '∤',\n nsmid: '∤',\n npar: '∦',\n parallel: '∥',\n spar: '∥',\n nparallel: '∦',\n nspar: '∦',\n and: '∧',\n wedge: '∧',\n or: '∨',\n vee: '∨',\n cap: '∩',\n cup: '∪',\n int: '∫',\n Integral: '∫',\n conint: '∮',\n ContourIntegral: '∮',\n Conint: '∯',\n DoubleContourIntegral: '∯',\n Cconint: '∰',\n there4: '∴',\n therefore: '∴',\n Therefore: '∴',\n becaus: '∵',\n because: '∵',\n Because: '∵',\n ratio: '∶',\n Proportion: '∷',\n minusd: '∸',\n dotminus: '∸',\n mDDot: '∺',\n homtht: '∻',\n sim: '∼',\n bsimg: '∽',\n backsim: '∽',\n ac: '∾',\n mstpos: '∾',\n acd: '∿',\n VerticalTilde: '≀',\n wr: '≀',\n wreath: '≀',\n nsime: '≄',\n nsimeq: '≄',\n ncong: '≇',\n simne: '≆',\n ncongdot: '⩭̸',\n ngsim: '≵',\n nsim: '≁',\n napprox: '≉',\n nap: '≉',\n ngeq: '≱',\n nge: '≱',\n nleq: '≰',\n nle: '≰',\n ngtr: '≯',\n ngt: '≯',\n nless: '≮',\n nlt: '≮',\n nprec: '⊀',\n npr: '⊀',\n nsucc: '⊁',\n nsc: '⊁',\n};\n\n/**\n * Arrows\n * @type {Record<string, string>}\n */\nexport const ARROWS = {\n larr: '←',\n leftarrow: '←',\n LeftArrow: '←',\n uarr: '↑',\n uparrow: '↑',\n UpArrow: '↑',\n rarr: '→',\n rightarrow: '→',\n RightArrow: '→',\n darr: '↓',\n downarrow: '↓',\n DownArrow: '↓',\n harr: '↔',\n leftrightarrow: '↔',\n LeftRightArrow: '↔',\n varr: '↕',\n updownarrow: '↕',\n UpDownArrow: '↕',\n nwarr: '↖',\n nwarrow: '↖',\n UpperLeftArrow: '↖',\n nearr: '↗',\n nearrow: '↗',\n UpperRightArrow: '↗',\n searr: '↘',\n searrow: '↘',\n LowerRightArrow: '↘',\n swarr: '↙',\n swarrow: '↙',\n LowerLeftArrow: '↙',\n lArr: '⇐',\n Leftarrow: '⇐',\n uArr: '⇑',\n Uparrow: '⇑',\n rArr: '⇒',\n Rightarrow: '⇒',\n dArr: '⇓',\n Downarrow: '⇓',\n hArr: '⇔',\n Leftrightarrow: '⇔',\n iff: '⇔',\n vArr: '⇕',\n Updownarrow: '⇕',\n lAarr: '⇚',\n Lleftarrow: '⇚',\n rAarr: '⇛',\n Rrightarrow: '⇛',\n lrarr: '⇆',\n leftrightarrows: '⇆',\n rlarr: '⇄',\n rightleftarrows: '⇄',\n lrhar: '⇋',\n leftrightharpoons: '⇋',\n ReverseEquilibrium: '⇋',\n rlhar: '⇌',\n rightleftharpoons: '⇌',\n Equilibrium: '⇌',\n udarr: '⇅',\n UpArrowDownArrow: '⇅',\n duarr: '⇵',\n DownArrowUpArrow: '⇵',\n llarr: '⇇',\n leftleftarrows: '⇇',\n rrarr: '⇉',\n rightrightarrows: '⇉',\n ddarr: '⇊',\n downdownarrows: '⇊',\n har: '↽',\n lhard: '↽',\n leftharpoondown: '↽',\n lharu: '↼',\n leftharpoonup: '↼',\n rhard: '⇁',\n rightharpoondown: '⇁',\n rharu: '⇀',\n rightharpoonup: '⇀',\n lsh: '↰',\n Lsh: '↰',\n rsh: '↱',\n Rsh: '↱',\n ldsh: '↲',\n rdsh: '↳',\n hookleftarrow: '↩',\n hookrightarrow: '↪',\n mapstoleft: '↤',\n mapstoup: '↥',\n map: '↦',\n mapsto: '↦',\n mapstodown: '↧',\n crarr: '↵',\n nleftarrow: '↚',\n nleftrightarrow: '↮',\n nrightarrow: '↛',\n nrarr: '↛',\n larrtl: '↢',\n rarrtl: '↣',\n leftarrowtail: '↢',\n rightarrowtail: '↣',\n twoheadleftarrow: '↞',\n twoheadrightarrow: '↠',\n Larr: '↞',\n Rarr: '↠',\n larrhk: '↩',\n rarrhk: '↪',\n larrlp: '↫',\n looparrowleft: '↫',\n rarrlp: '↬',\n looparrowright: '↬',\n harrw: '↭',\n leftrightsquigarrow: '↭',\n nrarrw: '↝̸',\n rarrw: '↝',\n rightsquigarrow: '↝',\n larrbfs: '⤟',\n rarrbfs: '⤠',\n nvHarr: '⤄',\n nvlArr: '⤂',\n nvrArr: '⤃',\n larrfs: '⤝',\n rarrfs: '⤞',\n Map: '⤅',\n larrsim: '⥳',\n rarrsim: '⥴',\n harrcir: '⥈',\n Uarrocir: '⥉',\n lurdshar: '⥊',\n ldrdhar: '⥧',\n ldrushar: '⥋',\n rdldhar: '⥩',\n lrhard: '⥭',\n uharr: '↾',\n uharl: '↿',\n dharr: '⇂',\n dharl: '⇃',\n Uarr: '↟',\n Darr: '↡',\n zigrarr: '⇝',\n nwArr: '⇖',\n neArr: '⇗',\n seArr: '⇘',\n swArr: '⇙',\n nharr: '↮',\n nhArr: '⇎',\n nlarr: '↚',\n nlArr: '⇍',\n nrArr: '⇏',\n larrb: '⇤',\n LeftArrowBar: '⇤',\n rarrb: '⇥',\n RightArrowBar: '⇥',\n};\n\n/**\n * Geometric Shapes\n * @type {Record<string, string>}\n */\nexport const SHAPES = {\n square: '□',\n Square: '□',\n squ: '□',\n squf: '▪',\n squarf: '▪',\n blacksquar: '▪',\n blacksquare: '▪',\n FilledVerySmallSquare: '▪',\n blk34: '▓',\n blk12: '▒',\n blk14: '░',\n block: '█',\n srect: '▭',\n rect: '▭',\n sdot: '⋅',\n sdotb: '⊡',\n dotsquare: '⊡',\n triangle: '▵',\n tri: '▵',\n trine: '▵',\n utri: '▵',\n triangledown: '▿',\n dtri: '▿',\n tridown: '▿',\n triangleleft: '◃',\n ltri: '◃',\n triangleright: '▹',\n rtri: '▹',\n blacktriangle: '▴',\n utrif: '▴',\n blacktriangledown: '▾',\n dtrif: '▾',\n blacktriangleleft: '◂',\n ltrif: '◂',\n blacktriangleright: '▸',\n rtrif: '▸',\n loz: '◊',\n lozenge: '◊',\n blacklozenge: '⧫',\n lozf: '⧫',\n bigcirc: '◯',\n xcirc: '◯',\n circ: 'ˆ',\n Circle: '○',\n cir: '○',\n o: '○',\n bullet: '•',\n bull: '•',\n hellip: '…',\n mldr: '…',\n nldr: '‥',\n boxh: '─',\n HorizontalLine: '─',\n boxv: '│',\n boxdr: '┌',\n boxdl: '┐',\n boxur: '└',\n boxul: '┘',\n boxvr: '├',\n boxvl: '┤',\n boxhd: '┬',\n boxhu: '┴',\n boxvh: '┼',\n boxH: '═',\n boxV: '║',\n boxdR: '╒',\n boxDr: '╓',\n boxDR: '╔',\n boxDl: '╕',\n boxdL: '╖',\n boxDL: '╗',\n boxuR: '╘',\n boxUr: '╙',\n boxUR: '╚',\n boxUl: '╜',\n boxuL: '╛',\n boxUL: '╝',\n boxvR: '╞',\n boxVr: '╟',\n boxVR: '╠',\n boxVl: '╢',\n boxvL: '╡',\n boxVL: '╣',\n boxHd: '╤',\n boxhD: '╥',\n boxHD: '╦',\n boxHu: '╧',\n boxhU: '╨',\n boxHU: '╩',\n boxvH: '╪',\n boxVh: '╫',\n boxVH: '╬',\n};\n\n/**\n * Punctuation & Diacritics\n * @type {Record<string, string>}\n */\nexport const PUNCTUATION = {\n excl: '!',\n iexcl: '¡',\n brvbar: '¦',\n sect: '§',\n uml: '¨',\n copy: '©',\n ordf: 'ª',\n laquo: '«',\n not: '¬',\n shy: '\\u00ad',\n reg: '®',\n macr: '¯',\n deg: '°',\n plusmn: '±',\n sup2: '²',\n sup3: '³',\n acute: '´',\n micro: 'µ',\n para: '¶',\n middot: '·',\n cedil: '¸',\n sup1: '¹',\n ordm: 'º',\n raquo: '»',\n frac14: '¼',\n frac12: '½',\n frac34: '¾',\n iquest: '¿',\n nbsp: '\\u00a0',\n comma: ',',\n period: '.',\n colon: ':',\n semi: ';',\n vert: '|',\n Verbar: '‖',\n verbar: '|',\n dblac: '˝',\n circ: 'ˆ',\n caron: 'ˇ',\n breve: '˘',\n dot: '˙',\n ring: '˚',\n ogon: '˛',\n tilde: '˜',\n DiacriticalGrave: '`',\n DiacriticalAcute: '´',\n DiacriticalTilde: '˜',\n DiacriticalDot: '˙',\n DiacriticalDoubleAcute: '˝',\n grave: '`',\n};\n\n/**\n * Currency Symbols\n * @type {Record<string, string>}\n */\nexport const CURRENCY = {\n cent: '¢',\n pound: '£',\n curren: '¤',\n yen: '¥',\n euro: '€',\n dollar: '$',\n fnof: 'ƒ',\n inr: '₹',\n af: '؋',\n birr: 'ብር',\n peso: '₱',\n rub: '₽',\n won: '₩',\n yuan: '¥',\n cedil: '¸',\n};\n\n/**\n * Fractions\n * @type {Record<string, string>}\n */\nexport const FRACTIONS = {\n frac12: '½',\n half: '½',\n frac13: '⅓',\n frac14: '¼',\n frac15: '⅕',\n frac16: '⅙',\n frac18: '⅛',\n frac23: '⅔',\n frac25: '⅖',\n frac34: '¾',\n frac35: '⅗',\n frac38: '⅜',\n frac45: '⅘',\n frac56: '⅚',\n frac58: '⅝',\n frac78: '⅞',\n frasl: '⁄',\n};\n\n/**\n * Miscellaneous Symbols\n * @type {Record<string, string>}\n */\nexport const MISC_SYMBOLS = {\n trade: '™',\n TRADE: '™',\n telrec: '⌕',\n target: '⌖',\n ulcorn: '⌜',\n ulcorner: '⌜',\n urcorn: '⌝',\n urcorner: '⌝',\n dlcorn: '⌞',\n llcorner: '⌞',\n drcorn: '⌟',\n lrcorner: '⌟',\n intercal: '⊺',\n intcal: '⊺',\n oplus: '⊕',\n CirclePlus: '⊕',\n ominus: '⊖',\n CircleMinus: '⊖',\n otimes: '⊗',\n CircleTimes: '⊗',\n osol: '⊘',\n odot: '⊙',\n CircleDot: '⊙',\n oast: '⊛',\n circledast: '⊛',\n odash: '⊝',\n circleddash: '⊝',\n ocirc: '⊚',\n circledcirc: '⊚',\n boxplus: '⊞',\n plusb: '⊞',\n boxminus: '⊟',\n minusb: '⊟',\n boxtimes: '⊠',\n timesb: '⊠',\n boxdot: '⊡',\n sdotb: '⊡',\n veebar: '⊻',\n vee: '∨',\n barvee: '⊽',\n and: '∧',\n wedge: '∧',\n Cap: '⋒',\n Cup: '⋓',\n Fork: '⋔',\n pitchfork: '⋔',\n epar: '⋕',\n ltlarr: '⥶',\n nvap: '≍⃒',\n nvsim: '∼⃒',\n nvge: '≥⃒',\n nvle: '≤⃒',\n nvlt: '<⃒',\n nvgt: '>⃒',\n nvltrie: '⊴⃒',\n nvrtrie: '⊵⃒',\n Vdash: '⊩',\n dashv: '⊣',\n vDash: '⊨',\n Vvdash: '⊪',\n nvdash: '⊬',\n nvDash: '⊭',\n nVdash: '⊮',\n nVDash: '⊯',\n};\n\nexport const XML = {\n amp: \"&\",\n apos: \"'\",\n gt: \">\",\n lt: \"<\",\n quot: \"\\\"\"\n}\nexport const COMMON_HTML = {\n nbsp: '\\u00a0',\n copy: '\\u00a9',\n reg: '\\u00ae',\n trade: '\\u2122',\n mdash: '\\u2014',\n ndash: '\\u2013',\n hellip: '\\u2026',\n laquo: '\\u00ab',\n raquo: '\\u00bb',\n lsquo: '\\u2018',\n rsquo: '\\u2019',\n ldquo: '\\u201c',\n rdquo: '\\u201d',\n bull: '\\u2022',\n para: '\\u00b6',\n sect: '\\u00a7',\n deg: '\\u00b0',\n frac12: '\\u00bd',\n frac14: '\\u00bc',\n frac34: '\\u00be',\n}\n// ---------------------------------------------------------------------------\n// Note: NUMERIC_ENTITIES (&#NNN; / &#xHH;) are handled by the scanner directly\n// via String.fromCodePoint() without any map lookup.\n// ---------------------------------------------------------------------------","// ---------------------------------------------------------------------------\n// Built-in named entity map (name → replacement string)\n// No regex, no {regex,val} objects — just flat key/value pairs.\n// ---------------------------------------------------------------------------\n\nimport { XML as DEFAULT_XML_ENTITIES } from \"./entities.js\"\n\n// ---------------------------------------------------------------------------\n// Entity hook action constants\n// ---------------------------------------------------------------------------\n\n/**\n * Action constants for `onExternalEntity` and `onInputEntity` hooks.\n *\n * Use these instead of raw strings to avoid typos:\n *\n * @example\n * import EntityDecoder, { ENTITY_ACTION } from './EntityDecoder.js';\n * const dec = new EntityDecoder({\n * onInputEntity: (name, value) => ENTITY_ACTION.BLOCK,\n * });\n */\nexport const ENTITY_ACTION = Object.freeze({\n /** Resolve and expand the entity normally. */\n ALLOW: 'allow',\n /** Silently skip this entity — it will not be registered. */\n BLOCK: 'block',\n /** Throw an error, aborting entity registration entirely. */\n THROW: 'throw',\n});\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\nconst SPECIAL_CHARS = new Set('!?\\\\\\\\/[]$%{}^&*()<>|+');\n\n/**\n * Validate that an entity name contains no dangerous characters.\n * @param {string} name\n * @returns {string} the name, unchanged\n * @throws {Error} on invalid characters\n */\nfunction validateEntityName(name) {\n if (name[0] === '#') {\n throw new Error(`[EntityReplacer] Invalid character '#' in entity name: \"${name}\"`);\n }\n for (const ch of name) {\n if (SPECIAL_CHARS.has(ch)) {\n throw new Error(`[EntityReplacer] Invalid character '${ch}' in entity name: \"${name}\"`);\n }\n }\n return name;\n}\n\n/**\n * Merge one or more entity maps into a flat name→string map.\n * Accepts either:\n * - plain string values: { amp: '&' }\n * - legacy {regex,val} / {regx,val}: { lt: { regex: /.../, val: '<' } }\n *\n * Values containing '&' are skipped (recursive expansion risk).\n *\n * @param {...object} maps\n * @returns {Record<string, string>}\n */\nfunction mergeEntityMaps(...maps) {\n const out = Object.create(null);\n for (const map of maps) {\n if (!map) continue;\n for (const key of Object.keys(map)) {\n const raw = map[key];\n if (typeof raw === 'string') {\n out[key] = raw;\n } else if (raw && typeof raw === 'object' && raw.val !== undefined) {\n // Legacy {regex,val} or {regx,val} — extract the string val only\n const val = raw.val;\n if (typeof val === 'string') {\n out[key] = val;\n }\n // function vals are not supported in the scanner — skip\n }\n }\n }\n return out;\n}\n\n// ---------------------------------------------------------------------------\n// applyLimitsTo helpers\n// ---------------------------------------------------------------------------\n\nconst LIMIT_TIER_EXTERNAL = 'external'; // input/runtime + persistent external maps\nconst LIMIT_TIER_BASE = 'base'; // DEFAULT_XML_ENTITIES + namedEntities (system) maps\nconst LIMIT_TIER_ALL = 'all'; // every entity regardless of tier\n\n/**\n * Resolve `applyLimitsTo` option into a normalised Set of tier strings.\n * Accepted values: 'external' | 'base' | 'all' | string[]\n * Default: 'external' (only untrusted injected entities are counted).\n * @param {string|string[]|undefined} raw\n * @returns {Set<string>}\n */\nfunction parseLimitTiers(raw) {\n if (!raw || raw === LIMIT_TIER_EXTERNAL) return new Set([LIMIT_TIER_EXTERNAL]);\n if (raw === LIMIT_TIER_ALL) return new Set([LIMIT_TIER_ALL]);\n if (raw === LIMIT_TIER_BASE) return new Set([LIMIT_TIER_BASE]);\n if (Array.isArray(raw)) return new Set(raw);\n return new Set([LIMIT_TIER_EXTERNAL]); // safe default for unrecognised values\n}\n\n// ---------------------------------------------------------------------------\n// NCR (Numeric Character Reference) classification\n// ---------------------------------------------------------------------------\n\n// Severity order — higher number = stricter action.\n// Used to enforce minimum action levels for specific codepoint ranges.\nconst NCR_LEVEL = Object.freeze({ allow: 0, leave: 1, remove: 2, throw: 3 });\n\n// XML 1.0 §2.2: allowed chars are #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]\n// Restricted C0: U+0001–U+001F excluding U+0009, U+000A, U+000D\nconst XML10_ALLOWED_C0 = new Set([0x09, 0x0A, 0x0D]);\n\n/**\n * Parse the `ncr` constructor option into flat, hot-path-friendly fields.\n * @param {object|undefined} ncr\n * @returns {{ xmlVersion: number, onLevel: number, nullLevel: number }}\n */\nfunction parseNCRConfig(ncr) {\n if (!ncr) {\n return { xmlVersion: 1.0, onLevel: NCR_LEVEL.allow, nullLevel: NCR_LEVEL.remove };\n }\n const xmlVersion = ncr.xmlVersion === 1.1 ? 1.1 : 1.0;\n const onLevel = NCR_LEVEL[ncr.onNCR] ?? NCR_LEVEL.allow;\n const nullLevel = NCR_LEVEL[ncr.nullNCR] ?? NCR_LEVEL.remove;\n // 'allow' is not meaningful for null — clamp to at least 'remove'\n const clampedNull = Math.max(nullLevel, NCR_LEVEL.remove);\n return { xmlVersion, onLevel, nullLevel: clampedNull };\n}\n\n// ---------------------------------------------------------------------------\n// EntityReplacer\n// ---------------------------------------------------------------------------\n\n/**\n * Single-pass, zero-regex entity replacer for XML/HTML content.\n *\n * Algorithm: scan the string once for '&', read to ';', resolve via map\n * or direct codepoint conversion, build output chunks, join once at the end.\n *\n * Entity lookup priority (highest → lowest):\n * 1. input / runtime (DOCTYPE entities for current document)\n * 2. persistent external (survive across documents)\n * 3. base named map (DEFAULT_XML_ENTITIES + user-supplied namedEntities)\n *\n * Both input and external resolve as the 'external' tier for limit purposes.\n * Base map entities resolve as the 'base' tier.\n *\n * Numeric / hex references (&#NNN; / &#xHH;) are resolved directly via\n * String.fromCodePoint() — no map needed. They count as 'base' tier.\n *\n * @example\n * const replacer = new EntityReplacer({ namedEntities: COMMON_HTML });\n * replacer.setExternalEntities({ brand: 'Acme' });\n *\n * const instance = replacer.reset();\n * instance.addInputEntities({ version: '1.0' });\n * instance.encode('&brand; v&version; &lt;'); // 'Acme v1.0 <'\n */\nexport default class EntityDecoder {\n /**\n * @param {object} [options]\n * @param {object|null} [options.namedEntities] — extra named entities merged into base map\n * @param {object} [options.limit] — security limits\n * @param {number} [options.limit.maxTotalExpansions=0] — 0 = unlimited\n * @param {number} [options.limit.maxExpandedLength=0] — 0 = unlimited\n * @param {'external'|'base'|'all'|string[]} [options.limit.applyLimitsTo='external']\n * Which entity tiers count against the security limits:\n * - 'external' (default) — only input/runtime + persistent external entities\n * - 'base' — only DEFAULT_XML_ENTITIES + namedEntities\n * - 'all' — every entity regardless of tier\n * - string[] — explicit combination, e.g. ['external', 'base']\n * @param {((resolved: string, original: string) => string)|null} [options.postCheck=null]\n * @param {string[]} [options.remove=[]] — entity names (e.g. ['nbsp', '#13']) to delete (replace with empty string)\n * @param {string[]} [options.leave=[]] — entity names to keep as literal (unchanged in output)\n * @param {object} [options.ncr] — Numeric Character Reference controls\n * @param {1.0|1.1} [options.ncr.xmlVersion=1.0]\n * XML version governing which codepoint ranges are restricted:\n * - 1.0 — C0 controls U+0001–U+001F (except U+0009/000A/000D) are prohibited\n * - 1.1 — C0 controls are allowed when written as NCRs; C1 (U+007F–U+009F) decoded as-is\n * @param {'allow'|'leave'|'remove'|'throw'} [options.ncr.onNCR='allow']\n * Base action for numeric references. Severity order: allow < leave < remove < throw.\n * For codepoint ranges that carry a minimum level (surrogates → remove, XML 1.0 C0 → remove),\n * the effective action is max(onNCR, rangeMinimum).\n * @param {'remove'|'throw'} [options.ncr.nullNCR='remove']\n * Action for U+0000 (null). 'allow' and 'leave' are clamped to 'remove' since null is never safe.\n * @param {((name: string, value: string) => 'allow'|'block'|'throw')|null} [options.onExternalEntity=null]\n * Hook called when an external entity is registered via `setExternalEntities()` or\n * `addExternalEntity()`. Return `ENTITY_ACTION.ALLOW` to accept the entity,\n * `ENTITY_ACTION.BLOCK` to silently skip it, or `ENTITY_ACTION.THROW` to abort with an error.\n * @param {((name: string, value: string) => 'allow'|'block'|'throw')|null} [options.onInputEntity=null]\n * Hook called when an input entity is registered via `addInputEntities()`. Return\n * `ENTITY_ACTION.ALLOW` to accept, `ENTITY_ACTION.BLOCK` to silently skip, or\n * `ENTITY_ACTION.THROW` to abort with an error.\n */\n constructor(options = {}) {\n this._limit = options.limit || {};\n this._maxTotalExpansions = this._limit.maxTotalExpansions || 0;\n this._maxExpandedLength = this._limit.maxExpandedLength || 0;\n this._postCheck = typeof options.postCheck === 'function' ? options.postCheck : r => r;\n this._limitTiers = parseLimitTiers(this._limit.applyLimitsTo ?? LIMIT_TIER_EXTERNAL);\n this._numericAllowed = options.numericAllowed ?? true;\n // Base map: DEFAULT_XML_ENTITIES + user-supplied extras. Immutable after construction.\n this._baseMap = mergeEntityMaps(DEFAULT_XML_ENTITIES, options.namedEntities || null);\n\n // Persistent external entities — survive across documents.\n // Stored as a separate map so reset() never touches them.\n /** @type {Record<string, string>} */\n this._externalMap = Object.create(null);\n\n // Input / runtime entities — current document only, wiped on reset().\n /** @type {Record<string, string>} */\n this._inputMap = Object.create(null);\n\n // Per-document counters\n this._totalExpansions = 0;\n this._expandedLength = 0;\n\n // --- New: remove / leave sets ---\n /** @type {Set<string>} */\n this._removeSet = new Set(options.remove && Array.isArray(options.remove) ? options.remove : []);\n /** @type {Set<string>} */\n this._leaveSet = new Set(options.leave && Array.isArray(options.leave) ? options.leave : []);\n\n // --- NCR config (parsed into flat fields for hot-path speed) ---\n const ncrCfg = parseNCRConfig(options.ncr);\n this._ncrXmlVersion = ncrCfg.xmlVersion;\n this._ncrOnLevel = ncrCfg.onLevel;\n this._ncrNullLevel = ncrCfg.nullLevel;\n\n // --- Registration hooks ---\n /** @type {((name: string, value: string) => 'allow'|'block'|'throw')|null} */\n this._onExternalEntity = typeof options.onExternalEntity === 'function'\n ? options.onExternalEntity\n : null;\n /** @type {((name: string, value: string) => 'allow'|'block'|'throw')|null} */\n this._onInputEntity = typeof options.onInputEntity === 'function'\n ? options.onInputEntity\n : null;\n }\n\n // -------------------------------------------------------------------------\n // Private: registration hook dispatch\n // -------------------------------------------------------------------------\n\n /**\n * Invoke a registration hook for a single entity name/value pair.\n * Returns true when the entity should be accepted, false when it should be\n * silently skipped (BLOCK), and throws when the hook returns THROW.\n *\n * @param {((name: string, value: string) => 'allow'|'block'|'throw')|null} hook\n * @param {string} name\n * @param {string} value\n * @param {string} context — used in error messages ('external' | 'input')\n * @returns {boolean} true = accept, false = skip\n */\n _applyRegistrationHook(hook, name, value, context) {\n if (!hook) return true; // no hook → always accept\n const action = hook(name, value);\n if (action === ENTITY_ACTION.BLOCK) return false;\n if (action === ENTITY_ACTION.THROW) {\n throw new Error(\n `[EntityDecoder] Registration of ${context} entity \"&${name};\" was rejected by hook`\n );\n }\n return true; // ALLOW or any unknown return value → accept\n }\n\n // -------------------------------------------------------------------------\n // Persistent external entity registration\n // -------------------------------------------------------------------------\n\n /**\n * Replace the full set of persistent external entities.\n * All keys are validated — throws on invalid characters.\n * If `onExternalEntity` is set, it is called once per entry; entries that\n * return `ENTITY_ACTION.BLOCK` are silently omitted, `ENTITY_ACTION.THROW`\n * aborts the whole call.\n * @param {Record<string, string | { regex?: RegExp, val: string }>} map\n */\n setExternalEntities(map) {\n if (map) {\n for (const key of Object.keys(map)) {\n validateEntityName(key);\n }\n }\n if (!this._onExternalEntity) {\n this._externalMap = mergeEntityMaps(map);\n return;\n }\n // Hook present — resolve values first, then filter\n const flat = mergeEntityMaps(map);\n const filtered = Object.create(null);\n for (const [name, value] of Object.entries(flat)) {\n if (this._applyRegistrationHook(this._onExternalEntity, name, value, 'external')) {\n filtered[name] = value;\n }\n }\n this._externalMap = filtered;\n }\n\n /**\n * Add a single persistent external entity.\n * If `onExternalEntity` is set it is called before the entity is stored;\n * `ENTITY_ACTION.BLOCK` silently skips storage, `ENTITY_ACTION.THROW` raises.\n * @param {string} key\n * @param {string} value\n */\n addExternalEntity(key, value) {\n validateEntityName(key);\n if (typeof value === 'string' && value.indexOf('&') === -1) {\n if (this._applyRegistrationHook(this._onExternalEntity, key, value, 'external')) {\n this._externalMap[key] = value;\n }\n }\n }\n\n // -------------------------------------------------------------------------\n // Input / runtime entity registration (per document)\n // -------------------------------------------------------------------------\n\n /**\n * Inject DOCTYPE entities for the current document.\n * Also resets per-document expansion counters.\n * If `onInputEntity` is set it is called once per entry; entries returning\n * `ENTITY_ACTION.BLOCK` are silently omitted, `ENTITY_ACTION.THROW` aborts.\n * @param {Record<string, string | { regx?: RegExp, regex?: RegExp, val: string }>} map\n */\n addInputEntities(map) {\n this._totalExpansions = 0;\n this._expandedLength = 0;\n if (!this._onInputEntity) {\n this._inputMap = mergeEntityMaps(map);\n return;\n }\n const flat = mergeEntityMaps(map);\n const filtered = Object.create(null);\n for (const [name, value] of Object.entries(flat)) {\n if (this._applyRegistrationHook(this._onInputEntity, name, value, 'input')) {\n filtered[name] = value;\n }\n }\n this._inputMap = filtered;\n }\n\n // -------------------------------------------------------------------------\n // Per-document reset\n // -------------------------------------------------------------------------\n\n /**\n * Wipe input/runtime entities and reset counters.\n * Call this before processing each new document.\n * @returns {this}\n */\n reset() {\n this._inputMap = Object.create(null);\n this._totalExpansions = 0;\n this._expandedLength = 0;\n return this;\n }\n\n // -------------------------------------------------------------------------\n // XML version (can be set after construction, e.g. once parser reads <?xml?>)\n // -------------------------------------------------------------------------\n\n /**\n * Update the XML version used for NCR classification.\n * Call this as soon as the document's `<?xml version=\"...\">` declaration is parsed.\n * @param {1.0|1.1|number} version\n */\n setXmlVersion(version) {\n this._ncrXmlVersion = version === 1.1 ? 1.1 : 1.0;\n }\n\n // -------------------------------------------------------------------------\n // Primary API\n // -------------------------------------------------------------------------\n\n /**\n * Replace all entity references in `str` in a single pass.\n *\n * @param {string} str\n * @returns {string}\n */\n decode(str) {\n if (typeof str !== 'string' || str.length === 0) return str;\n //TODO: check if needed\n if (str.indexOf('&') === -1) return str; // fast path — no entities at all\n\n const original = str;\n const chunks = [];\n const len = str.length;\n let last = 0; // start of next unprocessed literal chunk\n let i = 0;\n\n const limitExpansions = this._maxTotalExpansions > 0;\n const limitLength = this._maxExpandedLength > 0;\n const checkLimits = limitExpansions || limitLength;\n\n while (i < len) {\n // Scan forward to next '&'\n if (str.charCodeAt(i) !== 38 /* '&' */) { i++; continue; }\n\n // --- Found '&' at position i ---\n\n // Scan forward to ';'\n let j = i + 1;\n while (j < len && str.charCodeAt(j) !== 59 /* ';' */ && (j - i) <= 32) j++;\n\n if (j >= len || str.charCodeAt(j) !== 59) {\n // No closing ';' within window — treat '&' as literal\n i++;\n continue;\n }\n\n // Raw token between '&' and ';' (exclusive)\n const token = str.slice(i + 1, j);\n if (token.length === 0) { i++; continue; }\n\n let replacement;\n let tier; // which limit tier this entity belongs to\n\n if (this._removeSet.has(token)) {\n // Remove entity: replace with empty string\n replacement = '';\n // If entity was unknown (replacement undefined), we still need a tier for limits.\n // Treat as external tier because it's user-directed removal of an unknown reference.\n if (tier === undefined) {\n tier = LIMIT_TIER_EXTERNAL;\n }\n } else if (this._leaveSet.has(token)) {\n // Do not replace — keep original &token; as literal\n i++;\n continue;\n } else if (token.charCodeAt(0) === 35 /* '#' */) {\n // ---- Numeric / NCR reference ----\n // NCR classification always runs first — prohibited codepoints must be\n // caught regardless of numericAllowed.\n const ncrResult = this._resolveNCR(token);\n if (ncrResult === undefined) {\n // 'leave' action — keep original &token; as-is\n i++;\n continue;\n }\n replacement = ncrResult; // '' for remove, char string for allow\n tier = LIMIT_TIER_BASE;\n } else {\n // ---- Named reference ----\n const resolved = this._resolveName(token);\n replacement = resolved?.value;\n tier = resolved?.tier;\n }\n\n if (replacement === undefined) {\n // Unknown entity — leave as-is, advance past '&' only\n i++;\n continue;\n }\n\n // Flush literal chunk before this entity\n if (i > last) chunks.push(str.slice(last, i));\n chunks.push(replacement);\n last = j + 1; // skip past ';'\n i = last;\n\n // Apply expansion limits only if this tier is being tracked\n if (checkLimits && this._tierCounts(tier)) {\n if (limitExpansions) {\n this._totalExpansions++;\n if (this._totalExpansions > this._maxTotalExpansions) {\n throw new Error(\n `[EntityReplacer] Entity expansion count limit exceeded: ` +\n `${this._totalExpansions} > ${this._maxTotalExpansions}`\n );\n }\n }\n if (limitLength) {\n // delta: replacement.length minus the raw &token; length (token.length + 2 for '&' and ';')\n const delta = replacement.length - (token.length + 2);\n if (delta > 0) {\n this._expandedLength += delta;\n if (this._expandedLength > this._maxExpandedLength) {\n throw new Error(\n `[EntityReplacer] Expanded content length limit exceeded: ` +\n `${this._expandedLength} > ${this._maxExpandedLength}`\n );\n }\n }\n }\n }\n }\n\n // Flush trailing literal\n if (last < len) chunks.push(str.slice(last));\n\n // If nothing was replaced, chunks is empty — return original\n const result = chunks.length === 0 ? str : chunks.join('');\n\n return this._postCheck(result, original);\n }\n\n // -------------------------------------------------------------------------\n // Private: limit tier check\n // -------------------------------------------------------------------------\n\n /**\n * Returns true if a resolved entity of the given tier should count\n * against the expansion/length limits.\n * @param {string} tier — LIMIT_TIER_EXTERNAL | LIMIT_TIER_BASE\n * @returns {boolean}\n */\n _tierCounts(tier) {\n if (this._limitTiers.has(LIMIT_TIER_ALL)) return true;\n return this._limitTiers.has(tier);\n }\n\n // -------------------------------------------------------------------------\n // Private: entity resolution\n // -------------------------------------------------------------------------\n\n /**\n * Resolve a named entity token (without & and ;).\n * Priority: inputMap > externalMap > baseMap\n * Returns the resolved value tagged with its limit tier.\n *\n * @param {string} name\n * @returns {{ value: string, tier: string }|undefined}\n */\n _resolveName(name) {\n // input and external both count as 'external' tier for limit purposes —\n // they are injected at runtime and are the untrusted surface.\n if (name in this._inputMap) return { value: this._inputMap[name], tier: LIMIT_TIER_EXTERNAL };\n if (name in this._externalMap) return { value: this._externalMap[name], tier: LIMIT_TIER_EXTERNAL };\n if (name in this._baseMap) return { value: this._baseMap[name], tier: LIMIT_TIER_BASE };\n return undefined;\n }\n\n /**\n * Classify a codepoint and return the minimum action level that must be applied.\n * Returns -1 when no minimum is imposed (normal allow path).\n *\n * Ranges checked (in priority order):\n * 1. U+0000 — null, governed by nullNCR (always ≥ remove)\n * 2. U+D800–U+DFFF — surrogates, always prohibited (min: remove)\n * 3. U+0001–U+001F \\ {0x09,0x0A,0x0D} — XML 1.0 restricted C0 (min: remove)\n * (skipped in XML 1.1 — C0 controls are allowed when written as NCRs)\n *\n * @param {number} cp — codepoint\n * @returns {number} — minimum NCR_LEVEL value, or -1 for no restriction\n */\n _classifyNCR(cp) {\n // 1. Null\n if (cp === 0) return this._ncrNullLevel;\n\n // 2. Surrogates — always prohibited, minimum 'remove'\n if (cp >= 0xD800 && cp <= 0xDFFF) return NCR_LEVEL.remove;\n\n // 3. XML 1.0 restricted C0 controls\n if (this._ncrXmlVersion === 1.0) {\n if (cp >= 0x01 && cp <= 0x1F && !XML10_ALLOWED_C0.has(cp)) return NCR_LEVEL.remove;\n }\n\n return -1; // no restriction\n }\n\n /**\n * Execute a resolved NCR action.\n *\n * @param {number} action — NCR_LEVEL value\n * @param {string} token — raw token (e.g. '#38') for error messages\n * @param {number} cp — codepoint, used only for error messages\n * @returns {string|undefined}\n * - decoded character string → 'allow'\n * - '' → 'remove'\n * - undefined → 'leave' (caller must skip past '&' only)\n * - throws Error → 'throw'\n */\n _applyNCRAction(action, token, cp) {\n switch (action) {\n case NCR_LEVEL.allow: return String.fromCodePoint(cp);\n case NCR_LEVEL.remove: return '';\n case NCR_LEVEL.leave: return undefined; // signal: keep literal\n case NCR_LEVEL.throw:\n throw new Error(\n `[EntityDecoder] Prohibited numeric character reference ` +\n `&${token}; (U+${cp.toString(16).toUpperCase().padStart(4, '0')})`\n );\n default: return String.fromCodePoint(cp);\n }\n }\n\n /**\n * Full NCR resolution pipeline for a numeric token.\n *\n * Steps:\n * 1. Parse the codepoint (decimal or hex).\n * 2. Validate the raw codepoint range (NaN, <0, >0x10FFFF).\n * 3. If numericAllowed is false and no minimum restriction applies → leave as-is.\n * 4. Classify the codepoint to find the minimum required action level.\n * 5. Resolve effective action = max(onNCR, minimum).\n * 6. Apply and return.\n *\n * @param {string} token — e.g. '#38', '#x26', '#X26'\n * @returns {string|undefined}\n * - string (incl. '') — replacement ('' = remove)\n * - undefined — leave original &token; as-is\n */\n _resolveNCR(token) {\n // Step 1: parse codepoint\n const second = token.charCodeAt(1);\n let cp;\n if (second === 120 /* x */ || second === 88 /* X */) {\n cp = parseInt(token.slice(2), 16);\n } else {\n cp = parseInt(token.slice(1), 10);\n }\n\n // Step 2: out-of-range → leave as-is unconditionally\n if (Number.isNaN(cp) || cp < 0 || cp > 0x10FFFF) return undefined;\n\n // Step 3: classify to get minimum action level\n const minimum = this._classifyNCR(cp);\n\n // Step 4: if numericAllowed is false and no hard minimum → leave\n if (!this._numericAllowed && minimum < NCR_LEVEL.remove) return undefined;\n\n // Step 5: effective action = max(configured onNCR, range minimum)\n const effective = minimum === -1\n ? this._ncrOnLevel\n : Math.max(this._ncrOnLevel, minimum);\n\n // Step 6: apply\n return this._applyNCRAction(effective, token, cp);\n }\n}","import { DANGEROUS_PROPERTY_NAMES, criticalProperties } from \"../util.js\";\nimport { COMMON_HTML, CURRENCY } from '@nodable/entities';\n\nconst defaultOnDangerousProperty = (name) => {\n if (DANGEROUS_PROPERTY_NAMES.includes(name)) {\n return \"__\" + name;\n }\n return name;\n};\n\n\nexport const defaultOptions = {\n preserveOrder: false,\n attributeNamePrefix: '@_',\n attributesGroupName: false,\n textNodeName: '#text',\n ignoreAttributes: true,\n removeNSPrefix: false, // remove NS from tag name or attribute name if true\n allowBooleanAttributes: false, //a tag can have attributes without any value\n //ignoreRootElement : false,\n parseTagValue: true,\n parseAttributeValue: false,\n trimValues: true, //Trim string values of tag and attributes\n cdataPropName: false,\n numberParseOptions: {\n hex: true,\n leadingZeros: true,\n eNotation: true,\n unicode: false\n },\n tagValueProcessor: function (tagName, val) {\n return val;\n },\n attributeValueProcessor: function (attrName, val) {\n return val;\n },\n stopNodes: [], //nested tags will not be parsed even for errors\n alwaysCreateTextNode: false,\n isArray: () => false,\n commentPropName: false,\n unpairedTags: [],\n processEntities: true,\n htmlEntities: false,\n entityDecoder: null,\n ignoreDeclaration: false,\n ignorePiTags: false,\n transformTagName: false,\n transformAttributeName: false,\n updateTag: function (tagName, jPath, attrs) {\n return tagName\n },\n // skipEmptyListItem: false\n captureMetaData: false,\n maxNestedTags: 100,\n strictReservedNames: true,\n jPath: true, // if true, pass jPath string to callbacks; if false, pass matcher instance\n onDangerousProperty: defaultOnDangerousProperty\n};\n\n\n/**\n * Validates that a property name is safe to use\n * @param {string} propertyName - The property name to validate\n * @param {string} optionName - The option field name (for error message)\n * @throws {Error} If property name is dangerous\n */\nfunction validatePropertyName(propertyName, optionName) {\n if (typeof propertyName !== 'string') {\n return; // Only validate string property names\n }\n\n const normalized = propertyName.toLowerCase();\n if (DANGEROUS_PROPERTY_NAMES.some(dangerous => normalized === dangerous.toLowerCase())) {\n throw new Error(\n `[SECURITY] Invalid ${optionName}: \"${propertyName}\" is a reserved JavaScript keyword that could cause prototype pollution`\n );\n }\n\n if (criticalProperties.some(dangerous => normalized === dangerous.toLowerCase())) {\n throw new Error(\n `[SECURITY] Invalid ${optionName}: \"${propertyName}\" is a reserved JavaScript keyword that could cause prototype pollution`\n );\n }\n}\n\n/**\n * Normalizes processEntities option for backward compatibility\n * @param {boolean|object} value \n * @returns {object} Always returns normalized object\n */\nfunction normalizeProcessEntities(value, htmlEntities) {\n // Boolean backward compatibility\n if (typeof value === 'boolean') {\n return {\n enabled: value, // true or false\n maxEntitySize: 10000,\n maxExpansionDepth: 10000,\n maxTotalExpansions: Infinity,\n maxExpandedLength: 100000,\n maxEntityCount: 1000,\n allowedTags: null,\n tagFilter: null,\n appliesTo: \"all\",\n };\n }\n\n // Object config - merge with defaults\n if (typeof value === 'object' && value !== null) {\n return {\n enabled: value.enabled !== false,\n maxEntitySize: Math.max(1, value.maxEntitySize ?? 10000),\n maxExpansionDepth: Math.max(1, value.maxExpansionDepth ?? 10000),\n maxTotalExpansions: Math.max(1, value.maxTotalExpansions ?? Infinity),\n maxExpandedLength: Math.max(1, value.maxExpandedLength ?? 100000),\n maxEntityCount: Math.max(1, value.maxEntityCount ?? 1000),\n allowedTags: value.allowedTags ?? null,\n tagFilter: value.tagFilter ?? null,\n appliesTo: value.appliesTo ?? \"all\",\n };\n }\n\n // Default to enabled with limits\n return normalizeProcessEntities(true);\n}\n\nexport const buildOptions = function (options) {\n const built = Object.assign({}, defaultOptions, options);\n\n // Validate property names to prevent prototype pollution\n const propertyNameOptions = [\n { value: built.attributeNamePrefix, name: 'attributeNamePrefix' },\n { value: built.attributesGroupName, name: 'attributesGroupName' },\n { value: built.textNodeName, name: 'textNodeName' },\n { value: built.cdataPropName, name: 'cdataPropName' },\n { value: built.commentPropName, name: 'commentPropName' }\n ];\n\n for (const { value, name } of propertyNameOptions) {\n if (value) {\n validatePropertyName(value, name);\n }\n }\n\n if (built.onDangerousProperty === null) {\n built.onDangerousProperty = defaultOnDangerousProperty;\n }\n\n // Always normalize processEntities for backward compatibility and validation\n built.processEntities = normalizeProcessEntities(built.processEntities, built.htmlEntities);\n built.unpairedTagsSet = new Set(built.unpairedTags);\n // Convert old-style stopNodes for backward compatibility\n if (built.stopNodes && Array.isArray(built.stopNodes)) {\n built.stopNodes = built.stopNodes.map(node => {\n if (typeof node === 'string' && node.startsWith('*.')) {\n // Old syntax: *.tagname meant \"tagname anywhere\"\n // Convert to new syntax: ..tagname\n return '..' + node.substring(2);\n }\n return node;\n });\n }\n //console.debug(built.processEntities)\n return built;\n};","'use strict';\n\nlet METADATA_SYMBOL;\n\nif (typeof Symbol !== \"function\") {\n METADATA_SYMBOL = \"@@xmlMetadata\";\n} else {\n METADATA_SYMBOL = Symbol(\"XML Node Metadata\");\n}\n\nexport default class XmlNode {\n constructor(tagname) {\n this.tagname = tagname;\n this.child = []; //nested tags, text, cdata, comments in order\n this[\":@\"] = Object.create(null); //attributes map\n }\n add(key, val) {\n // this.child.push( {name : key, val: val, isCdata: isCdata });\n if (key === \"__proto__\") key = \"#__proto__\";\n this.child.push({ [key]: val });\n }\n addChild(node, startIndex) {\n if (node.tagname === \"__proto__\") node.tagname = \"#__proto__\";\n if (node[\":@\"] && Object.keys(node[\":@\"]).length > 0) {\n this.child.push({ [node.tagname]: node.child, [\":@\"]: node[\":@\"] });\n } else {\n this.child.push({ [node.tagname]: node.child });\n }\n // if requested, add the startIndex\n if (startIndex !== undefined) {\n // Note: for now we just overwrite the metadata. If we had more complex metadata,\n // we might need to do an object append here: metadata = { ...metadata, startIndex }\n this.child[this.child.length - 1][METADATA_SYMBOL] = { startIndex };\n }\n }\n /** symbol used for metadata */\n static getMetaDataSymbol() {\n return METADATA_SYMBOL;\n }\n}\n","/**\n * xml-naming\n * Validates XML Name productions as defined in the XML 1.0 and 1.1 specifications.\n * Covers: Name, NCName, QName, NMToken, NMTokens\n *\n * XML 1.0 spec: https://www.w3.org/TR/xml/#NT-Name\n * XML 1.1 spec: https://www.w3.org/TR/xml11/#NT-NameStartChar\n * XML NS spec: https://www.w3.org/TR/xml-names/#NT-NCName\n */\n\n// ---------------------------------------------------------------------------\n// Character class strings — XML 1.0\n//\n// NameStartChar ::= \":\" | [A-Z] | \"_\" | [a-z]\n// | [#xC0-#xD6] | [#xD8-#xF6] | [#xF8-#x2FF]\n// | [#x370-#x37D] | [#x37F-#x1FFF] <- split to exclude #x0487\n// | [#x200C-#x200D]\n// | [#x2070-#x218F] | [#x2C00-#x2FEF]\n// | [#x3001-#xD7FF] | [#xF900-#xFDCF] | [#xFDF0-#xFFFD]\n//\n// NameChar ::= NameStartChar | \"-\" | \".\" | [0-9]\n// | #xB7 | [#x0300-#x036F] | [#x203F-#x2040]\n//\n// Note: \\u0487 (Combining Cyrillic Millions Sign) was added in Unicode 4.0,\n// after XML 1.0 was defined against Unicode 2.0. It falls inside the range\n// \\u037F-\\u1FFF but must be excluded. We split that range into\n// \\u037F-\\u0486 and \\u0488-\\u1FFF to exclude it explicitly.\n// ---------------------------------------------------------------------------\n\nconst nameStartChar10 =\n ':A-Za-z_' +\n '\\u00C0-\\u00D6\\u00D8-\\u00F6\\u00F8-\\u02FF' +\n '\\u0370-\\u037D' +\n '\\u037F-\\u0486\\u0488-\\u1FFF' + // split to exclude \\u0487\n '\\u200C-\\u200D' +\n '\\u2070-\\u218F' +\n '\\u2C00-\\u2FEF' +\n '\\u3001-\\uD7FF' +\n '\\uF900-\\uFDCF' +\n '\\uFDF0-\\uFFFD';\n\nconst nameChar10 =\n nameStartChar10 +\n '\\\\-\\\\.\\\\d' +\n '\\u00B7' +\n '\\u0300-\\u036F' +\n '\\u203F-\\u2040';\n\n// ---------------------------------------------------------------------------\n// Character class strings — XML 1.1\n//\n// Differences from XML 1.0:\n//\n// NameStartChar:\n// 1.0 has split ranges: \\u00C0-\\u00D6, \\u00D8-\\u00F6, \\u00F8-\\u02FF\n// 1.1 merges them into: \\u00C0-\\u02FF\n// (\\u00D7 x and \\u00F7 / are division symbols, excluded in both versions)\n//\n// 1.0 tops out at \\uFFFD (BMP only)\n// 1.1 adds \\u{10000}-\\u{EFFFF} (supplementary planes)\n// These require the /u flag on the RegExp — see buildRegexes below.\n//\n// NameChar:\n// 1.1 adds \\u0487 (Combining Cyrillic Millions Sign, added in Unicode 4.0)\n// ---------------------------------------------------------------------------\n\nconst nameStartChar11 =\n ':A-Za-z_' +\n '\\u00C0-\\u02FF' + // merged — 1.0 had three split ranges here\n '\\u0370-\\u037D' +\n '\\u037F-\\u0486\\u0488-\\u1FFF' + // split to exclude \\u0487 (combining mark, never a NameStartChar)\n '\\u200C-\\u200D' +\n '\\u2070-\\u218F' +\n '\\u2C00-\\u2FEF' +\n '\\u3001-\\uD7FF' +\n '\\uF900-\\uFDCF' +\n '\\uFDF0-\\uFFFD' +\n '\\u{10000}-\\u{EFFFF}'; // supplementary planes — REQUIRES /u flag on RegExp\n\nconst nameChar11 =\n nameStartChar11 +\n '\\\\-\\\\.\\\\d' +\n '\\u00B7' +\n '\\u0300-\\u036F' +\n '\\u0487' + // Combining Cyrillic Millions Sign — valid in 1.1, not 1.0\n '\\u203F-\\u2040';\n\n// ---------------------------------------------------------------------------\n// Regex builders\n//\n// XML 1.0 regexes: no flags — BMP only, standard JS regex behaviour.\n// XML 1.1 regexes: /u flag — required for \\u{10000}-\\u{EFFFF} to match actual\n// supplementary code points rather than lone surrogates (which are illegal XML).\n// ---------------------------------------------------------------------------\n\nconst buildRegexes = (startChar, char, flags = '') => {\n const ncStart = startChar.replace(':', '');\n const ncChar = char.replace(':', '');\n const ncNamePat = `[${ncStart}][${ncChar}]*`;\n\n return {\n name: new RegExp(`^[${startChar}][${char}]*$`, flags),\n ncName: new RegExp(`^${ncNamePat}$`, flags),\n qName: new RegExp(`^${ncNamePat}(?::${ncNamePat})?$`, flags),\n nmToken: new RegExp(`^[${char}]+$`, flags),\n nmTokens: new RegExp(`^[${char}]+(?:\\\\s+[${char}]+)*$`, flags),\n };\n};\n\nconst regexes10 = buildRegexes(nameStartChar10, nameChar10); // no /u — BMP only\nconst regexes11 = buildRegexes(nameStartChar11, nameChar11, 'u'); // /u — enables \\u{10000}-\\u{EFFFF}\n\n// ---------------------------------------------------------------------------\n// ASCII-only fast path (opt-in, off by default)\n//\n// The XML 1.0 vs 1.1 NameStartChar/NameChar productions differ *only* in\n// their non-ASCII ranges (merged vs split Latin-1 ranges, \\u0487, and\n// supplementary planes). Restricted to ASCII, both versions collapse to the\n// same character classes, so a single regex pair covers both xmlVersion\n// values — no /u flag needed.\n//\n// Rationale: unicode-aware regexes (the /u flag, required for XML 1.1's\n// supplementary-plane range) are measurably slower in V8 than plain\n// non-unicode regexes on the same input, even when the input is pure ASCII.\n// For the common case — HTML/SVG ids, XML tags — names are ASCII, so callers\n// who know this can opt in to skip the unicode-aware matching path entirely.\n// This is a real but *conditional* win: mainly for XML 1.1 input (avoids /u),\n// or at scale where the larger unicode character classes add engine\n// overhead. It also changes behaviour (rejects legitimate non-ASCII XML\n// 1.0/1.1 names), so it must never be silently enabled — hence off by\n// default.\n// ---------------------------------------------------------------------------\n\nconst nameStartCharAscii = ':A-Za-z_';\nconst nameCharAscii = nameStartCharAscii + '\\\\-\\\\.\\\\d';\n\nconst regexesAscii = buildRegexes(nameStartCharAscii, nameCharAscii); // no /u — ASCII only\n\nconst getRegexes = (xmlVersion = '1.0', asciiOnly = false) => {\n if (asciiOnly) return regexesAscii;\n return xmlVersion === '1.1' ? regexes11 : regexes10;\n};\n\n// ---------------------------------------------------------------------------\n// Boolean validators\n// ---------------------------------------------------------------------------\n\n/**\n * Returns true if the string is a valid XML Name.\n * Colons are allowed anywhere (Name production).\n * Used for: DOCTYPE entity names, notation names, DTD element declarations.\n *\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * asciiOnly: skip unicode-aware matching, ASCII names only (default false).\n */\nexport const name = (str, { xmlVersion = '1.0', asciiOnly = false } = {}) =>\n getRegexes(xmlVersion, asciiOnly).name.test(str);\n\n/**\n * Returns true if the string is a valid NCName (Non-Colonized Name).\n * Colons are not permitted.\n * Used for: namespace prefixes, local names, SVG id attributes.\n *\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * asciiOnly: skip unicode-aware matching, ASCII names only (default false).\n */\nexport const ncName = (str, { xmlVersion = '1.0', asciiOnly = false } = {}) =>\n getRegexes(xmlVersion, asciiOnly).ncName.test(str);\n\n/**\n * Returns true if the string is a valid QName (Qualified Name).\n * Allows exactly one colon as a prefix separator: prefix:localName.\n * Used for: element and attribute names in namespace-aware XML/SVG.\n *\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * asciiOnly: skip unicode-aware matching, ASCII names only (default false).\n */\nexport const qName = (str, { xmlVersion = '1.0', asciiOnly = false } = {}) =>\n getRegexes(xmlVersion, asciiOnly).qName.test(str);\n\n/**\n * Returns true if the string is a valid NMToken.\n * Like Name but no restriction on the first character.\n * Used for: DTD NMTOKEN attribute values.\n *\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * asciiOnly: skip unicode-aware matching, ASCII names only (default false).\n */\nexport const nmToken = (str, { xmlVersion = '1.0', asciiOnly = false } = {}) =>\n getRegexes(xmlVersion, asciiOnly).nmToken.test(str);\n\n/**\n * Returns true if the string is a valid NMTokens value.\n * A whitespace-separated list of NMToken values.\n * Used for: DTD NMTOKENS attribute values.\n *\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * asciiOnly: skip unicode-aware matching, ASCII names only (default false).\n */\nexport const nmTokens = (str, { xmlVersion = '1.0', asciiOnly = false } = {}) =>\n getRegexes(xmlVersion, asciiOnly).nmTokens.test(str);\n\n// ---------------------------------------------------------------------------\n// Memoized validator factory\n//\n// Real documents reuse a small vocabulary of tag/attribute names across many\n// siblings (e.g. `id`, `class`, `href` repeated across hundreds of elements).\n// The plain boolean validators above re-run the regex on every call\n// regardless of repeats. `createValidator` returns a closure with a private\n// string -> boolean cache, so repeated names after the first become O(1)\n// lookups instead of regex tests.\n//\n// - opts (xmlVersion, asciiOnly) are fixed at creation time, so the regex is\n// resolved once, not on every call.\n// - The cache is private to the returned closure — no shared/global state,\n// no cross-caller pollution.\n// - `maxCacheSize` bounds memory: once the cache reaches this many entries,\n// it stops accepting new ones (existing entries keep serving hits; new\n// misses just fall through to the regex, uncached). This avoids unbounded\n// growth against adversarial/high-cardinality input (e.g. validating\n// attacker-supplied names with no repeats) without the cost/complexity of\n// a full LRU, and without the perf cliff of reset-and-refill thrashing.\n// - Call `.reset()` on the returned function to clear the cache manually\n// (e.g. between unrelated parse calls).\n// ---------------------------------------------------------------------------\n\nconst PRODUCTIONS = ['name', 'ncName', 'qName', 'nmToken', 'nmTokens'];\n\n/**\n * Returns a memoized boolean validator function for a single production,\n * with opts fixed at creation time.\n *\n * @param {'name'|'ncName'|'qName'|'nmToken'|'nmTokens'} production\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean, maxCacheSize?: number }} [opts]\n * maxCacheSize: max number of distinct strings to cache (default 2048).\n * Once reached, new strings are validated but not cached; existing cached\n * entries keep being served.\n * @returns {((str: string) => boolean) & { reset: () => void }}\n */\nexport const createValidator = (production, { xmlVersion = '1.0', asciiOnly = false, maxCacheSize = 2048 } = {}) => {\n if (!PRODUCTIONS.includes(production)) {\n throw new TypeError(\n `Unknown production \"${production}\". Must be one of: ${PRODUCTIONS.join(', ')}`\n );\n }\n\n const regex = getRegexes(xmlVersion, asciiOnly)[production];\n let cache = new Map();\n\n const validator = (str) => {\n const cached = cache.get(str);\n if (cached !== undefined) return cached;\n\n const result = regex.test(str);\n if (cache.size < maxCacheSize) cache.set(str, result);\n return result;\n };\n\n validator.reset = () => { cache = new Map(); };\n\n return validator;\n};\n\n// ---------------------------------------------------------------------------\n// Diagnostic validator\n// ---------------------------------------------------------------------------\n\n/**\n * Validates a string against a named production and returns a detailed result.\n *\n * @param {string} str\n * @param {'name'|'ncName'|'qName'|'nmToken'|'nmTokens'} production\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * @returns {{ valid: boolean, production: string, input: string, reason?: string, position?: number }}\n */\nexport const validate = (str, production, { xmlVersion = '1.0', asciiOnly = false } = {}) => {\n if (!PRODUCTIONS.includes(production)) {\n throw new TypeError(\n `Unknown production \"${production}\". Must be one of: ${PRODUCTIONS.join(', ')}`\n );\n }\n\n const validators = { name, ncName, qName, nmToken, nmTokens };\n const isValid = validators[production](str, { xmlVersion, asciiOnly });\n\n if (isValid) return { valid: true, production, input: str };\n\n let reason = 'Does not match the production rules';\n let position;\n\n // Diagnostic fallback char checks must mirror the same character set the\n // boolean validator above used, or the reported reason/position could\n // contradict the `valid: false` result (e.g. flagging a char as illegal\n // that the unicode-aware check would have accepted).\n const startCharPattern = asciiOnly ? /^[:A-Za-z_]/ : /^[:A-Za-z_\\u00C0-\\uFFFD]/;\n const namePattern = asciiOnly ? /[\\w\\-\\\\.:]/ : /[\\w\\-\\\\.:\\u00B7\\u00C0-\\uFFFD]/;\n\n if (str.length === 0) {\n reason = 'Input is empty';\n } else if (production === 'ncName' && str.includes(':')) {\n position = str.indexOf(':');\n reason = 'Colon is not allowed in NCName';\n } else if (production === 'qName' && str.startsWith(':')) {\n reason = 'QName cannot start with a colon';\n position = 0;\n } else if (production === 'qName' && str.endsWith(':')) {\n reason = 'QName cannot end with a colon';\n position = str.length - 1;\n } else if (production === 'qName' && (str.match(/:/g) || []).length > 1) {\n reason = 'QName can have at most one colon';\n position = str.lastIndexOf(':');\n } else if (\n ['name', 'ncName', 'qName'].includes(production) &&\n !startCharPattern.test(str[0])\n ) {\n reason = `First character \"${str[0]}\" is not a valid NameStartChar`;\n position = 0;\n } else {\n for (let i = 0; i < str.length; i++) {\n if (!namePattern.test(str[i])) {\n reason = `Character \"${str[i]}\" at position ${i} is not a valid NameChar`;\n position = i;\n break;\n }\n }\n }\n\n return { valid: false, production, input: str, reason, position };\n};\n\n// ---------------------------------------------------------------------------\n// Batch validator\n// ---------------------------------------------------------------------------\n\n/**\n * Validates an array of strings against a named production.\n *\n * @param {string[]} strings\n * @param {'name'|'ncName'|'qName'|'nmToken'|'nmTokens'} production\n * @param {{ xmlVersion?: '1.0'|'1.1', asciiOnly?: boolean }} [opts]\n * @returns {Array<{ valid: boolean, production: string, input: string, reason?: string, position?: number }>}\n */\nexport const validateAll = (strings, production, opts = {}) =>\n strings.map(str => validate(str, production, opts));\n\n// ---------------------------------------------------------------------------\n// Sanitizer\n// ---------------------------------------------------------------------------\n\n/**\n * Transforms an invalid string into the nearest valid XML name for the given production.\n *\n * @param {string} str\n * @param {'name'|'ncName'|'qName'|'nmToken'|'nmTokens'} production\n * @param {{ replacement?: string, asciiOnly?: boolean }} [opts]\n * asciiOnly: also replace any non-ASCII character, not just XML-illegal\n * ones (default false).\n * @returns {string}\n */\nexport const sanitize = (str, production = 'name', { replacement = '_', asciiOnly = false } = {}) => {\n if (!str) return replacement;\n\n let result = str;\n\n // Strip colons for NCName\n if (production === 'ncName') {\n result = result.replace(/:/g, '');\n }\n\n // Replace illegal characters\n const allowedCharPattern = asciiOnly ? /[^\\w\\-\\.:]/g : /[^\\w\\-\\.:\\u00B7\\u00C0-\\uFFFD]/g;\n result = result.replace(allowedCharPattern, replacement);\n\n // Fix invalid start character for Name / NCName / QName\n if (production !== 'nmToken' && production !== 'nmTokens') {\n if (/^[\\-\\.\\d]/.test(result)) {\n result = replacement + result;\n }\n }\n\n return result || replacement;\n};","import { qName as isName } from 'xml-naming';\n\nexport default class DocTypeReader {\n constructor(options, xmlVersion) {\n this.suppressValidationErr = !options;\n this.options = options;\n this.xmlVersion = xmlVersion || 1.0;\n }\n\n setXmlVersion(xmlVersion = 1.0) {\n this.xmlVersion = xmlVersion;\n }\n readDocType(xmlData, i) {\n const entities = Object.create(null);\n let entityCount = 0;\n\n if (xmlData[i + 3] === 'O' &&\n xmlData[i + 4] === 'C' &&\n xmlData[i + 5] === 'T' &&\n xmlData[i + 6] === 'Y' &&\n xmlData[i + 7] === 'P' &&\n xmlData[i + 8] === 'E') {\n i = i + 9;\n let angleBracketsCount = 1;\n let hasBody = false, comment = false;\n let exp = \"\";\n for (; i < xmlData.length; i++) {\n if (xmlData[i] === '<' && !comment) { //Determine the tag type\n if (hasBody && hasSeq(xmlData, \"!ENTITY\", i)) {\n i += 7;\n let entityName, val;\n [entityName, val, i] = this.readEntityExp(xmlData, i + 1, this.suppressValidationErr);\n if (val.indexOf(\"&\") === -1) { //Parameter entities are not supported\n if (this.options.enabled !== false &&\n this.options.maxEntityCount != null &&\n entityCount >= this.options.maxEntityCount) {\n throw new Error(\n `Entity count (${entityCount + 1}) exceeds maximum allowed (${this.options.maxEntityCount})`\n );\n }\n //const escaped = entityName.replace(/[.\\-+*:]/g, '\\\\.');\n //const escaped = entityName.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n entities[entityName] = val;\n entityCount++;\n }\n }\n else if (hasBody && hasSeq(xmlData, \"!ELEMENT\", i)) {\n i += 8;//Not supported\n const { index } = this.readElementExp(xmlData, i + 1);\n i = index;\n } else if (hasBody && hasSeq(xmlData, \"!ATTLIST\", i)) {\n i += 8;//Not supported\n // const {index} = this.readAttlistExp(xmlData,i+1);\n // i = index;\n } else if (hasBody && hasSeq(xmlData, \"!NOTATION\", i)) {\n i += 9;//Not supported\n const { index } = this.readNotationExp(xmlData, i + 1, this.suppressValidationErr);\n i = index;\n } else if (hasSeq(xmlData, \"!--\", i)) comment = true;\n else throw new Error(`Invalid DOCTYPE`);\n\n angleBracketsCount++;\n exp = \"\";\n } else if (xmlData[i] === '>') { //Read tag content\n if (comment) {\n if (xmlData[i - 1] === \"-\" && xmlData[i - 2] === \"-\") {\n comment = false;\n angleBracketsCount--;\n }\n } else {\n angleBracketsCount--;\n }\n if (angleBracketsCount === 0) {\n break;\n }\n } else if (xmlData[i] === '[') {\n hasBody = true;\n } else {\n exp += xmlData[i];\n }\n }\n if (angleBracketsCount !== 0) {\n throw new Error(`Unclosed DOCTYPE`);\n }\n } else {\n throw new Error(`Invalid Tag instead of DOCTYPE`);\n }\n return { entities, i };\n }\n readEntityExp(xmlData, i) {\n //External entities are not supported\n // <!ENTITY ext SYSTEM \"http://normal-website.com\" >\n\n //Parameter entities are not supported\n // <!ENTITY entityname \"&anotherElement;\">\n\n //Internal entities are supported\n // <!ENTITY entityname \"replacement text\">\n\n // Skip leading whitespace after <!ENTITY\n i = skipWhitespace(xmlData, i);\n\n // Read entity name\n const startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i]) && xmlData[i] !== '\"' && xmlData[i] !== \"'\") {\n i++;\n }\n let entityName = xmlData.substring(startIndex, i);\n\n validateEntityName(entityName, { xmlVersion: this.xmlVersion });\n\n // Skip whitespace after entity name\n i = skipWhitespace(xmlData, i);\n\n // Check for unsupported constructs (external entities or parameter entities)\n if (!this.suppressValidationErr) {\n if (xmlData.substring(i, i + 6).toUpperCase() === \"SYSTEM\") {\n throw new Error(\"External entities are not supported\");\n } else if (xmlData[i] === \"%\") {\n throw new Error(\"Parameter entities are not supported\");\n }\n }\n\n // Read entity value (internal entity)\n let entityValue = \"\";\n [i, entityValue] = this.readIdentifierVal(xmlData, i, \"entity\");\n\n // Validate entity size\n if (this.options.enabled !== false &&\n this.options.maxEntitySize != null &&\n entityValue.length > this.options.maxEntitySize) {\n throw new Error(\n `Entity \"${entityName}\" size (${entityValue.length}) exceeds maximum allowed size (${this.options.maxEntitySize})`\n );\n }\n\n i--;\n return [entityName, entityValue, i];\n }\n\n readNotationExp(xmlData, i) {\n // Skip leading whitespace after <!NOTATION\n i = skipWhitespace(xmlData, i);\n\n // Read notation name\n\n const startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n i++;\n }\n let notationName = xmlData.substring(startIndex, i);\n\n !this.suppressValidationErr && validateEntityName(notationName, { xmlVersion: this.xmlVersion });\n\n // Skip whitespace after notation name\n i = skipWhitespace(xmlData, i);\n\n // Check identifier type (SYSTEM or PUBLIC)\n const identifierType = xmlData.substring(i, i + 6).toUpperCase();\n if (!this.suppressValidationErr && identifierType !== \"SYSTEM\" && identifierType !== \"PUBLIC\") {\n throw new Error(`Expected SYSTEM or PUBLIC, found \"${identifierType}\"`);\n }\n i += identifierType.length;\n\n // Skip whitespace after identifier type\n i = skipWhitespace(xmlData, i);\n\n // Read public identifier (if PUBLIC)\n let publicIdentifier = null;\n let systemIdentifier = null;\n\n if (identifierType === \"PUBLIC\") {\n [i, publicIdentifier] = this.readIdentifierVal(xmlData, i, \"publicIdentifier\");\n\n // Skip whitespace after public identifier\n i = skipWhitespace(xmlData, i);\n\n // Optionally read system identifier\n if (xmlData[i] === '\"' || xmlData[i] === \"'\") {\n [i, systemIdentifier] = this.readIdentifierVal(xmlData, i, \"systemIdentifier\");\n }\n } else if (identifierType === \"SYSTEM\") {\n // Read system identifier (mandatory for SYSTEM)\n [i, systemIdentifier] = this.readIdentifierVal(xmlData, i, \"systemIdentifier\");\n\n if (!this.suppressValidationErr && !systemIdentifier) {\n throw new Error(\"Missing mandatory system identifier for SYSTEM notation\");\n }\n }\n\n return { notationName, publicIdentifier, systemIdentifier, index: --i };\n }\n\n readIdentifierVal(xmlData, i, type) {\n let identifierVal = \"\";\n const startChar = xmlData[i];\n if (startChar !== '\"' && startChar !== \"'\") {\n throw new Error(`Expected quoted string, found \"${startChar}\"`);\n }\n i++;\n\n const startIndex = i;\n while (i < xmlData.length && xmlData[i] !== startChar) {\n i++;\n }\n identifierVal = xmlData.substring(startIndex, i);\n\n if (xmlData[i] !== startChar) {\n throw new Error(`Unterminated ${type} value`);\n }\n i++;\n return [i, identifierVal];\n }\n\n readElementExp(xmlData, i) {\n // <!ELEMENT br EMPTY>\n // <!ELEMENT div ANY>\n // <!ELEMENT title (#PCDATA)>\n // <!ELEMENT book (title, author+)>\n // <!ELEMENT name (content-model)>\n\n // Skip leading whitespace after <!ELEMENT\n i = skipWhitespace(xmlData, i);\n\n // Read element name\n const startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n i++;\n }\n let elementName = xmlData.substring(startIndex, i);\n\n // Validate element name\n if (!this.suppressValidationErr && !isName(elementName, { xmlVersion: this.xmlVersion })) {\n throw new Error(`Invalid element name: \"${elementName}\"`);\n }\n\n // Skip whitespace after element name\n i = skipWhitespace(xmlData, i);\n let contentModel = \"\";\n // Expect '(' to start content model\n if (xmlData[i] === \"E\" && hasSeq(xmlData, \"MPTY\", i)) i += 4;\n else if (xmlData[i] === \"A\" && hasSeq(xmlData, \"NY\", i)) i += 2;\n else if (xmlData[i] === \"(\") {\n i++; // Move past '('\n\n // Read content model\n const startIndex = i;\n while (i < xmlData.length && xmlData[i] !== \")\") {\n i++;\n }\n contentModel = xmlData.substring(startIndex, i);\n\n if (xmlData[i] !== \")\") {\n throw new Error(\"Unterminated content model\");\n }\n\n } else if (!this.suppressValidationErr) {\n throw new Error(`Invalid Element Expression, found \"${xmlData[i]}\"`);\n }\n\n return {\n elementName,\n contentModel: contentModel.trim(),\n index: i\n };\n }\n\n readAttlistExp(xmlData, i) {\n // Skip leading whitespace after <!ATTLIST\n i = skipWhitespace(xmlData, i);\n\n // Read element name\n let startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n i++;\n }\n let elementName = xmlData.substring(startIndex, i);\n\n // Validate element name\n validateEntityName(elementName, { xmlVersion: this.xmlVersion })\n\n // Skip whitespace after element name\n i = skipWhitespace(xmlData, i);\n\n // Read attribute name\n startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n i++;\n }\n let attributeName = xmlData.substring(startIndex, i);\n\n // Validate attribute name\n if (!validateEntityName(attributeName, { xmlVersion: this.xmlVersion })) {\n throw new Error(`Invalid attribute name: \"${attributeName}\"`);\n }\n\n // Skip whitespace after attribute name\n i = skipWhitespace(xmlData, i);\n\n // Read attribute type\n let attributeType = \"\";\n if (xmlData.substring(i, i + 8).toUpperCase() === \"NOTATION\") {\n attributeType = \"NOTATION\";\n i += 8; // Move past \"NOTATION\"\n\n // Skip whitespace after \"NOTATION\"\n i = skipWhitespace(xmlData, i);\n\n // Expect '(' to start the list of notations\n if (xmlData[i] !== \"(\") {\n throw new Error(`Expected '(', found \"${xmlData[i]}\"`);\n }\n i++; // Move past '('\n\n // Read the list of allowed notations\n let allowedNotations = [];\n while (i < xmlData.length && xmlData[i] !== \")\") {\n\n\n const startIndex = i;\n while (i < xmlData.length && xmlData[i] !== \"|\" && xmlData[i] !== \")\") {\n i++;\n }\n let notation = xmlData.substring(startIndex, i);\n\n // Validate notation name\n notation = notation.trim();\n if (!validateEntityName(notation, { xmlVersion: this.xmlVersion })) {\n throw new Error(`Invalid notation name: \"${notation}\"`);\n }\n\n allowedNotations.push(notation);\n\n // Skip '|' separator or exit loop\n if (xmlData[i] === \"|\") {\n i++; // Move past '|'\n i = skipWhitespace(xmlData, i); // Skip optional whitespace after '|'\n }\n }\n\n if (xmlData[i] !== \")\") {\n throw new Error(\"Unterminated list of notations\");\n }\n i++; // Move past ')'\n\n // Store the allowed notations as part of the attribute type\n attributeType += \" (\" + allowedNotations.join(\"|\") + \")\";\n } else {\n // Handle simple types (e.g., CDATA, ID, IDREF, etc.)\n const startIndex = i;\n while (i < xmlData.length && !/\\s/.test(xmlData[i])) {\n i++;\n }\n attributeType += xmlData.substring(startIndex, i);\n\n // Validate simple attribute type\n const validTypes = [\"CDATA\", \"ID\", \"IDREF\", \"IDREFS\", \"ENTITY\", \"ENTITIES\", \"NMTOKEN\", \"NMTOKENS\"];\n if (!this.suppressValidationErr && !validTypes.includes(attributeType.toUpperCase())) {\n throw new Error(`Invalid attribute type: \"${attributeType}\"`);\n }\n }\n\n // Skip whitespace after attribute type\n i = skipWhitespace(xmlData, i);\n\n // Read default value\n let defaultValue = \"\";\n if (xmlData.substring(i, i + 8).toUpperCase() === \"#REQUIRED\") {\n defaultValue = \"#REQUIRED\";\n i += 8;\n } else if (xmlData.substring(i, i + 7).toUpperCase() === \"#IMPLIED\") {\n defaultValue = \"#IMPLIED\";\n i += 7;\n } else {\n [i, defaultValue] = this.readIdentifierVal(xmlData, i, \"ATTLIST\");\n }\n\n return {\n elementName,\n attributeName,\n attributeType,\n defaultValue,\n index: i\n }\n }\n}\n\n\n\nconst skipWhitespace = (data, index) => {\n while (index < data.length && /\\s/.test(data[index])) {\n index++;\n }\n return index;\n};\n\n\n\nfunction hasSeq(data, seq, i) {\n for (let j = 0; j < seq.length; j++) {\n if (seq[j] !== data[i + j + 1]) return false;\n }\n return true;\n}\n\nfunction validateEntityName(name, xmlVersion) {\n if (isName(name, { xmlVersion: xmlVersion }))\n return name;\n else\n throw new Error(`Invalid entity name ${name}`);\n}","/**\n * Flat lookup table: maps Unicode code point → ASCII digit (0-9).\n * Only decimal digit characters (Unicode category Nd) are included.\n *\n * Strategy: Int32Array of size (maxCodePoint - minCodePoint + 1).\n * Value 0xFF means \"not a digit\". Value 0-9 is the ASCII digit value.\n * This gives O(1) lookup with no branching, no bisect, no loop.\n *\n * Memory: range is 0x0660 to 0x1FBF0 → ~129,936 entries × 1 byte = ~127 KB.\n * Acceptable for a one-time init; lookup is a single array index.\n */\n\n// All known Unicode Nd (decimal digit) script zero code points.\n// Each script has exactly 10 consecutive digits: zero+0 .. zero+9.\nconst SCRIPT_ZEROS = [\n // Basic Latin (ASCII) — included for completeness / pass-through\n 0x0030, // 0-9\n\n // Arabic scripts\n 0x0660, // Arabic-Indic ٠١٢٣٤٥٦٧٨٩\n 0x06F0, // Extended Arabic-Indic (Urdu/Persian/Sindhi) ۰۱۲۳\n\n // Indic scripts\n 0x0966, // Devanagari ०१२३४५६७८९\n 0x09E6, // Bengali ০১২৩৪৫৬৭৮৯\n 0x0A66, // Gurmukhi ੦੧੨੩੪੫੬੭੮੯\n 0x0AE6, // Gujarati ૦૧૨૩૪૫૬૭૮૯\n 0x0B66, // Odia ୦୧୨୩୪୫୬୭୮୯\n 0x0BE6, // Tamil ௦௧௨௩௪௫௬௭௮௯\n 0x0C66, // Telugu ౦౧౨౩౪౫౬౭౮౯\n 0x0CE6, // Kannada ೦೧೨೩೪೫೬೭೮೯\n 0x0D66, // Malayalam ൦൧൨൩൪൫൬൭൮൯\n 0x0DE6, // Sinhala Archaic ෦෧෨෩෪෫෬෭෮෯\n\n // Southeast Asian scripts\n 0x0E50, // Thai ๐๑๒๓๔๕๖๗๘๙\n 0x0ED0, // Lao ໐໑໒໓໔໕໖໗໘໙\n 0x0F20, // Tibetan ༠༡༢༣༤༥༦༧༨༩\n 0x1040, // Myanmar ၀၁၂၃၄၅၆၇၈၉\n 0x1090, // Myanmar Shan ႐႑႒႓႔႕႖႗႘႙\n 0x17E0, // Khmer ០១២៣៤៥៦៧៨៩\n 0x1810, // Mongolian ᠐᠑᠒᠓᠔᠕᠖᠗᠘᠙\n 0x1946, // Limbu ᥆᥇᥈᥉᥊᥋᥌᥍᥎᥏\n 0x19D0, // New Tai Lue ᧐᧑᧒᧓᧔᧕᧖᧗᧘᧙\n 0x1A80, // Tai Tham Hora ᪀᪁᪂᪃᪄᪅᪆᪇᪈᪉\n 0x1A90, // Tai Tham Tham ᪐᪑᪒᪓᪔᪕᪖᪗᪘᪙\n 0x1B50, // Balinese ᭐᭑᭒᭓᭔᭕᭖᭗᭘᭙\n 0x1BB0, // Sundanese ᮰᮱᮲᮳᮴᮵᮶᮷᮸᮹\n 0x1C40, // Lepcha ᱀᱁᱂᱃᱄᱅᱆᱇᱈᱉\n 0x1C50, // Ol Chiki ᱐᱑᱒᱓᱔᱕᱖᱗᱘᱙\n\n // Fullwidth (CJK context)\n 0xFF10, // Fullwidth ０１２３４５６７８９\n\n // Mathematical digit variants (Unicode math block)\n 0x1D7CE, // Mathematical Bold\n 0x1D7D8, // Mathematical Double-Struck\n 0x1D7E2, // Mathematical Sans-Serif\n 0x1D7EC, // Mathematical Sans-Serif Bold\n 0x1D7F6, // Mathematical Monospace\n\n // Other scripts\n 0x104A0, // Osmanya 𐒠𐒡𐒢𐒣𐒤𐒥𐒦𐒧𐒨𐒩\n 0x10D30, // Hanifi Rohingya 𐴰𐴱𐴲𐴳𐴴𐴵𐴶𐴷𐴸𐴹\n 0x11066, // Brahmi 𑁦𑁧𑁨𑁩𑁪𑁫𑁬𑁭𑁮𑁯\n 0x110F0, // Sora Sompeng 𑃰𑃱𑃲𑃳𑃴𑃵𑃶𑃷𑃸𑃹\n 0x11136, // Chakma 𑄶𑄷𑄸𑄹𑄺𑄻𑄼𑄽𑄾𑄿\n 0x111D0, // Sharada 𑇐𑇑𑇒𑇓𑇔𑇕𑇖𑇗𑇘𑇙\n 0x112F0, // Khudawadi 𑋰𑋱𑋲𑋳𑋴𑋵𑋶𑋷𑋸𑋹\n 0x11450, // Newa 𑑐𑑑𑑒𑑓𑑔𑑕𑑖𑑗𑑘𑑙\n 0x114D0, // Tirhuta 𑓐𑓑𑓒𑓓𑓔𑓕𑓖𑓗𑓘𑓙\n 0x11650, // Modi 𑙐𑙑𑙒𑙓𑙔𑙕𑙖𑙗𑙘𑙙\n 0x116C0, // Takri 𑛀𑛁𑛂𑛃𑛄𑛅𑛆𑛇𑛈𑛉\n 0x11730, // Ahom 𑜰𑜱𑜲𑜳𑜴𑜵𑜶𑜷𑜸𑜹\n 0x118E0, // Warang Citi 𑣠𑣡𑣢𑣣𑣤𑣥𑣦𑣧𑣨𑣩\n 0x11950, // Dives Akuru 𑥐𑥑𑥒𑥓𑥔𑥕𑥖𑥗𑥘𑥙\n 0x11BF0, // Khitan Small Script 𑯰𑯱𑯲𑯳𑯴𑯵𑯶𑯷𑯸𑯹\n 0x11C50, // Bhaiksuki 𑱐𑱑𑱒𑱓𑱔𑱕𑱖𑱗𑱘𑱙\n 0x11D50, // Masaram Gondi 𑵐𑵑𑵒𑵓𑵔𑵕𑵖𑵗𑵘𑵙\n 0x11DA0, // Gunjala Gondi 𑶠𑶡𑶢𑶣𑶤𑶥𑶦𑶧𑶨𑶩\n 0x11F50, // Kawi 𑽐𑽑𑽒𑽓𑽔𑽕𑽖𑽗𑽘𑽙\n 0x16A60, // Mro 𖩠𖩡𖩢𖩣𖩤𖩥𖩦𖩧𖩨𖩩\n 0x16AC0, // Tangsa 𖫀𖫁𖫂𖫃𖫄𖫅𖫆𖫇𖫈𖫉\n 0x16B50, // Pahawh Hmong 𖭐𖭑𖭒𖭓𖭔𖭕𖭖𖭗𖭘𖭙\n 0x1E140, // Nyiakeng Puachue Hmong 𞅀𞅁𞅂𞅃𞅄𞅅𞅆𞅇𞅈𞅉\n 0x1E2F0, // Wancho 𞋰𞋱𞋲𞋳𞋴𞋵𞋶𞋷𞋸𞋹\n 0x1E4F0, // Nag Mundari 𞓰𞓱𞓲𞓳𞓴𞓵𞓶𞓷𞓸𞓹\n 0x1E950, // Adlam 𞥐𞥑𞥒𞥓𞥔𞥕𞥖𞥗𞥘𞥙\n 0x1FBF0, // Segmented digit symbols 🯰🯱🯲🯳🯴🯵🯶🯷🯸🯹\n];\n\n// Build a sparse Map for scripts above 0xFFFF (surrogate-pair range).\n// These can't go into a flat Uint8Array indexed by code point efficiently.\nconst NOT_DIGIT = 0xFF;\nconst HIGH_MAP = new Map(); // codePoint → digit value (0-9)\n\nconst LOW_MAX = 0xFFFF;\nconst LOW_MIN = 0x0660; // first non-ASCII digit script\n\n// Flat Uint8Array covering 0x0660 .. 0xFFFF\nconst TABLE_OFFSET = LOW_MIN;\nconst TABLE_SIZE = LOW_MAX - LOW_MIN + 1;\nconst TABLE = new Uint8Array(TABLE_SIZE).fill(NOT_DIGIT);\n\nfor (const zero of SCRIPT_ZEROS) {\n for (let d = 0; d < 10; d++) {\n const cp = zero + d;\n if (cp <= LOW_MAX) {\n TABLE[cp - TABLE_OFFSET] = d;\n } else {\n HIGH_MAP.set(cp, d);\n }\n }\n}\n\nexport { TABLE, TABLE_OFFSET, HIGH_MAP, NOT_DIGIT };\n","'use strict';\n\nimport { TABLE, TABLE_OFFSET, HIGH_MAP, NOT_DIGIT } from './digitTable.js';\n\nconst CHAR_0 = 48; // '0'.charCodeAt(0)\nconst CHAR_9 = 57; // '9'.charCodeAt(0)\nconst CHAR_MINUS = 45; // '-'.charCodeAt(0)\n\n// Unicode minus/hyphen variants worth normalizing to ASCII '-' in numeric context:\n// U+2212 MINUS SIGN − (mathematically correct minus)\n// U+FF0D FULLWIDTH HYPHEN-MINUS － (Japanese fullwidth context)\n// U+FE63 SMALL HYPHEN-MINUS ﹣ (small form variant)\n//\n// NOT normalized (deliberate):\n// U+2013 EN DASH – (punctuation, not a numeric sign)\n// U+2014 EM DASH — (punctuation)\n// U+2010 HYPHEN ‐ (typographic hyphen)\n//\n// Rationale: only characters a human or locale formatter would plausibly use\n// as a numeric minus sign are normalized. Dashes used for punctuation are left\n// alone to avoid mangling non-numeric strings.\nconst MINUS_SET = new Set([0x2212, 0xFF0D, 0xFE63]);\n\n/**\n * Normalize all Unicode decimal digit characters in a string to ASCII (0-9),\n * and normalize Unicode minus variants to ASCII '-' (U+002D).\n *\n * Non-digit, non-minus characters are passed through unchanged.\n *\n * Performance design:\n * - Fast path: if the string has no convertible characters, return it unchanged\n * (zero allocation).\n * - BMP digits (0x0660..0xFFFF excl. surrogates): flat Uint8Array lookup (O(1)).\n * - Supplementary plane digits (> 0xFFFF, encoded as surrogate pairs): Map lookup.\n * - Minus variants: checked inline with a small fixed Set.\n *\n * @param {string} str\n * @returns {string}\n */\nfunction anynum(str) {\n if (typeof str !== 'string') return str;\n\n const len = str.length;\n if (len === 0) return str;\n\n // Scan for first character needing conversion.\n // If none found, return original string (zero allocation).\n let firstHit = -1;\n\n for (let i = 0; i < len; i++) {\n const cc = str.charCodeAt(i);\n\n // ASCII digit or ASCII minus — already normalized, skip fast\n if ((cc >= CHAR_0 && cc <= CHAR_9) || cc === CHAR_MINUS) continue;\n\n // Below first unicode digit script — check minus variants only\n if (cc < TABLE_OFFSET) {\n if (MINUS_SET.has(cc)) { firstHit = i; break; }\n continue;\n }\n\n // Surrogate pairs live in BMP range 0xD800-0xDFFF — check before TABLE\n if (cc >= 0xD800 && cc <= 0xDBFF) {\n if (i + 1 < len) {\n const low = str.charCodeAt(i + 1);\n if (low >= 0xDC00 && low <= 0xDFFF) {\n const cp = 0x10000 + ((cc - 0xD800) << 10) + (low - 0xDC00);\n if (HIGH_MAP.has(cp)) { firstHit = i; break; }\n }\n }\n continue;\n }\n\n // BMP non-surrogate: flat table lookup; also check minus variants in this range\n if (TABLE[cc - TABLE_OFFSET] !== NOT_DIGIT || MINUS_SET.has(cc)) {\n firstHit = i;\n break;\n }\n }\n\n // Nothing to replace — return original, zero allocation\n if (firstHit === -1) return str;\n\n // Build result: copy unchanged prefix, then convert from firstHit onward\n const chars = [];\n\n if (firstHit > 0) chars.push(str.slice(0, firstHit));\n\n for (let i = firstHit; i < len; i++) {\n const cc = str.charCodeAt(i);\n\n // ASCII digit or ASCII minus — pass through\n if ((cc >= CHAR_0 && cc <= CHAR_9) || cc === CHAR_MINUS) {\n chars.push(str[i]);\n continue;\n }\n\n // Below TABLE_OFFSET — check minus variants, else pass through\n if (cc < TABLE_OFFSET) {\n chars.push(MINUS_SET.has(cc) ? '-' : str[i]);\n continue;\n }\n\n // Surrogate pairs\n if (cc >= 0xD800 && cc <= 0xDBFF) {\n if (i + 1 < len) {\n const low = str.charCodeAt(i + 1);\n if (low >= 0xDC00 && low <= 0xDFFF) {\n const cp = 0x10000 + ((cc - 0xD800) << 10) + (low - 0xDC00);\n const d = HIGH_MAP.get(cp);\n if (d !== undefined) {\n chars.push(String.fromCharCode(d + 48));\n i++; // consume low surrogate\n continue;\n }\n }\n }\n chars.push(str[i]);\n continue;\n }\n\n // BMP non-surrogate: flat table lookup + minus variants\n if (MINUS_SET.has(cc)) {\n chars.push('-');\n continue;\n }\n const d = TABLE[cc - TABLE_OFFSET];\n chars.push(d !== NOT_DIGIT ? String.fromCharCode(d + 48) : str[i]);\n }\n\n return chars.join('');\n}\n\nexport { anynum };\nexport default anynum;","const hexRegex = /^[-+]?0x[a-fA-F0-9]+$/;\nconst binRegex = /^0b[01]+$/;\nconst octRegex = /^0o[0-7]+$/;\nconst numRegex = /^([\\-\\+])?(0*)([0-9]*(\\.[0-9]*)?)$/;\n\nimport anynum from \"anynum\";\n\nconst consider = {\n hex: true,\n binary: false,\n octal: false,\n leadingZeros: true,\n decimalPoint: \"\\.\",\n eNotation: true,\n //skipLike: /regex/,\n infinity: \"original\", // \"null\", \"infinity\" (Infinity type), \"string\" (\"Infinity\" (the string literal))\n unicode: false,\n};\n\nexport default function toNumber(str, options = {}) {\n options = Object.assign({}, consider, options);\n if (!str || typeof str !== \"string\") return str;\n\n let trimmedStr = str.trim();\n\n if (trimmedStr.length === 0) return str;\n else if (options.skipLike !== undefined && options.skipLike.test(trimmedStr)) return str;\n else if (trimmedStr === \"0\") return 0;\n\n if (options.unicode) {\n trimmedStr = anynum(trimmedStr);\n if (trimmedStr === \"0\") return 0; // re-check after normalization\n }\n if (options.hex && hexRegex.test(trimmedStr)) {\n return parse_int(trimmedStr, 16);\n } else if (options.binary && binRegex.test(trimmedStr)) {\n return parse_int(trimmedStr, 2);\n } else if (options.octal && octRegex.test(trimmedStr)) {\n return parse_int(trimmedStr, 8);\n } else if (!isFinite(trimmedStr)) { //Infinity\n return handleInfinity(str, Number(trimmedStr), options);\n } else if (trimmedStr.includes('e') || trimmedStr.includes('E')) { //eNotation\n return resolveEnotation(str, trimmedStr, options);\n } else {\n //separate negative sign, leading zeros, and rest number\n const match = numRegex.exec(trimmedStr);\n // +00.123 => [ , '+', '00', '.123', ..\n if (match) {\n const sign = match[1] || \"\";\n const leadingZeros = match[2];\n let numTrimmedByZeros = trimZeros(match[3]); //complete num without leading zeros\n const decimalAdjacentToLeadingZeros = sign ? // 0., -00., 000.\n str[leadingZeros.length + 1] === \".\"\n : str[leadingZeros.length] === \".\";\n\n //trim ending zeros for floating number\n if (!options.leadingZeros //leading zeros are not allowed\n && (leadingZeros.length > 1\n || (leadingZeros.length === 1 && !decimalAdjacentToLeadingZeros))) {\n // 00, 00.3, +03.24, 03, 03.24\n return str;\n }\n else {//no leading zeros or leading zeros are allowed\n const num = Number(trimmedStr);\n const parsedStr = String(num);\n\n if (num === 0) return num;\n if (parsedStr.search(/[eE]/) !== -1) { //given number is long and parsed to eNotation\n if (options.eNotation) return num;\n else return str;\n } else if (trimmedStr.indexOf(\".\") !== -1) { //floating number\n if (parsedStr === \"0\") return num; //0.0\n else if (parsedStr === numTrimmedByZeros) return num; //0.456. 0.79000\n else if (parsedStr === `${sign}${numTrimmedByZeros}`) return num;\n else return str;\n }\n\n let n = leadingZeros ? numTrimmedByZeros : trimmedStr;\n if (leadingZeros) {\n // -009 => -9\n return (n === parsedStr) || (sign + n === parsedStr) ? num : str\n } else {\n // +9\n return (n === parsedStr) || (n === sign + parsedStr) ? num : str\n }\n }\n } else { //non-numeric string\n return str;\n }\n }\n}\n\nconst eNotationRegx = /^([-+])?(0*)(\\d*(\\.\\d*)?[eE][-\\+]?\\d+)$/;\nfunction resolveEnotation(str, trimmedStr, options) {\n if (!options.eNotation) return str;\n const notation = trimmedStr.match(eNotationRegx);\n if (notation) {\n let sign = notation[1] || \"\";\n const eChar = notation[3].indexOf(\"e\") === -1 ? \"E\" : \"e\";\n const leadingZeros = notation[2];\n const eAdjacentToLeadingZeros = sign ? // 0E.\n str[leadingZeros.length + 1] === eChar\n : str[leadingZeros.length] === eChar;\n\n if (leadingZeros.length > 1 && eAdjacentToLeadingZeros) return str;\n else if (leadingZeros.length === 1\n && (notation[3].startsWith(`.${eChar}`) || notation[3][0] === eChar)) {\n return Number(trimmedStr);\n } else if (leadingZeros.length > 0) {\n // Has leading zeros — only accept if leadingZeros option allows it\n if (options.leadingZeros && !eAdjacentToLeadingZeros) {\n trimmedStr = (notation[1] || \"\") + notation[3];\n return Number(trimmedStr);\n } else return str;\n } else {\n // No leading zeros — always valid e-notation, parse it\n return Number(trimmedStr);\n }\n } else {\n return str;\n }\n}\n\n/**\n * \n * @param {string} numStr without leading zeros\n * @returns \n */\nfunction trimZeros(numStr) {\n if (numStr && numStr.indexOf(\".\") !== -1) {//float\n numStr = numStr.replace(/0+$/, \"\"); //remove ending zeros\n if (numStr === \".\") numStr = \"0\";\n else if (numStr[0] === \".\") numStr = \"0\" + numStr;\n else if (numStr[numStr.length - 1] === \".\") numStr = numStr.substring(0, numStr.length - 1);\n return numStr;\n }\n return numStr;\n}\n\nfunction parse_int(numStr, base) {\n const str = numStr.trim();\n if (base === 2 || base === 8) numStr = str.substring(2);\n\n if (parseInt) return parseInt(numStr, base);\n else if (Number.parseInt) return Number.parseInt(numStr, base);\n else if (window && window.parseInt) return window.parseInt(numStr, base);\n else throw new Error(\"parseInt, Number.parseInt, window.parseInt are not supported\");\n}\n\n/**\n * Handle infinite values based on user option\n * @param {string} str - original input string\n * @param {number} num - parsed number (Infinity or -Infinity)\n * @param {object} options - user options\n * @returns {string|number|null} based on infinity option\n */\nfunction handleInfinity(str, num, options) {\n const isPositive = num === Infinity;\n\n switch (options.infinity.toLowerCase()) {\n case \"null\":\n return null;\n case \"infinity\":\n return num; // Return Infinity or -Infinity\n case \"string\":\n return isPositive ? \"Infinity\" : \"-Infinity\";\n case \"original\":\n default:\n return str; // Return original string like \"1e1000\"\n }\n}","export default function getIgnoreAttributesFn(ignoreAttributes) {\n if (typeof ignoreAttributes === 'function') {\n return ignoreAttributes\n }\n if (Array.isArray(ignoreAttributes)) {\n return (attrName) => {\n for (const pattern of ignoreAttributes) {\n if (typeof pattern === 'string' && attrName === pattern) {\n return true\n }\n if (pattern instanceof RegExp && pattern.test(attrName)) {\n return true\n }\n }\n }\n }\n return () => false\n}","/**\n * Expression - Parses and stores a tag pattern expression\n * \n * Patterns are parsed once and stored in an optimized structure for fast matching.\n * \n * @example\n * const expr = new Expression(\"root.users.user\");\n * const expr2 = new Expression(\"..user[id]:first\");\n * const expr3 = new Expression(\"root/users/user\", { separator: '/' });\n */\nexport default class Expression {\n /**\n * Create a new Expression\n * @param {string} pattern - Pattern string (e.g., \"root.users.user\", \"..user[id]\")\n * @param {Object} options - Configuration options\n * @param {string} options.separator - Path separator (default: '.')\n */\n constructor(pattern, options = {}, data) {\n this.pattern = pattern;\n this.separator = options.separator || '.';\n this.segments = this._parse(pattern);\n this.data = data;\n // Cache expensive checks for performance (O(1) instead of O(n))\n this._hasDeepWildcard = this.segments.some(seg => seg.type === 'deep-wildcard');\n this._hasAttributeCondition = this.segments.some(seg => seg.attrName !== undefined);\n this._hasPositionSelector = this.segments.some(seg => seg.position !== undefined);\n }\n\n /**\n * Parse pattern string into segments\n * @private\n * @param {string} pattern - Pattern to parse\n * @returns {Array} Array of segment objects\n */\n _parse(pattern) {\n const segments = [];\n\n // Split by separator but handle \"..\" specially\n let i = 0;\n let currentPart = '';\n\n while (i < pattern.length) {\n if (pattern[i] === this.separator) {\n // Check if next char is also separator (deep wildcard)\n if (i + 1 < pattern.length && pattern[i + 1] === this.separator) {\n // Flush current part if any\n if (currentPart.trim()) {\n segments.push(this._parseSegment(currentPart.trim()));\n currentPart = '';\n }\n // Add deep wildcard\n segments.push({ type: 'deep-wildcard' });\n i += 2; // Skip both separators\n } else {\n // Regular separator\n if (currentPart.trim()) {\n segments.push(this._parseSegment(currentPart.trim()));\n }\n currentPart = '';\n i++;\n }\n } else {\n currentPart += pattern[i];\n i++;\n }\n }\n\n // Flush remaining part\n if (currentPart.trim()) {\n segments.push(this._parseSegment(currentPart.trim()));\n }\n\n return segments;\n }\n\n /**\n * Parse a single segment\n * @private\n * @param {string} part - Segment string (e.g., \"user\", \"ns::user\", \"user[id]\", \"ns::user:first\")\n * @returns {Object} Segment object\n */\n _parseSegment(part) {\n const segment = { type: 'tag' };\n\n // NEW NAMESPACE SYNTAX (v2.0):\n // ============================\n // Namespace uses DOUBLE colon (::)\n // Position uses SINGLE colon (:)\n // \n // Examples:\n // \"user\" → tag\n // \"user:first\" → tag + position\n // \"user[id]\" → tag + attribute\n // \"user[id]:first\" → tag + attribute + position\n // \"ns::user\" → namespace + tag\n // \"ns::user:first\" → namespace + tag + position\n // \"ns::user[id]\" → namespace + tag + attribute\n // \"ns::user[id]:first\" → namespace + tag + attribute + position\n // \"ns::first\" → namespace + tag named \"first\" (NO ambiguity!)\n //\n // This eliminates all ambiguity:\n // :: = namespace separator\n // : = position selector\n // [] = attributes\n\n // Step 1: Extract brackets [attr] or [attr=value]\n let bracketContent = null;\n let withoutBrackets = part;\n\n const bracketMatch = part.match(/^([^\\[]+)(\\[[^\\]]*\\])(.*)$/);\n if (bracketMatch) {\n withoutBrackets = bracketMatch[1] + bracketMatch[3];\n if (bracketMatch[2]) {\n const content = bracketMatch[2].slice(1, -1);\n if (content) {\n bracketContent = content;\n }\n }\n }\n\n // Step 2: Check for namespace (double colon ::)\n let namespace = undefined;\n let tagAndPosition = withoutBrackets;\n\n if (withoutBrackets.includes('::')) {\n const nsIndex = withoutBrackets.indexOf('::');\n namespace = withoutBrackets.substring(0, nsIndex).trim();\n tagAndPosition = withoutBrackets.substring(nsIndex + 2).trim(); // Skip ::\n\n if (!namespace) {\n throw new Error(`Invalid namespace in pattern: ${part}`);\n }\n }\n\n // Step 3: Parse tag and position (single colon :)\n let tag = undefined;\n let positionMatch = null;\n\n if (tagAndPosition.includes(':')) {\n const colonIndex = tagAndPosition.lastIndexOf(':'); // Use last colon for position\n const tagPart = tagAndPosition.substring(0, colonIndex).trim();\n const posPart = tagAndPosition.substring(colonIndex + 1).trim();\n\n // Verify position is a valid keyword\n const isPositionKeyword = ['first', 'last', 'odd', 'even'].includes(posPart) ||\n /^nth\\(\\d+\\)$/.test(posPart);\n\n if (isPositionKeyword) {\n tag = tagPart;\n positionMatch = posPart;\n } else {\n // Not a valid position keyword, treat whole thing as tag\n tag = tagAndPosition;\n }\n } else {\n tag = tagAndPosition;\n }\n\n if (!tag) {\n throw new Error(`Invalid segment pattern: ${part}`);\n }\n\n segment.tag = tag;\n if (namespace) {\n segment.namespace = namespace;\n }\n\n // Step 4: Parse attributes\n if (bracketContent) {\n if (bracketContent.includes('=')) {\n const eqIndex = bracketContent.indexOf('=');\n segment.attrName = bracketContent.substring(0, eqIndex).trim();\n segment.attrValue = bracketContent.substring(eqIndex + 1).trim();\n } else {\n segment.attrName = bracketContent.trim();\n }\n }\n\n // Step 5: Parse position selector\n if (positionMatch) {\n const nthMatch = positionMatch.match(/^nth\\((\\d+)\\)$/);\n if (nthMatch) {\n segment.position = 'nth';\n segment.positionValue = parseInt(nthMatch[1], 10);\n } else {\n segment.position = positionMatch;\n }\n }\n\n return segment;\n }\n\n /**\n * Get the number of segments\n * @returns {number}\n */\n get length() {\n return this.segments.length;\n }\n\n /**\n * Check if expression contains deep wildcard\n * @returns {boolean}\n */\n hasDeepWildcard() {\n return this._hasDeepWildcard;\n }\n\n /**\n * Check if expression has attribute conditions\n * @returns {boolean}\n */\n hasAttributeCondition() {\n return this._hasAttributeCondition;\n }\n\n /**\n * Check if expression has position selectors\n * @returns {boolean}\n */\n hasPositionSelector() {\n return this._hasPositionSelector;\n }\n\n /**\n * Get string representation\n * @returns {string}\n */\n toString() {\n return this.pattern;\n }\n}","/**\n * ExpressionSet - An indexed collection of Expressions for efficient bulk matching\n *\n * Instead of iterating all expressions on every tag, ExpressionSet pre-indexes\n * them at insertion time by depth and terminal tag name. At match time, only\n * the relevant bucket is evaluated — typically reducing checks from O(E) to O(1)\n * lookup plus O(small bucket) matches.\n *\n * Three buckets are maintained:\n * - `_byDepthAndTag` — exact depth + exact tag name (tightest, used first)\n * - `_wildcardByDepth` — exact depth + wildcard tag `*` (depth-matched only)\n * - `_deepWildcards` — expressions containing `..` (cannot be depth-indexed)\n *\n * @example\n * import { Expression, ExpressionSet } from 'fast-xml-tagger';\n *\n * // Build once at config time\n * const stopNodes = new ExpressionSet();\n * stopNodes.add(new Expression('root.users.user'));\n * stopNodes.add(new Expression('root.config.setting'));\n * stopNodes.add(new Expression('..script'));\n *\n * // Query on every tag — hot path\n * if (stopNodes.matchesAny(matcher)) { ... }\n */\nexport default class ExpressionSet {\n constructor() {\n /** @type {Map<string, import('./Expression.js').default[]>} depth:tag → expressions */\n this._byDepthAndTag = new Map();\n\n /** @type {Map<number, import('./Expression.js').default[]>} depth → wildcard-tag expressions */\n this._wildcardByDepth = new Map();\n\n /** @type {import('./Expression.js').default[]} expressions containing deep wildcard (..) */\n this._deepWildcards = [];\n\n /** @type {Map<string, import('./Expression.js').default[]>} terminalTag → deep wildcard expressions */\n this._deepByTerminalTag = new Map();\n\n /** @type {Set<string>} pattern strings already added — used for deduplication */\n this._patterns = new Set();\n\n /** @type {boolean} whether the set is sealed against further additions */\n this._sealed = false;\n }\n\n /**\n * Add an Expression to the set.\n * Duplicate patterns (same pattern string) are silently ignored.\n *\n * @param {import('./Expression.js').default} expression - A pre-constructed Expression instance\n * @returns {this} for chaining\n * @throws {TypeError} if called after seal()\n *\n * @example\n * set.add(new Expression('root.users.user'));\n * set.add(new Expression('..script'));\n */\n add(expression) {\n if (this._sealed) {\n throw new TypeError(\n 'ExpressionSet is sealed. Create a new ExpressionSet to add more expressions.'\n );\n }\n\n // Deduplicate by pattern string\n if (this._patterns.has(expression.pattern)) return this;\n this._patterns.add(expression.pattern);\n\n if (expression.hasDeepWildcard()) {\n const lastSeg = expression.segments[expression.segments.length - 1];\n if (lastSeg && lastSeg.type !== 'deep-wildcard' && lastSeg.tag !== '*') {\n const tag = lastSeg.tag;\n if (!this._deepByTerminalTag.has(tag)) this._deepByTerminalTag.set(tag, []);\n this._deepByTerminalTag.get(tag).push(expression);\n } else {\n this._deepWildcards.push(expression);\n }\n return this;\n }\n\n const depth = expression.length;\n const lastSeg = expression.segments[expression.segments.length - 1];\n const tag = lastSeg?.tag;\n\n if (!tag || tag === '*') {\n // Can index by depth but not by tag\n if (!this._wildcardByDepth.has(depth)) this._wildcardByDepth.set(depth, []);\n this._wildcardByDepth.get(depth).push(expression);\n } else {\n // Tightest bucket: depth + tag\n const key = `${depth}:${tag}`;\n if (!this._byDepthAndTag.has(key)) this._byDepthAndTag.set(key, []);\n this._byDepthAndTag.get(key).push(expression);\n }\n\n return this;\n }\n\n /**\n * Add multiple expressions at once.\n *\n * @param {import('./Expression.js').default[]} expressions - Array of Expression instances\n * @returns {this} for chaining\n *\n * @example\n * set.addAll([\n * new Expression('root.users.user'),\n * new Expression('root.config.setting'),\n * ]);\n */\n addAll(expressions) {\n for (const expr of expressions) this.add(expr);\n return this;\n }\n\n /**\n * Check whether a pattern string is already present in the set.\n *\n * @param {import('./Expression.js').default} expression\n * @returns {boolean}\n */\n has(expression) {\n return this._patterns.has(expression.pattern);\n }\n\n /**\n * Number of expressions in the set.\n * @type {number}\n */\n get size() {\n return this._patterns.size;\n }\n\n /**\n * Seal the set against further modifications.\n * Useful to prevent accidental mutations after config is built.\n * Calling add() or addAll() on a sealed set throws a TypeError.\n *\n * @returns {this}\n */\n seal() {\n this._sealed = true;\n return this;\n }\n\n /**\n * Whether the set has been sealed.\n * @type {boolean}\n */\n get isSealed() {\n return this._sealed;\n }\n\n /**\n * Test whether the matcher's current path matches any expression in the set.\n *\n * Evaluation order (cheapest → most expensive):\n * 1. Exact depth + tag bucket — O(1) lookup, typically 0–2 expressions\n * 2. Depth-only wildcard bucket — O(1) lookup, rare\n * 3. Deep-wildcard list — always checked, but usually small\n *\n * @param {import('./Matcher.js').default} matcher - Matcher instance (or readOnly view)\n * @returns {boolean} true if any expression matches the current path\n *\n * @example\n * if (stopNodes.matchesAny(matcher)) {\n * // handle stop node\n * }\n */\n matchesAny(matcher) {\n return this.findMatch(matcher) !== null;\n }\n /**\n * Find and return the first Expression that matches the matcher's current path.\n *\n * Uses the same evaluation order as matchesAny (cheapest → most expensive):\n * 1. Exact depth + tag bucket\n * 2. Depth-only wildcard bucket\n * 3. Deep-wildcard list\n *\n * @param {import('./Matcher.js').default} matcher - Matcher instance (or readOnly view)\n * @returns {import('./Expression.js').default | null} the first matching Expression, or null\n *\n * @example\n * const expr = stopNodes.findMatch(matcher);\n * if (expr) {\n * // access expr.config, expr.pattern, etc.\n * }\n */\n findMatch(matcher) {\n const depth = matcher.getDepth();\n const tag = matcher.getCurrentTag();\n\n // 1. Tightest bucket — most expressions live here\n const exactKey = `${depth}:${tag}`;\n const exactBucket = this._byDepthAndTag.get(exactKey);\n if (exactBucket) {\n for (let i = 0; i < exactBucket.length; i++) {\n if (matcher.matches(exactBucket[i])) return exactBucket[i];\n }\n }\n\n // 2. Depth-matched wildcard-tag expressions\n const wildcardBucket = this._wildcardByDepth.get(depth);\n if (wildcardBucket) {\n for (let i = 0; i < wildcardBucket.length; i++) {\n if (matcher.matches(wildcardBucket[i])) return wildcardBucket[i];\n }\n }\n\n // 3. Deep wildcards — indexed by terminal tag, then unindexed fallback\n const deepBucket = this._deepByTerminalTag.get(tag);\n if (deepBucket) {\n for (let i = 0; i < deepBucket.length; i++) {\n if (matcher.matches(deepBucket[i])) return deepBucket[i];\n }\n }\n for (let i = 0; i < this._deepWildcards.length; i++) {\n if (matcher.matches(this._deepWildcards[i])) return this._deepWildcards[i];\n }\n\n return null;\n }\n}\n","import ExpressionSet from \"./ExpressionSet.js\";\n\n/**\n * MatcherView - A lightweight read-only view over a Matcher's internal state.\n *\n * Created once by Matcher and reused across all callbacks. Holds a direct\n * reference to the parent Matcher so it always reflects current parser state\n * with zero copying or freezing overhead.\n *\n * Users receive this via {@link Matcher#readOnly} or directly from parser\n * callbacks. It exposes all query and matching methods but has no mutation\n * methods — misuse is caught at the TypeScript level rather than at runtime.\n *\n * @example\n * const matcher = new Matcher();\n * const view = matcher.readOnly();\n *\n * matcher.push(\"root\", {});\n * view.getCurrentTag(); // \"root\"\n * view.getDepth(); // 1\n */\nexport class MatcherView {\n /**\n * @param {Matcher} matcher - The parent Matcher instance to read from.\n */\n constructor(matcher) {\n this._matcher = matcher;\n }\n\n /**\n * Get the path separator used by the parent matcher.\n * @returns {string}\n */\n get separator() {\n return this._matcher.separator;\n }\n\n /**\n * Get current tag name.\n * @returns {string|undefined}\n */\n getCurrentTag() {\n const path = this._matcher.path;\n return path.length > 0 ? path[path.length - 1].tag : undefined;\n }\n\n /**\n * Get current namespace.\n * @returns {string|undefined}\n */\n getCurrentNamespace() {\n const path = this._matcher.path;\n return path.length > 0 ? path[path.length - 1].namespace : undefined;\n }\n\n /**\n * Get current node's attribute value.\n * @param {string} attrName\n * @returns {*}\n */\n getAttrValue(attrName) {\n const path = this._matcher.path;\n if (path.length === 0) return undefined;\n return path[path.length - 1].values?.[attrName];\n }\n\n /**\n * Check if current node has an attribute.\n * @param {string} attrName\n * @returns {boolean}\n */\n hasAttr(attrName) {\n const path = this._matcher.path;\n if (path.length === 0) return false;\n const current = path[path.length - 1];\n return current.values !== undefined && attrName in current.values;\n }\n\n /**\n * Get the value of a \"kept\" attribute from the nearest ancestor (or\n * current node) that declared it via `push(tag, attrs, ns, { keep: [...] })`.\n * @param {string} attrName\n * @returns {*}\n */\n getAnyParentAttr(attrName) {\n return this._matcher.getAnyParentAttr(attrName);\n }\n\n /**\n * Check whether any ancestor (or the current node) kept the given\n * attribute via `push(tag, attrs, ns, { keep: [...] })`.\n * @param {string} attrName\n * @returns {boolean}\n */\n hasAnyParentAttr(attrName) {\n return this._matcher.hasAnyParentAttr(attrName);\n }\n\n /**\n * Get current node's sibling position (child index in parent).\n * @returns {number}\n */\n getPosition() {\n const path = this._matcher.path;\n if (path.length === 0) return -1;\n return path[path.length - 1].position ?? 0;\n }\n\n /**\n * Get current node's repeat counter (occurrence count of this tag name).\n * @returns {number}\n */\n getCounter() {\n const path = this._matcher.path;\n if (path.length === 0) return -1;\n return path[path.length - 1].counter ?? 0;\n }\n\n /**\n * Get current node's sibling index (alias for getPosition).\n * @returns {number}\n * @deprecated Use getPosition() or getCounter() instead\n */\n getIndex() {\n return this.getPosition();\n }\n\n /**\n * Get current path depth.\n * @returns {number}\n */\n getDepth() {\n return this._matcher.path.length;\n }\n\n /**\n * Get path as string.\n * @param {string} [separator] - Optional separator (uses default if not provided)\n * @param {boolean} [includeNamespace=true]\n * @returns {string}\n */\n toString(separator, includeNamespace = true) {\n return this._matcher.toString(separator, includeNamespace);\n }\n\n /**\n * Get path as array of tag names.\n * @returns {string[]}\n */\n toArray() {\n return this._matcher.path.map(n => n.tag);\n }\n\n /**\n * Match current path against an Expression.\n * @param {Expression} expression\n * @returns {boolean}\n */\n matches(expression) {\n return this._matcher.matches(expression);\n }\n\n /**\n * Match any expression in the given set against the current path.\n * @param {ExpressionSet} exprSet\n * @returns {boolean}\n */\n matchesAny(exprSet) {\n return exprSet.matchesAny(this._matcher);\n }\n}\n\n/**\n * Matcher - Tracks current path in XML/JSON tree and matches against Expressions.\n *\n * The matcher maintains a stack of nodes representing the current path from root to\n * current tag. It only stores attribute values for the current (top) node to minimize\n * memory usage. Sibling tracking is used to auto-calculate position and counter.\n *\n * Use {@link Matcher#readOnly} to obtain a {@link MatcherView} safe to pass to\n * user callbacks — it always reflects current state with no Proxy overhead.\n *\n * @example\n * const matcher = new Matcher();\n * matcher.push(\"root\", {});\n * matcher.push(\"users\", {});\n * matcher.push(\"user\", { id: \"123\", type: \"admin\" });\n *\n * const expr = new Expression(\"root.users.user\");\n * matcher.matches(expr); // true\n */\nexport default class Matcher {\n /**\n * Create a new Matcher.\n * @param {Object} [options={}]\n * @param {string} [options.separator='.'] - Default path separator\n */\n constructor(options = {}) {\n this.separator = options.separator || '.';\n this.path = [];\n this.siblingStacks = [];\n // Each path node: { tag, values, position, counter, namespace? }\n // values only present for current (last) node\n // Each siblingStacks entry: Map<tagName, count> tracking occurrences at each level\n this._pathStringCache = null;\n this._view = new MatcherView(this);\n\n // Kept-attribute stack: only populated when push() is called with options.keep.\n this._keptAttrs = [];\n }\n\n /**\n * Push a new tag onto the path.\n * @param {string} tagName\n * @param {Object|null} [attrValues=null]\n * @param {string|null} [namespace=null]\n * @param {Object|null} [options=null]\n * @param {string[]} [options.keep] - Names of attributes (from attrValues)\n */\n push(tagName, attrValues = null, namespace = null, options = null) {\n this._pathStringCache = null;\n\n // Remove values from previous current node (now becoming ancestor)\n if (this.path.length > 0) {\n this.path[this.path.length - 1].values = undefined;\n }\n\n // Get or create sibling tracking for current level\n const currentLevel = this.path.length;\n let level = this.siblingStacks[currentLevel];\n if (!level) {\n // `counts` tells same-name siblings apart (the \"counter\" — nth <item>\n // among other <item>s). `total` is every child seen at this level so\n // far, kept as a running number instead of re-added from `counts` on\n // every push — a parent with many differently-named children would\n // otherwise cost more per child the more distinct names it has.\n level = { counts: new Map(), total: 0 };\n this.siblingStacks[currentLevel] = level;\n }\n\n // Create a unique key for sibling tracking that includes namespace\n const siblingKey = namespace ? `${namespace}:${tagName}` : tagName;\n\n // Calculate counter (how many times this tag appeared at this level)\n const counter = level.counts.get(siblingKey) || 0;\n\n // Position = total children at this level seen before this one.\n const position = level.total;\n\n // Update sibling count for this tag, and the level's running total.\n level.counts.set(siblingKey, counter + 1);\n level.total++;\n\n // Create new node\n const node = {\n tag: tagName,\n position: position,\n counter: counter\n };\n\n if (namespace !== null && namespace !== undefined) {\n node.namespace = namespace;\n }\n\n if (attrValues !== null && attrValues !== undefined) {\n node.values = attrValues;\n }\n\n this.path.push(node);\n\n // Depth of the node we just pushed (1-based, matches this.path.length)\n const depth = this.path.length;\n\n // Copy only the requested attributes into the kept-attrs stack. This is\n // the one part of push() whose cost scales with input (O(keep.length))\n // rather than being O(1) — by design, since the caller is explicitly\n // opting in for specific attribute names. No options/keep => zero added\n // cost beyond the two property reads below.\n const keep = options !== null ? options.keep : null;\n if (keep !== null && keep !== undefined && keep.length > 0 && attrValues) {\n for (let i = 0; i < keep.length; i++) {\n const name = keep[i];\n if (attrValues[name] !== undefined) {\n this._keptAttrs.push({ depth, name, value: attrValues[name] });\n }\n }\n }\n }\n\n /**\n * Pop the last tag from the path.\n * @returns {Object|undefined} The popped node\n */\n pop() {\n if (this.path.length === 0) return undefined;\n this._pathStringCache = null;\n\n const node = this.path.pop();\n\n if (this.siblingStacks.length > this.path.length + 1) {\n this.siblingStacks.length = this.path.length + 1;\n }\n\n // Drop any kept attributes that belonged to the popped node (or deeper).\n // _keptAttrs is depth-ordered (push only ever appends increasing depths),\n // so this is a backward scan that stops at the first surviving entry —\n // typically O(1) since kept attrs are rare by design.\n const poppedDepth = this.path.length + 1;\n while (\n this._keptAttrs.length > 0 &&\n this._keptAttrs[this._keptAttrs.length - 1].depth >= poppedDepth\n ) {\n this._keptAttrs.pop();\n }\n\n return node;\n }\n\n /**\n * Update current node's attribute values.\n * Useful when attributes are parsed after push.\n * @param {Object} attrValues\n */\n updateCurrent(attrValues) {\n if (this.path.length > 0) {\n const current = this.path[this.path.length - 1];\n if (attrValues !== null && attrValues !== undefined) {\n current.values = attrValues;\n }\n }\n }\n\n /**\n * Get current tag name.\n * @returns {string|undefined}\n */\n getCurrentTag() {\n return this.path.length > 0 ? this.path[this.path.length - 1].tag : undefined;\n }\n\n /**\n * Get current namespace.\n * @returns {string|undefined}\n */\n getCurrentNamespace() {\n return this.path.length > 0 ? this.path[this.path.length - 1].namespace : undefined;\n }\n\n /**\n * Get current node's attribute value.\n * @param {string} attrName\n * @returns {*}\n */\n getAttrValue(attrName) {\n if (this.path.length === 0) return undefined;\n return this.path[this.path.length - 1].values?.[attrName];\n }\n\n /**\n * Check if current node has an attribute.\n * @param {string} attrName\n * @returns {boolean}\n */\n hasAttr(attrName) {\n if (this.path.length === 0) return false;\n const current = this.path[this.path.length - 1];\n return current.values !== undefined && attrName in current.values;\n }\n\n /**\n * Get the value of a \"kept\" attribute from the nearest ancestor (or\n * current node) that declared it via `push(tag, attrs, ns, { keep: [...] })`.\n * Unlike getAttrValue(), this works regardless of how deep the path has\n * gone since the attribute was pushed — but only for attribute names that\n * were explicitly marked with `keep` at push time. Cost is proportional to\n * the number of currently-kept attributes (typically 0-3), not path depth.\n * @param {string} attrName\n * @returns {*} the value, or undefined if no ancestor kept this attribute\n */\n getAnyParentAttr(attrName) {\n const kept = this._keptAttrs;\n for (let i = kept.length - 1; i >= 0; i--) {\n if (kept[i].name === attrName) return kept[i].value;\n }\n return undefined;\n }\n\n /**\n * Check whether any ancestor (or the current node) kept the given\n * attribute via `push(tag, attrs, ns, { keep: [...] })`.\n * @param {string} attrName\n * @returns {boolean}\n */\n hasAnyParentAttr(attrName) {\n const kept = this._keptAttrs;\n for (let i = kept.length - 1; i >= 0; i--) {\n if (kept[i].name === attrName) return true;\n }\n return false;\n }\n\n /**\n * Get current node's sibling position (child index in parent).\n * @returns {number}\n */\n getPosition() {\n if (this.path.length === 0) return -1;\n return this.path[this.path.length - 1].position ?? 0;\n }\n\n /**\n * Get current node's repeat counter (occurrence count of this tag name).\n * @returns {number}\n */\n getCounter() {\n if (this.path.length === 0) return -1;\n return this.path[this.path.length - 1].counter ?? 0;\n }\n\n /**\n * Get current node's sibling index (alias for getPosition).\n * @returns {number}\n * @deprecated Use getPosition() or getCounter() instead\n */\n getIndex() {\n return this.getPosition();\n }\n\n /**\n * Get current path depth.\n * @returns {number}\n */\n getDepth() {\n return this.path.length;\n }\n\n /**\n * Get path as string.\n * @param {string} [separator] - Optional separator (uses default if not provided)\n * @param {boolean} [includeNamespace=true]\n * @returns {string}\n */\n toString(separator, includeNamespace = true) {\n const sep = separator || this.separator;\n const isDefault = (sep === this.separator && includeNamespace === true);\n\n if (isDefault) {\n if (this._pathStringCache !== null) {\n return this._pathStringCache;\n }\n const result = this.path.map(n =>\n (n.namespace) ? `${n.namespace}:${n.tag}` : n.tag\n ).join(sep);\n this._pathStringCache = result;\n return result;\n }\n\n return this.path.map(n =>\n (includeNamespace && n.namespace) ? `${n.namespace}:${n.tag}` : n.tag\n ).join(sep);\n }\n\n /**\n * Get path as array of tag names.\n * @returns {string[]}\n */\n toArray() {\n return this.path.map(n => n.tag);\n }\n\n /**\n * Reset the path to empty.\n */\n reset() {\n this._pathStringCache = null;\n this.path = [];\n this.siblingStacks = [];\n this._keptAttrs = [];\n }\n\n /**\n * Match current path against an Expression.\n * @param {Expression} expression\n * @returns {boolean}\n */\n matches(expression) {\n const segments = expression.segments;\n\n if (segments.length === 0) {\n return false;\n }\n\n if (expression.hasDeepWildcard()) {\n return this._matchWithDeepWildcard(segments);\n }\n\n return this._matchSimple(segments);\n }\n\n /**\n * @private\n */\n _matchSimple(segments) {\n if (this.path.length !== segments.length) {\n return false;\n }\n\n for (let i = 0; i < segments.length; i++) {\n if (!this._matchSegment(segments[i], this.path[i], i === this.path.length - 1)) {\n return false;\n }\n }\n\n return true;\n }\n\n /**\n * @private\n */\n _matchWithDeepWildcard(segments) {\n let pathIdx = this.path.length - 1;\n let segIdx = segments.length - 1;\n\n while (segIdx >= 0 && pathIdx >= 0) {\n const segment = segments[segIdx];\n\n if (segment.type === 'deep-wildcard') {\n segIdx--;\n\n if (segIdx < 0) {\n return true;\n }\n\n const nextSeg = segments[segIdx];\n let found = false;\n\n for (let i = pathIdx; i >= 0; i--) {\n if (this._matchSegment(nextSeg, this.path[i], i === this.path.length - 1)) {\n pathIdx = i - 1;\n segIdx--;\n found = true;\n break;\n }\n }\n\n if (!found) {\n return false;\n }\n } else {\n if (!this._matchSegment(segment, this.path[pathIdx], pathIdx === this.path.length - 1)) {\n return false;\n }\n pathIdx--;\n segIdx--;\n }\n }\n\n return segIdx < 0;\n }\n\n /**\n * @private\n */\n _matchSegment(segment, node, isCurrentNode) {\n if (segment.tag !== '*' && segment.tag !== node.tag) {\n return false;\n }\n\n if (segment.namespace !== undefined) {\n if (segment.namespace !== '*' && segment.namespace !== node.namespace) {\n return false;\n }\n }\n\n if (segment.attrName !== undefined) {\n if (!isCurrentNode) {\n return false;\n }\n\n if (!node.values || !(segment.attrName in node.values)) {\n return false;\n }\n\n if (segment.attrValue !== undefined) {\n if (String(node.values[segment.attrName]) !== String(segment.attrValue)) {\n return false;\n }\n }\n }\n\n if (segment.position !== undefined) {\n if (!isCurrentNode) {\n return false;\n }\n\n const counter = node.counter ?? 0;\n\n if (segment.position === 'first' && counter !== 0) {\n return false;\n } else if (segment.position === 'odd' && counter % 2 !== 1) {\n return false;\n } else if (segment.position === 'even' && counter % 2 !== 0) {\n return false;\n } else if (segment.position === 'nth' && counter !== segment.positionValue) {\n return false;\n }\n }\n\n return true;\n }\n\n /**\n * Match any expression in the given set against the current path.\n * @param {ExpressionSet} exprSet\n * @returns {boolean}\n */\n matchesAny(exprSet) {\n return exprSet.matchesAny(this);\n }\n\n /**\n * Create a snapshot of current state.\n * @returns {Object}\n */\n snapshot() {\n return {\n path: this.path.map(node => ({ ...node })),\n siblingStacks: this.siblingStacks.map(level => level ? { counts: new Map(level.counts), total: level.total } : level),\n keptAttrs: this._keptAttrs.map(entry => ({ ...entry }))\n };\n }\n\n /**\n * Restore state from snapshot.\n * @param {Object} snapshot\n */\n restore(snapshot) {\n this._pathStringCache = null;\n this.path = snapshot.path.map(node => ({ ...node }));\n this.siblingStacks = snapshot.siblingStacks.map(level => level ? { counts: new Map(level.counts), total: level.total } : level);\n this._keptAttrs = (snapshot.keptAttrs || []).map(entry => ({ ...entry }));\n }\n\n /**\n * Return the read-only {@link MatcherView} for this matcher.\n *\n * The same instance is returned on every call — no allocation occurs.\n * It always reflects the current parser state and is safe to pass to\n * user callbacks without risk of accidental mutation.\n *\n * @returns {MatcherView}\n *\n * @example\n * const view = matcher.readOnly();\n * // pass view to callbacks — it stays in sync automatically\n * view.matches(expr); // ✓\n * view.getCurrentTag(); // ✓\n * // view.push(...) // ✗ method does not exist — caught by TypeScript\n */\n readOnly() {\n return this._view;\n }\n}\n","/**\n * HTML context patterns.\n *\n * Detects XSS vectors that are dangerous when a string ends up rendered as HTML.\n * All patterns use bounded quantifiers to ensure linear-time matching (ReDoS-safe).\n *\n * Each entry is { pattern: RegExp, id: string, description: string }\n * so callers can inspect which rule fired if they need to.\n */\n\nconst HTML_PATTERNS = [\n {\n id: 'html-script-open',\n description: '<script opening tag',\n pattern: /<script[\\s>/]/i,\n },\n {\n id: 'html-script-close',\n description: '</script closing tag',\n pattern: /<\\/script[\\s>]/i,\n },\n {\n id: 'html-javascript-protocol',\n description: 'javascript: URI scheme (with optional whitespace/encoding)',\n // Handles j&#x61;vascript:, j\\u0061vascript:, and whitespace variants\n pattern: /j[\\t\\n\\r ]*a[\\t\\n\\r ]*v[\\t\\n\\r ]*a[\\t\\n\\r ]*s[\\t\\n\\r ]*c[\\t\\n\\r ]*r[\\t\\n\\r ]*i[\\t\\n\\r ]*p[\\t\\n\\r ]*t[\\t\\n\\r ]*:/i,\n },\n {\n id: 'html-vbscript-protocol',\n description: 'vbscript: URI scheme',\n pattern: /vbscript[\\t\\n\\r ]*:/i,\n },\n {\n id: 'html-data-html',\n description: 'data:text/html URI — can execute scripts in browsers',\n pattern: /data[\\t\\n\\r ]*:[\\t\\n\\r ]*text\\/html/i,\n },\n {\n id: 'html-data-xhtml',\n description: 'data:application/xhtml+xml URI',\n pattern: /data[\\t\\n\\r ]*:[\\t\\n\\r ]*application\\/xhtml/i,\n },\n {\n id: 'html-data-svg',\n description: 'data:image/svg+xml URI — can execute scripts',\n pattern: /data[\\t\\n\\r ]*:[\\t\\n\\r ]*image\\/svg\\+xml/i,\n },\n {\n id: 'html-inline-event-handler',\n description: 'Inline event handler attributes: onclick=, onerror=, onload=, etc.',\n // \\bon ensures we match a word boundary so \"phonetic=\" is not caught\n pattern: /\\bon\\w{1,30}\\s*=/i,\n },\n {\n id: 'html-entity-obfuscated-script',\n description: 'HTML-entity-encoded <script (e.g. &#x3C;script or &lt;script)',\n // Entities include optional trailing semicolon: &#x3C; or &#x3C (both valid in HTML5)\n pattern: /(?:&#x0*3[Cc];?|&#0*60;?|&lt;)\\s*script/i,\n },\n {\n id: 'html-entity-obfuscated-javascript',\n description: 'HTML-entity-encoded javascript: (partial — catches common &#106; or &#x6a; for \"j\")',\n pattern: /(?:&#x0*6[Aa];?|&#0*106;?)\\s*(?:&#x0*61;?|a)[\\s\\S]{0,80}script\\s*:/i,\n },\n {\n id: 'html-style-expression',\n description: 'CSS expression() — IE-era code execution in style attributes',\n pattern: /style[\\s\\S]{0,20}expression\\s*\\(/i,\n },\n {\n id: 'html-object-embed',\n description: '<object or <embed tags that can load active content',\n pattern: /<(?:object|embed)[\\s>/]/i,\n },\n {\n id: 'html-base-tag',\n description: '<base href= — can hijack all relative URLs on a page',\n pattern: /<base[\\s>]/i,\n },\n {\n id: 'html-meta-refresh',\n description: '<meta http-equiv=\"refresh\" — can redirect users',\n pattern: /<meta[\\s\\S]{0,40}http-equiv[\\s\\S]{0,20}refresh/i,\n },\n {\n id: 'html-srcdoc',\n description: 'srcdoc= attribute on iframes — embeds HTML that can run scripts',\n pattern: /srcdoc\\s*=/i,\n },\n {\n id: 'html-iframe',\n description: '<iframe tag',\n pattern: /<iframe[\\s>/]/i,\n },\n {\n id: 'html-form',\n description: '<form tag — can be used for phishing / credential harvesting injection',\n pattern: /<form[\\s>/]/i,\n },\n];\n\nexport default HTML_PATTERNS;\n","/**\n * XML context patterns.\n *\n * Detects injection vectors that are specifically dangerous when a string\n * is inserted into an XML document (not HTML rendering context).\n *\n * Key distinction from HTML: these patterns target parser-level attacks —\n * things that can confuse or subvert an XML parser, trigger external entity\n * resolution, or inject DTD content. HTML rendering concerns (XSS) belong\n * in the HTML context.\n */\n\nconst XML_PATTERNS = [\n {\n id: 'xml-cdata-injection',\n description: 'CDATA section injection: <![CDATA[ breaks out of text node context',\n pattern: /<!\\[CDATA\\[/i,\n },\n {\n id: 'xml-cdata-close',\n description: 'CDATA close sequence: ]]> can terminate an enclosing CDATA section',\n pattern: /\\]\\]>/,\n },\n {\n id: 'xml-processing-instruction',\n description: 'XML processing instruction: <?xml-stylesheet or <?php etc.',\n pattern: /<\\?(?:xml[\\- ]|php|asp)/i,\n },\n {\n id: 'xml-doctype-injection',\n description: 'DOCTYPE declaration embedded in content — can define entities',\n // Match <!DOCTYPE followed by end-of-string, whitespace, or [ (internal subset)\n pattern: /<!DOCTYPE(?:[\\s[]|$)/i,\n },\n {\n id: 'xml-entity-system',\n description: 'SYSTEM keyword — used in external entity declarations (XXE)',\n pattern: /\\bSYSTEM\\s+[\"']/i,\n },\n {\n id: 'xml-entity-public',\n description: 'PUBLIC keyword — used in external entity declarations (XXE)',\n pattern: /\\bPUBLIC\\s+[\"']/i,\n },\n {\n id: 'xml-entity-declaration',\n description: '<!ENTITY declaration — defines entities, potential XXE or entity expansion',\n pattern: /<!ENTITY[\\s%]/i,\n },\n {\n id: 'xml-billion-laughs',\n description: 'Entity reference chaining / billion laughs: repeated &eX; style references',\n // Heuristic: 3+ consecutive entity refs suggests expansion attack\n pattern: /(?:&\\w{1,20};){3,}/,\n },\n {\n id: 'xml-namespace-confusion',\n description: 'xmlns: attribute injection — can redefine namespaces to confuse parsers',\n pattern: /\\bxmlns\\s*(?::\\w{1,40})?\\s*=/i,\n },\n {\n id: 'xml-comment-injection',\n description: '<!-- comment injection — can hide content from some parsers',\n pattern: /<!--/,\n },\n {\n id: 'xml-comment-close',\n description: '--> closes an enclosing XML comment',\n pattern: /-->/,\n },\n {\n id: 'xml-pi-close',\n description: '?> closes an enclosing processing instruction',\n pattern: /\\?>/,\n },\n];\n\nexport default XML_PATTERNS;\n","/**\n * SVG context patterns.\n *\n * SVG is XML-based but renders in browsers, giving it a unique attack surface\n * that combines XML parser behaviour with browser rendering and JavaScript execution.\n *\n * Many of these vectors bypass HTML sanitizers that don't understand SVG semantics\n * (DOMPurify has documented bypass vulnerabilities specifically in SVG/XML context).\n */\n\nconst SVG_PATTERNS = [\n {\n id: 'svg-script-element',\n description: '<script element inside SVG executes JavaScript',\n pattern: /<script[\\s>/]/i,\n },\n {\n id: 'svg-xlink-href-javascript',\n description: 'xlink:href with javascript: — classic SVG XSS via <a> or <use>',\n pattern: /xlink\\s*:\\s*href\\s*=\\s*[\"']?\\s*javascript\\s*:/i,\n },\n {\n id: 'svg-href-javascript',\n description: 'href= with javascript: in SVG context (<a>, <animate>, etc.)',\n pattern: /href\\s*=\\s*[\"']?\\s*javascript\\s*:/i,\n },\n {\n id: 'svg-foreignobject',\n description: '<foreignObject embeds HTML inside SVG — can execute scripts',\n pattern: /<foreignObject[\\s>/]/i,\n },\n {\n id: 'svg-use-external',\n description: '<use xlink:href or href pointing to external resource (non-fragment URL)',\n // Match <use with href= where the value starts with a non-# character (external URL)\n // [\\\"'][^#] catches quoted values not starting with #; [^\\\"'#\\s>] catches unquoted\n pattern: /<use[\\s\\S]{0,60}(?:xlink\\s*:\\s*)?href\\s*=\\s*(?:[\"'][^#]|[^\"'#\\s>])/i,\n },\n {\n id: 'svg-animate-href',\n description: '<animate attributeName=\"href\" — can dynamically change href to javascript:',\n pattern: /<animate[\\s\\S]{0,80}attributeName\\s*=\\s*[\"'][\\s]*href[\"']/i,\n },\n {\n id: 'svg-animate-xlinkhref',\n description: '<animate attributeName=\"xlink:href\"',\n pattern: /<animate[\\s\\S]{0,80}attributeName\\s*=\\s*[\"'][\\s]*xlink\\s*:\\s*href[\"']/i,\n },\n {\n id: 'svg-set-javascript',\n description: '<set to=\"javascript:...\" — sets an attribute to a javascript: URI',\n pattern: /<set[\\s\\S]{0,80}to\\s*=\\s*[\"']?\\s*javascript\\s*:/i,\n },\n {\n id: 'svg-event-handler',\n description: 'SVG-specific event handler attributes: onload=, onerror=, onactivate=, etc.',\n pattern: /\\bon(?:load|error|activate|begin|end|repeat|focus|blur|click|mouse\\w{1,20}|key\\w{1,20})\\s*=/i,\n },\n {\n id: 'svg-handler-generic',\n description: 'Generic on* handler catch-all for SVG attributes',\n pattern: /\\bon\\w{1,30}\\s*=/i,\n },\n {\n id: 'svg-filter-feimage',\n description: '<feImage href= — filter primitive that can load external resources',\n pattern: /<feImage[\\s\\S]{0,80}(?:xlink\\s*:\\s*)?href\\s*=/i,\n },\n {\n id: 'svg-image-external',\n description: '<image xlink:href with http/https or javascript protocol',\n pattern: /<image[\\s\\S]{0,80}(?:xlink\\s*:\\s*)?href\\s*=\\s*[\"']?\\s*(?:https?|javascript)\\s*:/i,\n },\n {\n id: 'svg-style-javascript',\n description: 'style= attribute containing javascript: (e.g. background:url(javascript:...))',\n pattern: /style\\s*=[\\s\\S]{0,60}javascript\\s*:/i,\n },\n];\n\nexport default SVG_PATTERNS;\n","/**\n * SQL context patterns — high-precision rules only.\n *\n * These rules have very low false-positive risk and are safe to apply to\n * general user text (names, descriptions, search queries, etc.).\n * All patterns are ReDoS-safe — unlike the `sql-injection` npm package\n * which has an active CVE on its own detection regexes.\n *\n * For exhaustive coverage including noisier heuristics (comment sequences,\n * hex literals, stacked queries with semicolons), use 'SQL-STRICT' instead.\n * Apply 'SQL-STRICT' only to strings that are specifically SQL fragments,\n * not to general free-text fields.\n */\n\nconst SQL_PATTERNS = [\n {\n id: 'sql-block-comment-open',\n description: 'SQL block comment open: /* ... */ — unusual in legitimate user text',\n pattern: /\\/\\*/,\n },\n {\n id: 'sql-union-select',\n description: 'UNION SELECT — most common SQL injection aggregation attack',\n pattern: /\\bUNION\\s{1,20}(?:ALL\\s{1,20})?SELECT\\b/i,\n },\n {\n id: 'sql-drop-table',\n description: 'DROP TABLE — destructive DDL injection',\n pattern: /\\bDROP\\s{1,20}TABLE\\b/i,\n },\n {\n id: 'sql-drop-database',\n description: 'DROP DATABASE — destructive DDL injection',\n pattern: /\\bDROP\\s{1,20}DATABASE\\b/i,\n },\n {\n id: 'sql-insert-into',\n description: 'INSERT INTO — data injection',\n pattern: /\\bINSERT\\s{1,20}INTO\\b/i,\n },\n {\n id: 'sql-delete-from',\n description: 'DELETE FROM — data deletion injection',\n pattern: /\\bDELETE\\s{1,20}FROM\\b/i,\n },\n {\n id: 'sql-update-set',\n description: 'UPDATE ... SET — data modification injection',\n // Allows arbitrary content between UPDATE and SET (table name, alias, etc.)\n pattern: /\\bUPDATE\\b[\\s\\S]{1,60}\\bSET\\b/i,\n },\n {\n id: 'sql-exec-xp',\n description: 'EXEC xp_ — MSSQL extended stored procedure execution',\n pattern: /\\bEXEC(?:UTE)?\\s{1,20}xp_/i,\n },\n {\n id: 'sql-tautology-string',\n description: \"Classic string tautology: ' OR '1'='1 or \\\" OR \\\"1\\\"=\\\"1\\\"\",\n // Last quote is optional — injection may truncate it: ' OR '1'='1--\n pattern: /'\\s{0,10}OR\\s{0,10}'[^']{0,20}'\\s*=\\s*'[^']{0,20}/i,\n },\n {\n id: 'sql-tautology-numeric',\n description: 'Numeric tautology: OR 1=1',\n pattern: /\\bOR\\s{1,10}1\\s*=\\s*1\\b/i,\n },\n {\n id: 'sql-always-true-zero',\n description: 'Numeric tautology: OR 0=0',\n pattern: /\\bOR\\s{1,10}0\\s*=\\s*0\\b/i,\n },\n {\n id: 'sql-sleep-benchmark',\n description: 'Time-based blind injection: SLEEP() or BENCHMARK()',\n pattern: /\\b(?:SLEEP|BENCHMARK)\\s*\\(/i,\n },\n {\n id: 'sql-waitfor-delay',\n description: 'MSSQL time-based blind injection: WAITFOR DELAY',\n pattern: /\\bWAITFOR\\s{1,20}DELAY\\b/i,\n },\n {\n id: 'sql-char-function',\n description: 'CHAR() function — used to obfuscate injected strings',\n pattern: /\\bCHAR\\s*\\(\\s*\\d{1,3}/i,\n },\n {\n id: 'sql-information-schema',\n description: 'INFORMATION_SCHEMA — reconnaissance query for table/column enumeration',\n pattern: /\\bINFORMATION_SCHEMA\\b/i,\n },\n];\n\nexport default SQL_PATTERNS;\n","/**\n * SHELL context patterns.\n *\n * Detects shell injection vectors and path traversal patterns.\n * Designed for use when a string will be passed to a shell command,\n * used as a file path, or interpolated into OS-level operations.\n */\n\nconst SHELL_PATTERNS = [\n {\n id: 'shell-path-traversal-unix',\n description: 'Unix path traversal: ../ — climbing the directory tree',\n pattern: /\\.\\.\\//,\n },\n {\n id: 'shell-path-traversal-windows',\n description: 'Windows path traversal: ..\\\\ — climbing the directory tree',\n pattern: /\\.\\.\\\\/,\n },\n {\n id: 'shell-path-traversal-encoded',\n description: 'URL-encoded path traversal: %2e%2e or %2f variants',\n pattern: /%2e%2e|%2f\\.\\.|\\.\\.%2f/i,\n },\n {\n id: 'shell-null-byte',\n description: 'Null byte injection: \\\\x00 or %00 — truncates strings in C-backed functions',\n pattern: /\\x00|%00/,\n },\n {\n id: 'shell-semicolon',\n description: 'Semicolon command separator: cmd1; cmd2',\n pattern: /;/,\n },\n {\n id: 'shell-pipe',\n description: 'Pipe operator: cmd1 | cmd2',\n pattern: /\\|/,\n },\n {\n id: 'shell-and-operator',\n description: 'AND operator: cmd1 && cmd2',\n pattern: /&&/,\n },\n {\n id: 'shell-or-operator',\n description: 'OR operator: cmd1 || cmd2',\n pattern: /\\|\\|/,\n },\n {\n id: 'shell-backtick',\n description: 'Backtick command substitution: `cmd`',\n pattern: /`/,\n },\n {\n id: 'shell-dollar-paren',\n description: 'Dollar-paren command substitution: $(cmd)',\n pattern: /\\$\\(/,\n },\n {\n id: 'shell-dollar-brace',\n description: 'Dollar-brace variable expansion: ${var} — can be abused for injection',\n pattern: /\\$\\{/,\n },\n {\n id: 'shell-redirect-out',\n description: 'Output redirection: cmd > file or cmd >> file',\n pattern: />{1,2}/,\n },\n {\n id: 'shell-redirect-in',\n description: 'Input redirection: cmd < file',\n pattern: /</,\n },\n {\n id: 'shell-newline-injection',\n description: 'Newline injection: \\\\n or \\\\r — can inject new shell commands',\n pattern: /[\\n\\r]/,\n },\n {\n id: 'shell-glob-star',\n description: 'Glob expansion: * or ? — can expand to unintended files',\n // Only flag when combined with path separators to reduce false positives\n pattern: /[/\\\\][*?]/,\n },\n {\n id: 'shell-absolute-root',\n description: 'Absolute root path injection: string starting with / or \\\\ (Windows UNC)',\n pattern: /^(?:\\/|\\\\\\\\)/,\n },\n {\n id: 'shell-windows-drive',\n description: 'Windows drive letter path injection: C:\\\\ or D:/',\n pattern: /^[a-zA-Z]:[/\\\\]/,\n },\n {\n id: 'shell-curl-wget',\n description: 'curl/wget with URL or flags — can exfiltrate data or download payloads',\n // Require a URL scheme (http/https/ftp) or a flag (-) to reduce false positives\n // \"curl is a tool\" won't match; \"curl http://...\" or \"curl -s ...\" will\n pattern: /\\b(?:curl|wget)\\s+(?:https?:\\/\\/|ftp:\\/\\/|-)/i,\n },\n];\n\nexport default SHELL_PATTERNS;\n","/**\n * REDOS context patterns.\n *\n * Detects strings that, if used as regular expressions, could cause\n * catastrophic backtracking (ReDoS — Regular Expression Denial of Service).\n *\n * These patterns detect the structural forms that lead to exponential or\n * polynomial backtracking in NFA-based regex engines (V8, PCRE, Java, etc.).\n *\n * Use this context when user-supplied strings will be compiled into RegExp objects.\n */\n\nconst REDOS_PATTERNS = [\n {\n id: 'redos-nested-quantifier-plus',\n description: 'Nested + quantifier inside a group with outer quantifier: (a+)+, (.+b)*, etc.',\n // Matches any group containing a + quantifier, with an outer * or + — catches (a+)+, (.+b)*, etc.\n pattern: /\\([^)]*\\+[^)]*\\)[+*]/,\n },\n {\n id: 'redos-nested-quantifier-star',\n description: 'Nested * quantifier: (a*)* or (a*)+ — catastrophic backtracking',\n pattern: /\\([^)]*\\*[^)]*\\)[*+]/,\n },\n {\n id: 'redos-nested-groups',\n description: 'Doubly nested quantified groups: ((a+)+) — guaranteed catastrophic',\n pattern: /\\(\\([^)]{0,40}\\)[+*]\\)[+*]/,\n },\n {\n id: 'redos-alternation-overlap',\n description: 'Overlapping alternation under quantifier: (a|a)+ — ambiguous NFA paths',\n // Detect repeated identical alternatives under a quantifier\n pattern: /\\(([^|()]{1,20})\\|(?:\\1)(?:\\|[^|()]{1,20}){0,5}\\)[+*?]{1,2}/,\n },\n {\n id: 'redos-star-plus-concat',\n description: '(x*x)+ pattern — triggers super-linear backtracking',\n pattern: /\\([^)]{0,10}\\*[^)]{0,10}\\)[+*]/,\n },\n {\n id: 'redos-dot-star-greedy',\n description: '(.*){n,} or (.+){n,} — repeated greedy dot quantifiers',\n pattern: /\\(\\.[*+]\\)\\{?\\d/,\n },\n {\n id: 'redos-large-repetition',\n description: 'Very large fixed or range repetition count {1000,} or {1000,n} — denial of service via backtracking',\n // Matches { followed by 4+ digits (≥1000), then optional ,digits }\n pattern: /\\{\\d{4,}(?:,\\d*)?\\}/,\n },\n {\n id: 'redos-catastrophic-alternation',\n description: 'Long alternation with many similar branches — polynomial backtracking risk',\n // Heuristic: 10+ pipe-separated alternatives in a single group\n pattern: /\\([^)]{0,200}(?:\\|[^|)]{0,50}){9,}\\)/,\n },\n];\n\nexport default REDOS_PATTERNS;\n","/**\n * NOSQL context patterns.\n *\n * Detects injection vectors specific to NoSQL databases (primarily MongoDB)\n * and JavaScript-evaluated queries.\n *\n * Attack categories:\n * 1. MongoDB query operator injection: $where, $ne, $gt, $regex, $or, $and, etc.\n * These operators, when injected into a JSON query object, can bypass\n * authentication or exfiltrate data without knowing passwords.\n *\n * 2. JavaScript execution: $where clauses execute arbitrary JS server-side.\n *\n * 3. Prototype pollution: __proto__, constructor.prototype — can corrupt\n * the prototype chain of all objects in the Node.js process.\n *\n * Pattern note: MongoDB operators appear as JSON keys. In JSON, keys are\n * quoted: {\"$where\": ...} so the pattern must allow an optional closing\n * quote between the operator name and the colon: /\\$where[\"'\\s]*:/\n */\n\n// Shared suffix: optional closing quote/whitespace before the colon\n// Handles: $op: (bare), \"$op\": (JSON), '$op': (single-quoted)\nconst SEP = /[\"'\\s]*:/;\nconst sep = '[\"\\'\\\\s]*:';\n\nconst NOSQL_PATTERNS = [\n // ─── MongoDB $ operator injection ────────────────────────────────────────\n {\n id: 'nosql-where-operator',\n description: '$where — executes arbitrary JavaScript server-side in MongoDB',\n pattern: new RegExp(`\\\\$where${sep}`, 'i'),\n },\n {\n id: 'nosql-ne-operator',\n description: '$ne — \"not equal\" operator used to bypass equality checks',\n pattern: new RegExp(`\\\\$ne${sep}`, 'i'),\n },\n {\n id: 'nosql-gt-operator',\n description: '$gt — \"greater than\" used to bypass password/value checks',\n pattern: new RegExp(`\\\\$gte?${sep}`, 'i'),\n },\n {\n id: 'nosql-lt-operator',\n description: '$lt / $lte — \"less than\" bypass variants',\n pattern: new RegExp(`\\\\$lte?${sep}`, 'i'),\n },\n {\n id: 'nosql-regex-operator',\n description: '$regex — can be used to extract data character by character (blind injection)',\n pattern: new RegExp(`\\\\$regex${sep}`, 'i'),\n },\n {\n id: 'nosql-or-operator',\n description: '$or — logical OR; used to create always-true conditions',\n pattern: new RegExp(`\\\\$or${sep}\\\\s*\\\\[`, 'i'),\n },\n {\n id: 'nosql-and-operator',\n description: '$and — logical AND operator injection',\n pattern: new RegExp(`\\\\$and${sep}\\\\s*\\\\[`, 'i'),\n },\n {\n id: 'nosql-nor-operator',\n description: '$nor — logical NOR operator injection',\n pattern: new RegExp(`\\\\$nor${sep}\\\\s*\\\\[`, 'i'),\n },\n {\n id: 'nosql-exists-operator',\n description: '$exists — can enumerate fields to determine schema',\n pattern: new RegExp(`\\\\$exists${sep}`, 'i'),\n },\n {\n id: 'nosql-in-operator',\n description: '$in — matches any value in a list; can enumerate values',\n pattern: new RegExp(`\\\\$in${sep}\\\\s*\\\\[`, 'i'),\n },\n {\n id: 'nosql-expr-operator',\n description: '$expr — allows aggregation expressions in queries (MongoDB 3.6+)',\n pattern: new RegExp(`\\\\$expr${sep}`, 'i'),\n },\n {\n id: 'nosql-function-operator',\n description: '$function — executes arbitrary JavaScript in MongoDB 4.4+',\n pattern: new RegExp(`\\\\$function${sep}`, 'i'),\n },\n {\n id: 'nosql-accumulator-operator',\n description: '$accumulator — custom aggregation with arbitrary JS execution',\n pattern: new RegExp(`\\\\$accumulator${sep}`, 'i'),\n },\n // ─── Prototype pollution ─────────────────────────────────────────────────\n {\n id: 'nosql-proto-pollution',\n description: '__proto__ — prototype pollution via object key injection',\n pattern: /__proto__/,\n },\n {\n id: 'nosql-constructor-prototype',\n description: 'constructor.prototype — alternative prototype pollution vector (dot notation or JSON key)',\n // Matches dot-notation (obj.constructor.prototype) and JSON key adjacency\n // (\"constructor\": {\"prototype\": ...})\n pattern: /constructor[\\s\"':.,{\\[]*prototype/i,\n },\n {\n id: 'nosql-proto-bracket',\n description: '[\"__proto__\"] — bracket-notation prototype pollution',\n pattern: /\\[[\"']__proto__[\"']\\]/,\n },\n];\n\nexport default NOSQL_PATTERNS;\n","/**\n * LOG context patterns.\n *\n * Detects injection vectors that are dangerous when a string is written\n * to a log file, passed to a logging framework, or interpolated into\n * a log message that will be parsed or displayed.\n *\n * Attack categories:\n * 1. CRLF injection — injects fake log lines by embedding newlines\n * 2. Log4Shell (CVE-2021-44228) — ${jndi:...} triggers JNDI lookup in Log4j\n * 3. SSTI in log templates — {{...}}, #{...} trigger template evaluation\n * if the log message is passed through a template engine\n * 4. Null byte injection — truncates log entries in some implementations\n * 5. ANSI escape injection — manipulates terminal output when logs are\n * tailed in a terminal (colour codes, cursor movement, etc.)\n *\n * Note: Newline characters (\\n, \\r) will produce false positives for\n * multi-line legitimate values. Use this context only for single-line\n * log field values (usernames, IDs, request parameters, etc.).\n */\n\nconst LOG_PATTERNS = [\n // ─── CRLF / newline injection ─────────────────────────────────────────────\n {\n id: 'log-crlf-injection',\n description: 'CRLF injection: literal \\\\r or \\\\n embeds fake log lines',\n pattern: /[\\r\\n]/,\n },\n {\n id: 'log-url-encoded-crlf',\n description: 'URL-encoded CRLF: %0d, %0a, %0D, %0A — decoded by some log parsers',\n pattern: /%0[dDaA]/,\n },\n {\n id: 'log-unicode-newline',\n description: 'Unicode newline variants: U+2028 (line separator), U+2029 (paragraph separator)',\n pattern: /[\\u2028\\u2029]/,\n },\n\n // ─── Log4Shell / JNDI injection (CVE-2021-44228) ─────────────────────────\n {\n id: 'log-log4shell-jndi',\n description: 'Log4Shell: ${jndi:...} triggers remote code execution in Apache Log4j',\n pattern: /\\$\\{jndi\\s*:/i,\n },\n {\n id: 'log-log4shell-obfuscated',\n description: 'Obfuscated Log4Shell: ${::-j}... lookup-bypass prefix used to evade WAF detection',\n // ${::- is the Log4j lookup-bypass escape sequence; presence alone is suspicious\n pattern: /\\$\\{::-/,\n },\n {\n id: 'log-log4j-lookup',\n description: 'Log4j lookup syntax: ${env:...}, ${sys:...}, ${ctx:...} — data exfiltration',\n pattern: /\\$\\{(?:env|sys|ctx|main|map|sd|web|docker|k8s|spring)\\s*:/i,\n },\n\n // ─── Server-Side Template Injection (SSTI) in log messages ───────────────\n {\n id: 'log-ssti-double-brace',\n description: 'SSTI double-brace: {{expression}} — Jinja2, Twig, Handlebars, etc.',\n pattern: /\\{\\{[\\s\\S]{0,80}\\}\\}/,\n },\n {\n id: 'log-ssti-hash-brace',\n description: 'SSTI hash-brace: #{expression} — Thymeleaf, Velocity, Ruby ERB',\n pattern: /#\\{[\\s\\S]{0,80}\\}/,\n },\n {\n id: 'log-ssti-dollar-brace',\n description: 'SSTI/EL injection: ${expression with operators or method calls} — JSP EL, Freemarker, SpEL',\n // Require that the ${...} content looks like an expression, not a plain variable name.\n // Flags if the content contains: . ( * + operators, or known SSTI keywords.\n // This avoids flagging ${PATH}, ${HOME} etc. (plain shell variables).\n pattern: /\\$\\{[^}]*(?:\\.|\\(|\\*|\\+|\\bclass\\b|\\bruntime\\b|\\bprocess\\b|\\bexec\\b)[^}]{0,80}\\}/i,\n },\n {\n id: 'log-ssti-percent-tag',\n description: 'SSTI ERB/ASP tag: <%= expression %> — Ruby ERB, ASP',\n pattern: /<%=[\\s\\S]{0,80}%>/,\n },\n\n // ─── Null byte ────────────────────────────────────────────────────────────\n {\n id: 'log-null-byte',\n description: 'Null byte: \\\\x00 or %00 — can truncate log entries in C-backed loggers',\n pattern: /\\x00|%00/,\n },\n\n // ─── ANSI escape injection ────────────────────────────────────────────────\n {\n id: 'log-ansi-escape',\n description: 'ANSI escape sequence: ESC[ — can manipulate terminal output when logs are tailed',\n pattern: /\\x1b\\[/,\n },\n];\n\nexport default LOG_PATTERNS;\n","/**\n * SQL-STRICT context patterns.\n *\n * Extends the base 'SQL' context with three additional rules that are\n * effective at detecting real injections but carry a higher false-positive\n * risk on general free-text input.\n *\n * Use 'SQL-STRICT' when:\n * - The string is specifically a SQL fragment or database identifier\n * - You control the input domain (e.g. a dedicated SQL search field)\n * - You can tolerate occasional false positives in exchange for broader coverage\n *\n * Use 'SQL' (not STRICT) when:\n * - The field is general user text (names, descriptions, comments)\n * - False positives would block legitimate content (e.g. \"see note -- above\")\n *\n * Rules moved here from 'SQL' due to false-positive risk:\n *\n * sql-line-comment — \"--\" fires on \"see note -- above\", \"value--\", CSS var(--primary)\n * sql-stacked-query — \"; SELECT\" fires on legitimate prose with semicolons + SQL words\n * sql-hex-encoding — \"0xDEAD\" fires on hex values in technical docs and log output\n */\n\nimport SQL_PATTERNS from './sql.js';\n\nconst SQL_STRICT_EXTRA = [\n {\n id: 'sql-line-comment',\n description: 'SQL line comment: -- followed by whitespace or end of string',\n pattern: /--(?:\\s|$)/,\n },\n {\n id: 'sql-stacked-query',\n description: 'Stacked queries: semicolon immediately followed by a SQL keyword',\n pattern: /;\\s{0,10}(?:SELECT|INSERT|UPDATE|DELETE|DROP|CREATE|ALTER|EXEC)\\b/i,\n },\n {\n id: 'sql-hex-encoding',\n description: 'Hex-encoded string injection: 0x41414141 style (MySQL)',\n pattern: /\\b0x[0-9a-f]{4,}/i,\n },\n];\n\n// SQL-STRICT = all base SQL rules + the three noisy extras\nconst SQL_STRICT_PATTERNS = [...SQL_PATTERNS, ...SQL_STRICT_EXTRA];\n\nexport default SQL_STRICT_PATTERNS;\n","/**\n * is-unsafe v2\n *\n * Zero-dependency, DOM-free, pure predicate for detecting unsafe strings\n * across HTML, XML, SVG, SQL, SQL-STRICT, SHELL, REDOS, NOSQL, and LOG contexts.\n *\n * v2 change: contexts are imported as named pattern arrays rather than resolved\n * via a string-keyed registry. This makes each context independently\n * tree-shakeable — bundlers can drop any context you never import.\n *\n * @module is-unsafe\n */\n\n// ─── Context pattern arrays (named exports) ────────────────────────────────\n// Import only the ones you need. Each is independently tree-shakeable.\n\nexport { default as HTML } from './contexts/html.js';\nexport { default as XML } from './contexts/xml.js';\nexport { default as SVG } from './contexts/svg.js';\nexport { default as SQL } from './contexts/sql.js';\nexport { default as SHELL } from './contexts/shell.js';\nexport { default as REDOS } from './contexts/redos.js';\nexport { default as NOSQL } from './contexts/nosql.js';\nexport { default as LOG } from './contexts/log.js';\n\n// SQL-STRICT needs a quoted identifier because of the hyphen\nimport SQL_STRICT from './contexts/sql-strict.js';\nexport { SQL_STRICT };\n\n// ─── VALID_CONTEXTS convenience re-export ─────────────────────────────────\n// Importing this pulls in ALL contexts. Use it only when you need all of them\n// (e.g. for validation UI, tooling, or exhaustive audits).\n// If you only need a subset, import the named contexts directly instead.\n\nimport HTML from './contexts/html.js';\nimport XML from './contexts/xml.js';\nimport SVG from './contexts/svg.js';\nimport SQL from './contexts/sql.js';\nimport SHELL from './contexts/shell.js';\nimport REDOS from './contexts/redos.js';\nimport NOSQL from './contexts/nosql.js';\nimport LOG from './contexts/log.js';\n\n// ─── Attach labels to named contexts ──────────────────────────────────────\n// Each built-in PatternList carries its canonical name so matchList can read\n// list.label directly — no registry lookup needed at match time.\n// Custom PatternLists default to 'CUSTOM' unless the caller sets list.label.\n\nHTML.label = 'HTML';\nXML.label = 'XML';\nSVG.label = 'SVG';\nSQL.label = 'SQL';\nSQL_STRICT.label = 'SQL-STRICT';\nSHELL.label = 'SHELL';\nREDOS.label = 'REDOS';\nNOSQL.label = 'NOSQL';\nLOG.label = 'LOG';\n\nexport const VALID_CONTEXTS = Object.freeze({\n HTML,\n XML,\n SVG,\n SQL,\n 'SQL-STRICT': SQL_STRICT,\n SHELL,\n REDOS,\n NOSQL,\n LOG,\n});\n\n// ─── Types ────────────────────────────────────────────────────────────────\n\n/**\n * @typedef {{ id: string, description: string, pattern: RegExp }} Rule\n */\n\n/**\n * @typedef {Rule[]} PatternList\n */\n\n/**\n * @typedef {Object} MatchResult\n * @property {string} context - Label identifying which context matched ('HTML', 'CUSTOM', etc.)\n * @property {string} id - Rule identifier\n * @property {string} description - Human-readable description of what was matched\n * @property {RegExp} pattern - The pattern that matched\n */\n\n// ─── Internal helpers ──────────────────────────────────────────────────────\n\n/**\n * @param {unknown} value\n */\nfunction assertString(value) {\n if (typeof value !== 'string') {\n throw new TypeError(\n `is-unsafe: first argument must be a string, got ${typeof value}`\n );\n }\n}\n\n/**\n * @param {unknown} context\n */\nfunction assertContext(context) {\n if (context instanceof RegExp) return;\n\n if (Array.isArray(context)) {\n if (context.length === 0) {\n throw new TypeError('is-unsafe: context must not be an empty array');\n }\n // Detect array-of-arrays vs flat pattern list\n if (Array.isArray(context[0])) {\n // Array of PatternLists\n for (const list of context) {\n if (!Array.isArray(list) || list.length === 0) {\n throw new TypeError(\n 'is-unsafe: each context in the array must be a non-empty pattern array (PatternList)'\n );\n }\n }\n }\n // else: flat PatternList — trust it, no deep validation needed\n return;\n }\n\n throw new TypeError(\n `is-unsafe: second argument must be a PatternList (e.g. HTML), ` +\n `an array of PatternLists (e.g. [HTML, XML]), or a RegExp. Got: ${typeof context}`\n );\n}\n\n/**\n * Normalise any valid context arg into an array of PatternLists.\n *\n * @param {Rule[]|Rule[][]|RegExp} context\n * @returns {{ lists: Rule[][]|null, regex: RegExp|null }}\n */\nfunction normalise(context) {\n if (context instanceof RegExp) return { lists: null, regex: context };\n // Distinguish PatternList (array of rule objects) from array of PatternLists\n if (Array.isArray(context[0])) return { lists: context, regex: null };\n return { lists: [context], regex: null };\n}\n\n/**\n * Test value against a single PatternList. Returns the first MatchResult or null.\n *\n * @param {string} value\n * @param {Rule[]} list\n * @returns {MatchResult|null}\n */\nfunction matchList(value, list) {\n const label = list.label ?? 'CUSTOM';\n for (const rule of list) {\n if (rule.pattern.test(value)) {\n return { context: label, id: rule.id, description: rule.description, pattern: rule.pattern };\n }\n }\n return null;\n}\n\n// ─── Public API ───────────────────────────────────────────────────────────\n\n/**\n * Returns `true` if `value` is unsafe in the given context(s), `false` otherwise.\n *\n * @param {string} value - The string to test\n * @param {PatternList | PatternList[] | RegExp} context\n * - A PatternList imported from is-unsafe (e.g. `HTML`, `XML`)\n * - An array of PatternLists — returns true if unsafe in **any** of them\n * - A custom RegExp — returns true if the pattern matches\n * @returns {boolean}\n *\n * @example\n * import { isUnsafe, HTML, SQL } from 'is-unsafe';\n *\n * isUnsafe('<script>alert(1)</script>', HTML) // true\n * isUnsafe('hello world', HTML) // false\n * isUnsafe('value', [HTML, SQL]) // false\n * isUnsafe('value', /my-pattern/i) // false\n */\nfunction isUnsafe(value, context) {\n assertString(value);\n assertContext(context);\n\n const { lists, regex } = normalise(context);\n\n if (regex) return regex.test(value);\n\n for (const list of lists) {\n if (matchList(value, list) !== null) return true;\n }\n return false;\n}\n\n/**\n * Like `isUnsafe`, but returns the first `MatchResult` describing **why**\n * the value was flagged, or `null` if it is safe.\n *\n * @param {string} value\n * @param {PatternList | PatternList[] | RegExp} context\n * @returns {MatchResult|null}\n *\n * @example\n * import { whyUnsafe, HTML } from 'is-unsafe';\n *\n * whyUnsafe('<script>alert(1)</script>', HTML)\n * // { context: 'HTML', id: 'html-script-open', description: '...', pattern: /.../ }\n */\nfunction whyUnsafe(value, context) {\n assertString(value);\n assertContext(context);\n\n const { lists, regex } = normalise(context);\n\n if (regex) {\n return regex.test(value)\n ? { context: 'CUSTOM', id: 'custom-regex', description: 'Matched caller-supplied pattern', pattern: regex }\n : null;\n }\n\n for (const list of lists) {\n const result = matchList(value, list);\n if (result !== null) return result;\n }\n return null;\n}\n\n/**\n * Returns **all** matching rules across the given context(s), or an empty\n * array if the value is safe. Useful for comprehensive auditing.\n *\n * @param {string} value\n * @param {PatternList | PatternList[] | RegExp} context\n * @returns {MatchResult[]}\n */\nfunction allUnsafe(value, context) {\n assertString(value);\n assertContext(context);\n\n const { lists, regex } = normalise(context);\n const results = [];\n\n if (regex) {\n if (regex.test(value)) {\n results.push({ context: 'CUSTOM', id: 'custom-regex', description: 'Matched caller-supplied pattern', pattern: regex });\n }\n return results;\n }\n\n for (const list of lists) {\n const label = list.label ?? 'CUSTOM';\n for (const rule of list) {\n if (rule.pattern.test(value)) {\n results.push({ context: label, id: rule.id, description: rule.description, pattern: rule.pattern });\n }\n }\n }\n\n return results;\n}\n\nexport { isUnsafe, whyUnsafe, allUnsafe };\nexport default isUnsafe;\n","'use strict';\n///@ts-check\n\nimport { getAllMatches, isExist, DANGEROUS_PROPERTY_NAMES, criticalProperties } from '../util.js';\nimport xmlNode from './xmlNode.js';\nimport DocTypeReader from './DocTypeReader.js';\nimport toNumber from \"strnum\";\nimport getIgnoreAttributesFn from \"../ignoreAttributes.js\";\nimport { Expression, Matcher } from 'path-expression-matcher';\nimport { ExpressionSet } from 'path-expression-matcher';\nimport { EntityDecoder, XML, CURRENCY, COMMON_HTML, ENTITY_ACTION } from '@nodable/entities';\nimport { isUnsafe, HTML as HTML_CONTEXT, XML as XML_CONTEXT } from \"is-unsafe\"\n\n\n// const regx =\n// '<((!\\\\[CDATA\\\\[([\\\\s\\\\S]*?)(]]>))|((NAME:)?(NAME))([^>]*)>|((\\\\/)(NAME)\\\\s*>))([^<]*)'\n// .replace(/NAME/g, util.nameRegexp);\n\n//const tagsRegx = new RegExp(\"<(\\\\/?[\\\\w:\\\\-\\._]+)([^>]*)>(\\\\s*\"+cdataRegx+\")*([^<]+)?\",\"g\");\n//const tagsRegx = new RegExp(\"<(\\\\/?)((\\\\w*:)?([\\\\w:\\\\-\\._]+))([^>]*)>([^<]*)(\"+cdataRegx+\"([^<]*))*([^<]+)?\",\"g\");\n\n// Helper functions for attribute and namespace handling\n\n/**\n * Extract raw attributes (without prefix) from prefixed attribute map\n * @param {object} prefixedAttrs - Attributes with prefix from buildAttributesMap\n * @param {object} options - Parser options containing attributeNamePrefix\n * @returns {object} Raw attributes for matcher\n */\nfunction extractRawAttributes(prefixedAttrs, options) {\n if (!prefixedAttrs) return {};\n\n // Handle attributesGroupName option\n const attrs = options.attributesGroupName\n ? prefixedAttrs[options.attributesGroupName]\n : prefixedAttrs;\n\n if (!attrs) return {};\n\n const rawAttrs = {};\n for (const key in attrs) {\n // Remove the attribute prefix to get raw name\n if (key.startsWith(options.attributeNamePrefix)) {\n const rawName = key.substring(options.attributeNamePrefix.length);\n rawAttrs[rawName] = attrs[key];\n } else {\n // Attribute without prefix (shouldn't normally happen, but be safe)\n rawAttrs[key] = attrs[key];\n }\n }\n return rawAttrs;\n}\n\n/**\n * Extract namespace from raw tag name\n * @param {string} rawTagName - Tag name possibly with namespace (e.g., \"soap:Envelope\")\n * @returns {string|undefined} Namespace or undefined\n */\nfunction extractNamespace(rawTagName) {\n if (!rawTagName || typeof rawTagName !== 'string') return undefined;\n\n const colonIndex = rawTagName.indexOf(':');\n if (colonIndex !== -1 && colonIndex > 0) {\n const ns = rawTagName.substring(0, colonIndex);\n // Don't treat xmlns as a namespace\n if (ns !== 'xmlns') {\n return ns;\n }\n }\n return undefined;\n}\n\nexport default class OrderedObjParser {\n constructor(options, externalEntities) {\n this.options = options;\n this.currentNode = null;\n this.tagsNodeStack = [];\n this.parseXml = parseXml;\n this.parseTextData = parseTextData;\n this.resolveNameSpace = resolveNameSpace;\n this.buildAttributesMap = buildAttributesMap;\n this.isItStopNode = isItStopNode;\n this.replaceEntitiesValue = replaceEntitiesValue;\n this.readStopNodeData = readStopNodeData;\n this.saveTextToParentTag = saveTextToParentTag;\n this.addChild = addChild;\n this.ignoreAttributesFn = getIgnoreAttributesFn(this.options.ignoreAttributes)\n this.entityExpansionCount = 0;\n this.currentExpandedLength = 0;\n this.doctypefound = false;\n let namedEntities = { ...XML };\n if (this.options.entityDecoder) {\n this.entityDecoder = this.options.entityDecoder\n } else {\n if (typeof this.options.htmlEntities === \"object\") namedEntities = this.options.htmlEntities;\n else if (this.options.htmlEntities === true) namedEntities = { ...COMMON_HTML, ...CURRENCY };\n this.entityDecoder = new EntityDecoder({\n namedEntities: { ...namedEntities, ...externalEntities },\n numericAllowed: this.options.htmlEntities,\n limit: {\n maxTotalExpansions: this.options.processEntities.maxTotalExpansions,\n maxExpandedLength: this.options.processEntities.maxExpandedLength,\n applyLimitsTo: this.options.processEntities.appliesTo,\n },\n // onExternalEntity: (name, value) => isUnsafe(value) ? 'block' : 'allow',\n onInputEntity: (name, value) =>\n //TODO: VALID_CONTEXTS.HTML should be set only if this.options.htmlEntities\n isUnsafe(value, [HTML_CONTEXT, XML_CONTEXT]) ? ENTITY_ACTION.BLOCK : ENTITY_ACTION.ALLOW,\n\n //postCheck: resolved => resolved\n });\n }\n\n // Initialize path matcher for path-expression-matcher\n this.matcher = new Matcher();\n this.readonlyMatcher = this.matcher.readOnly();\n\n // Flag to track if current node is a stop node (optimization)\n this.isCurrentNodeStopNode = false;\n\n // Pre-compile stopNodes expressions\n this.stopNodeExpressionsSet = new ExpressionSet();\n const stopNodesOpts = this.options.stopNodes;\n if (stopNodesOpts && stopNodesOpts.length > 0) {\n for (let i = 0; i < stopNodesOpts.length; i++) {\n const stopNodeExp = stopNodesOpts[i];\n if (typeof stopNodeExp === 'string') {\n // Convert string to Expression object\n this.stopNodeExpressionsSet.add(new Expression(stopNodeExp));\n } else if (stopNodeExp instanceof Expression) {\n // Already an Expression object\n this.stopNodeExpressionsSet.add(stopNodeExp);\n }\n }\n this.stopNodeExpressionsSet.seal();\n }\n }\n\n}\n\n\n/**\n * @param {string} val\n * @param {string} tagName\n * @param {string|Matcher} jPath - jPath string or Matcher instance based on options.jPath\n * @param {boolean} dontTrim\n * @param {boolean} hasAttributes\n * @param {boolean} isLeafNode\n * @param {boolean} escapeEntities\n */\nfunction parseTextData(val, tagName, jPath, dontTrim, hasAttributes, isLeafNode, escapeEntities) {\n const options = this.options;\n if (val !== undefined) {\n if (options.trimValues && !dontTrim) {\n val = val.trim();\n }\n if (val.length > 0) {\n if (!escapeEntities) val = this.replaceEntitiesValue(val, tagName, jPath);\n\n // Pass jPath string or matcher based on options.jPath setting\n const jPathOrMatcher = options.jPath ? jPath.toString() : jPath;\n const newval = options.tagValueProcessor(tagName, val, jPathOrMatcher, hasAttributes, isLeafNode);\n if (newval === null || newval === undefined) {\n //don't parse\n return val;\n } else if (typeof newval !== typeof val || newval !== val) {\n //overwrite\n return newval;\n } else if (options.trimValues) {\n return parseValue(val, options.parseTagValue, options.numberParseOptions);\n } else {\n const trimmedVal = val.trim();\n if (trimmedVal === val) {\n return parseValue(val, options.parseTagValue, options.numberParseOptions);\n } else {\n return val;\n }\n }\n }\n }\n}\n\nfunction resolveNameSpace(tagname) {\n if (this.options.removeNSPrefix) {\n const tags = tagname.split(':');\n const prefix = tagname.charAt(0) === '/' ? '/' : '';\n if (tags[0] === 'xmlns') {\n return '';\n }\n if (tags.length === 2) {\n tagname = prefix + tags[1];\n }\n }\n return tagname;\n}\n\n//TODO: change regex to capture NS\n//const attrsRegx = new RegExp(\"([\\\\w\\\\-\\\\.\\\\:]+)\\\\s*=\\\\s*(['\\\"])((.|\\n)*?)\\\\2\",\"gm\");\nconst attrsRegx = new RegExp('([^\\\\s=]+)\\\\s*(=\\\\s*([\\'\"])([\\\\s\\\\S]*?)\\\\3)?', 'gm');\n\nfunction buildAttributesMap(attrStr, jPath, tagName, force = false) {\n const options = this.options;\n if (force === true || (options.ignoreAttributes !== true && typeof attrStr === 'string')) {\n // attrStr = attrStr.replace(/\\r?\\n/g, ' ');\n //attrStr = attrStr || attrStr.trim();\n\n const matches = getAllMatches(attrStr, attrsRegx);\n const len = matches.length; //don't make it inline\n const attrs = {};\n\n // Pre-process values once: trim + entity replacement\n // Reused in both matcher update and second pass\n const processedVals = new Array(len);\n let hasRawAttrs = false;\n const rawAttrsForMatcher = {};\n\n for (let i = 0; i < len; i++) {\n const attrName = this.resolveNameSpace(matches[i][1]);\n const oldVal = matches[i][4];\n\n if (attrName.length && oldVal !== undefined) {\n let val = oldVal;\n if (options.trimValues) val = val.trim();\n val = this.replaceEntitiesValue(val, tagName, this.readonlyMatcher);\n processedVals[i] = val;\n\n rawAttrsForMatcher[attrName] = val;\n hasRawAttrs = true;\n }\n }\n\n // Update matcher ONCE before second pass, if applicable\n if (hasRawAttrs && typeof jPath === 'object' && jPath.updateCurrent) {\n jPath.updateCurrent(rawAttrsForMatcher);\n }\n\n // Hoist toString() once — path doesn't change during attribute processing\n const jPathStr = options.jPath ? jPath.toString() : this.readonlyMatcher;\n\n // Second pass: apply processors, build final attrs\n let hasAttrs = false;\n for (let i = 0; i < len; i++) {\n const attrName = this.resolveNameSpace(matches[i][1]);\n\n if (this.ignoreAttributesFn(attrName, jPathStr)) continue;\n\n let aName = options.attributeNamePrefix + attrName;\n\n if (attrName.length) {\n if (options.transformAttributeName) {\n aName = options.transformAttributeName(aName);\n }\n aName = sanitizeName(aName, options);\n\n if (matches[i][4] !== undefined) {\n // Reuse already-processed value — no double entity replacement\n const oldVal = processedVals[i];\n\n const newVal = options.attributeValueProcessor(attrName, oldVal, jPathStr);\n if (newVal === null || newVal === undefined) {\n attrs[aName] = oldVal;\n } else if (typeof newVal !== typeof oldVal || newVal !== oldVal) {\n attrs[aName] = newVal;\n } else {\n attrs[aName] = parseValue(oldVal, options.parseAttributeValue, options.numberParseOptions);\n }\n hasAttrs = true;\n } else if (options.allowBooleanAttributes) {\n attrs[aName] = true;\n hasAttrs = true;\n }\n }\n }\n\n if (!hasAttrs) return;\n\n if (options.attributesGroupName && !options.preserveOrder) {\n const attrCollection = {};\n attrCollection[options.attributesGroupName] = attrs;\n return attrCollection;\n }\n return attrs;\n }\n}\nconst parseXml = function (xmlData) {\n xmlData = xmlData.replace(/\\r\\n?/g, \"\\n\"); //TODO: remove this line\n const xmlObj = new xmlNode('!xml');\n let currentNode = xmlObj;\n let textData = \"\";\n\n // Reset matcher for new document\n this.matcher.reset();\n this.entityDecoder.reset();\n\n // Reset entity expansion counters for this document\n this.entityExpansionCount = 0;\n this.currentExpandedLength = 0;\n this.doctypefound = false;\n const options = this.options;\n const docTypeReader = new DocTypeReader(options.processEntities);\n const xmlLen = xmlData.length;\n for (let i = 0; i < xmlLen; i++) {//for each char in XML data\n const ch = xmlData[i];\n if (ch === '<') {\n // const nextIndex = i+1;\n // const _2ndChar = xmlData[nextIndex];\n const c1 = xmlData.charCodeAt(i + 1);\n if (c1 === 47) {//Closing Tag '/'\n const closeIndex = findClosingIndex(xmlData, \">\", i, \"Closing Tag is not closed.\")\n let tagName = xmlData.substring(i + 2, closeIndex).trim();\n\n if (options.removeNSPrefix) {\n const colonIndex = tagName.indexOf(\":\");\n if (colonIndex !== -1) {\n tagName = tagName.substr(colonIndex + 1);\n }\n }\n\n tagName = transformTagName(options.transformTagName, tagName, \"\", options).tagName;\n\n if (currentNode) {\n textData = this.saveTextToParentTag(textData, currentNode, this.readonlyMatcher);\n }\n\n //check if last tag of nested tag was unpaired tag\n const lastTagName = this.matcher.getCurrentTag();\n if (tagName && options.unpairedTagsSet.has(tagName)) {\n throw new Error(`Unpaired tag can not be used as closing tag: </${tagName}>`);\n }\n if (lastTagName && options.unpairedTagsSet.has(lastTagName)) {\n // Pop the unpaired tag\n this.matcher.pop();\n this.tagsNodeStack.pop();\n }\n // Pop the closing tag\n this.matcher.pop();\n this.isCurrentNodeStopNode = false; // Reset flag when closing tag\n\n currentNode = this.tagsNodeStack.pop();//avoid recursion, set the parent tag scope\n textData = \"\";\n i = closeIndex;\n } else if (c1 === 63) { //'?'\n\n let tagData = readTagExp(xmlData, i, false, \"?>\");\n if (!tagData) throw new Error(\"Pi Tag is not closed.\");\n\n textData = this.saveTextToParentTag(textData, currentNode, this.readonlyMatcher);\n const attsMap = this.buildAttributesMap(tagData.tagExp, this.matcher, tagData.tagName, true);\n if (attsMap) {\n const ver = attsMap[this.options.attributeNamePrefix + \"version\"];\n this.entityDecoder.setXmlVersion(Number(ver) || 1.0);\n docTypeReader.setXmlVersion(Number(ver) || 1.0);\n }\n if ((options.ignoreDeclaration && tagData.tagName === \"?xml\") || options.ignorePiTags) {\n //do nothing\n } else {\n\n const childNode = new xmlNode(tagData.tagName);\n childNode.add(options.textNodeName, \"\");\n\n if (tagData.tagName !== tagData.tagExp && tagData.attrExpPresent && options.ignoreAttributes !== true) {\n childNode[\":@\"] = attsMap\n }\n this.addChild(currentNode, childNode, this.readonlyMatcher, i);\n }\n\n\n i = tagData.closeIndex + 1;\n } else if (c1 === 33\n && xmlData.charCodeAt(i + 2) === 45\n && xmlData.charCodeAt(i + 3) === 45) { //'!--'\n const endIndex = findClosingIndex(xmlData, \"-->\", i + 4, \"Comment is not closed.\")\n if (options.commentPropName) {\n const comment = xmlData.substring(i + 4, endIndex - 2);\n\n textData = this.saveTextToParentTag(textData, currentNode, this.readonlyMatcher);\n\n currentNode.add(options.commentPropName, [{ [options.textNodeName]: comment }]);\n }\n i = endIndex;\n } else if (c1 === 33\n && xmlData.charCodeAt(i + 2) === 68) { //'!D'\n if (this.doctypefound) throw new Error(\"Multiple DOCTYPE declarations found.\");\n this.doctypefound = true;\n const result = docTypeReader.readDocType(xmlData, i);\n this.entityDecoder.addInputEntities(result.entities);\n i = result.i;\n } else if (c1 === 33\n && xmlData.charCodeAt(i + 2) === 91) { // '!['\n const closeIndex = findClosingIndex(xmlData, \"]]>\", i, \"CDATA is not closed.\") - 2;\n const tagExp = xmlData.substring(i + 9, closeIndex);\n\n textData = this.saveTextToParentTag(textData, currentNode, this.readonlyMatcher);\n\n let val = this.parseTextData(tagExp, currentNode.tagname, this.readonlyMatcher, true, false, true, true);\n if (val == undefined) val = \"\";\n\n //cdata should be set even if it is 0 length string\n if (options.cdataPropName) {\n currentNode.add(options.cdataPropName, [{ [options.textNodeName]: tagExp }]);\n } else {\n currentNode.add(options.textNodeName, val);\n }\n\n i = closeIndex + 2;\n } else {//Opening tag\n let result = readTagExp(xmlData, i, options.removeNSPrefix);\n\n // Safety check: readTagExp can return undefined\n if (!result) {\n // Log context for debugging\n const context = xmlData.substring(Math.max(0, i - 50), Math.min(xmlLen, i + 50));\n throw new Error(`readTagExp returned undefined at position ${i}. Context: \"${context}\"`);\n }\n\n let tagName = result.tagName;\n const rawTagName = result.rawTagName;\n let tagExp = result.tagExp;\n let attrExpPresent = result.attrExpPresent;\n let closeIndex = result.closeIndex;\n\n ({ tagName, tagExp } = transformTagName(options.transformTagName, tagName, tagExp, options));\n\n if (options.strictReservedNames &&\n (tagName === options.commentPropName\n || tagName === options.cdataPropName\n || tagName === options.textNodeName\n || tagName === options.attributesGroupName\n )) {\n throw new Error(`Invalid tag name: ${tagName}`);\n }\n\n //save text as child node\n if (currentNode && textData) {\n if (currentNode.tagname !== '!xml') {\n //when nested tag is found\n textData = this.saveTextToParentTag(textData, currentNode, this.readonlyMatcher, false);\n }\n }\n\n //check if last tag was unpaired tag\n const lastTag = currentNode;\n if (lastTag && options.unpairedTagsSet.has(lastTag.tagname)) {\n currentNode = this.tagsNodeStack.pop();\n this.matcher.pop();\n }\n\n // Clean up self-closing syntax BEFORE processing attributes\n // This is where tagExp gets the trailing / removed\n let isSelfClosing = false;\n if (tagExp.length > 0 && tagExp.lastIndexOf(\"/\") === tagExp.length - 1) {\n isSelfClosing = true;\n if (tagName[tagName.length - 1] === \"/\") {\n tagName = tagName.substr(0, tagName.length - 1);\n tagExp = tagName;\n } else {\n tagExp = tagExp.substr(0, tagExp.length - 1);\n }\n\n // Re-check attrExpPresent after cleaning\n attrExpPresent = (tagName !== tagExp);\n }\n\n // Now process attributes with CLEAN tagExp (no trailing /)\n let prefixedAttrs = null;\n let rawAttrs = {};\n let namespace = undefined;\n\n // Extract namespace from rawTagName\n namespace = extractNamespace(rawTagName);\n\n // Push tag to matcher FIRST (with empty attrs for now) so callbacks see correct path\n if (tagName !== xmlObj.tagname) {\n this.matcher.push(tagName, {}, namespace);\n }\n\n // Now build attributes - callbacks will see correct matcher state\n if (tagName !== tagExp && attrExpPresent) {\n // Build attributes (returns prefixed attributes for the tree)\n // Note: buildAttributesMap now internally updates the matcher with raw attributes\n prefixedAttrs = this.buildAttributesMap(tagExp, this.matcher, tagName);\n\n if (prefixedAttrs) {\n // Extract raw attributes (without prefix) for our use\n //TODO: seems a performance overhead\n rawAttrs = extractRawAttributes(prefixedAttrs, options);\n }\n }\n\n // Now check if this is a stop node (after attributes are set)\n if (tagName !== xmlObj.tagname) {\n this.isCurrentNodeStopNode = this.isItStopNode();\n }\n\n const startIndex = i;\n if (this.isCurrentNodeStopNode) {\n let tagContent = \"\";\n\n // For self-closing tags, content is empty\n if (isSelfClosing) {\n i = result.closeIndex;\n }\n //unpaired tag\n else if (options.unpairedTagsSet.has(tagName)) {\n i = result.closeIndex;\n }\n //normal tag\n else {\n //read until closing tag is found\n const result = this.readStopNodeData(xmlData, rawTagName, closeIndex + 1);\n if (!result) throw new Error(`Unexpected end of ${rawTagName}`);\n i = result.i;\n tagContent = result.tagContent;\n }\n\n const childNode = new xmlNode(tagName);\n\n if (prefixedAttrs) {\n childNode[\":@\"] = prefixedAttrs;\n }\n\n // For stop nodes, store raw content as-is without any processing\n childNode.add(options.textNodeName, tagContent);\n\n this.matcher.pop(); // Pop the stop node tag\n this.isCurrentNodeStopNode = false; // Reset flag\n\n this.addChild(currentNode, childNode, this.readonlyMatcher, startIndex);\n } else {\n //selfClosing tag\n if (isSelfClosing) {\n ({ tagName, tagExp } = transformTagName(options.transformTagName, tagName, tagExp, options));\n\n const childNode = new xmlNode(tagName);\n if (prefixedAttrs) {\n childNode[\":@\"] = prefixedAttrs;\n }\n this.addChild(currentNode, childNode, this.readonlyMatcher, startIndex);\n this.matcher.pop(); // Pop self-closing tag\n this.isCurrentNodeStopNode = false; // Reset flag\n }\n else if (options.unpairedTagsSet.has(tagName)) {//unpaired tag\n const childNode = new xmlNode(tagName);\n if (prefixedAttrs) {\n childNode[\":@\"] = prefixedAttrs;\n }\n this.addChild(currentNode, childNode, this.readonlyMatcher, startIndex);\n this.matcher.pop(); // Pop unpaired tag\n this.isCurrentNodeStopNode = false; // Reset flag\n i = result.closeIndex;\n // Continue to next iteration without changing currentNode\n continue;\n }\n //opening tag\n else {\n const childNode = new xmlNode(tagName);\n if (this.tagsNodeStack.length > options.maxNestedTags) {\n throw new Error(\"Maximum nested tags exceeded\");\n }\n this.tagsNodeStack.push(currentNode);\n\n if (prefixedAttrs) {\n childNode[\":@\"] = prefixedAttrs;\n }\n this.addChild(currentNode, childNode, this.readonlyMatcher, startIndex);\n currentNode = childNode;\n }\n textData = \"\";\n i = closeIndex;\n }\n }\n } else {\n textData += xmlData[i];\n }\n }\n return xmlObj.child;\n}\n\nfunction addChild(currentNode, childNode, matcher, startIndex) {\n // unset startIndex if not requested\n if (!this.options.captureMetaData) startIndex = undefined;\n\n // Pass jPath string or matcher based on options.jPath setting\n const jPathOrMatcher = this.options.jPath ? matcher.toString() : matcher;\n const result = this.options.updateTag(childNode.tagname, jPathOrMatcher, childNode[\":@\"])\n if (result === false) {\n //do nothing\n } else if (typeof result === \"string\") {\n childNode.tagname = result\n currentNode.addChild(childNode, startIndex);\n } else {\n currentNode.addChild(childNode, startIndex);\n }\n}\n\n/**\n * @param {object} val - Entity object with regex and val properties\n * @param {string} tagName - Tag name\n * @param {string|Matcher} jPath - jPath string or Matcher instance based on options.jPath\n */\nfunction replaceEntitiesValue(val, tagName, jPath) {\n const entityConfig = this.options.processEntities;\n\n if (!entityConfig || !entityConfig.enabled) {\n return val;\n }\n\n // Check if tag is allowed to contain entities\n if (entityConfig.allowedTags) {\n const jPathOrMatcher = this.options.jPath ? jPath.toString() : jPath;\n const allowed = Array.isArray(entityConfig.allowedTags)\n ? entityConfig.allowedTags.includes(tagName)\n : entityConfig.allowedTags(tagName, jPathOrMatcher);\n\n if (!allowed) {\n return val;\n }\n }\n\n // Apply custom tag filter if provided\n if (entityConfig.tagFilter) {\n const jPathOrMatcher = this.options.jPath ? jPath.toString() : jPath;\n if (!entityConfig.tagFilter(tagName, jPathOrMatcher)) {\n return val; // Skip based on custom filter\n }\n }\n\n return this.entityDecoder.decode(val);\n}\n\n\nfunction saveTextToParentTag(textData, parentNode, matcher, isLeafNode) {\n if (textData) { //store previously collected data as textNode\n if (isLeafNode === undefined) isLeafNode = parentNode.child.length === 0\n\n textData = this.parseTextData(textData,\n parentNode.tagname,\n matcher,\n false,\n parentNode[\":@\"] ? Object.keys(parentNode[\":@\"]).length !== 0 : false,\n isLeafNode);\n\n if (textData !== undefined && textData !== \"\")\n parentNode.add(this.options.textNodeName, textData);\n textData = \"\";\n }\n return textData;\n}\n\n/**\n * @param {Array<Expression>} stopNodeExpressions - Array of compiled Expression objects\n * @param {Matcher} matcher - Current path matcher\n */\nfunction isItStopNode() {\n if (this.stopNodeExpressionsSet.size === 0) return false;\n\n return this.matcher.matchesAny(this.stopNodeExpressionsSet);\n}\n\n/**\n * Returns the tag Expression and where it is ending handling single-double quotes situation\n * @param {string} xmlData \n * @param {number} i starting index\n * @returns \n */\nfunction tagExpWithClosingIndex(xmlData, i, closingChar = \">\") {\n //TODO: ignore boolean attributes in tag expression\n //TODO: if ignore attributes, dont read full attribute expression but the end. But read for xml declaration\n let attrBoundary = 0;\n const len = xmlData.length;\n const closeCode0 = closingChar.charCodeAt(0);\n const closeCode1 = closingChar.length > 1 ? closingChar.charCodeAt(1) : -1;\n\n let result = '';\n let segmentStart = i;\n\n for (let index = i; index < len; index++) {\n const code = xmlData.charCodeAt(index);\n\n if (attrBoundary) {\n if (code === attrBoundary) attrBoundary = 0;\n } else if (code === 34 || code === 39) { // \" or '\n attrBoundary = code;\n } else if (code === closeCode0) {\n if (closeCode1 !== -1) {\n if (xmlData.charCodeAt(index + 1) === closeCode1) {\n result += xmlData.substring(segmentStart, index);\n return { data: result, index };\n }\n } else {\n result += xmlData.substring(segmentStart, index);\n return { data: result, index };\n }\n } else if (code === 9 && !attrBoundary) { // \\t - only replace with space outside attribute values\n // Flush accumulated segment, add space, start new segment\n result += xmlData.substring(segmentStart, index) + ' ';\n segmentStart = index + 1;\n }\n }\n}\n\nfunction findClosingIndex(xmlData, str, i, errMsg) {\n const closingIndex = xmlData.indexOf(str, i);\n if (closingIndex === -1) {\n throw new Error(errMsg)\n } else {\n return closingIndex + str.length - 1;\n }\n}\n\nfunction findClosingChar(xmlData, char, i, errMsg) {\n const closingIndex = xmlData.indexOf(char, i);\n if (closingIndex === -1) throw new Error(errMsg);\n return closingIndex; // no offset needed\n}\n\nfunction readTagExp(xmlData, i, removeNSPrefix, closingChar = \">\") {\n const result = tagExpWithClosingIndex(xmlData, i + 1, closingChar);\n if (!result) return;\n let tagExp = result.data;\n const closeIndex = result.index;\n const separatorIndex = tagExp.search(/\\s/);\n let tagName = tagExp;\n let attrExpPresent = true;\n if (separatorIndex !== -1) {//separate tag name and attributes expression\n tagName = tagExp.substring(0, separatorIndex);\n tagExp = tagExp.substring(separatorIndex + 1).trimStart();\n }\n\n const rawTagName = tagName;\n if (removeNSPrefix) {\n const colonIndex = tagName.indexOf(\":\");\n if (colonIndex !== -1) {\n tagName = tagName.substr(colonIndex + 1);\n attrExpPresent = tagName !== result.data.substr(colonIndex + 1);\n }\n }\n\n return {\n tagName: tagName,\n tagExp: tagExp,\n closeIndex: closeIndex,\n attrExpPresent: attrExpPresent,\n rawTagName: rawTagName,\n }\n}\n/**\n * find paired tag for a stop node\n * @param {string} xmlData \n * @param {string} tagName \n * @param {number} i \n */\nfunction readStopNodeData(xmlData, tagName, i) {\n const startIndex = i;\n // Starting at 1 since we already have an open tag\n let openTagCount = 1;\n\n const xmllen = xmlData.length;\n for (; i < xmllen; i++) {\n if (xmlData[i] === \"<\") {\n const c1 = xmlData.charCodeAt(i + 1);\n if (c1 === 47) {//close tag '/'\n const closeIndex = findClosingChar(xmlData, \">\", i, `${tagName} is not closed`);\n let closeTagName = xmlData.substring(i + 2, closeIndex).trim();\n if (closeTagName === tagName) {\n openTagCount--;\n if (openTagCount === 0) {\n return {\n tagContent: xmlData.substring(startIndex, i),\n i: closeIndex\n }\n }\n }\n i = closeIndex;\n } else if (c1 === 63) { //?\n const closeIndex = findClosingIndex(xmlData, \"?>\", i + 1, \"StopNode is not closed.\")\n i = closeIndex;\n } else if (c1 === 33\n && xmlData.charCodeAt(i + 2) === 45\n && xmlData.charCodeAt(i + 3) === 45) { // '!--'\n const closeIndex = findClosingIndex(xmlData, \"-->\", i + 3, \"StopNode is not closed.\")\n i = closeIndex;\n } else if (c1 === 33\n && xmlData.charCodeAt(i + 2) === 91) { // '!['\n const closeIndex = findClosingIndex(xmlData, \"]]>\", i, \"StopNode is not closed.\") - 2;\n i = closeIndex;\n } else {\n const tagData = readTagExp(xmlData, i, false)\n\n if (tagData) {\n const openTagName = tagData && tagData.tagName;\n if (openTagName === tagName && tagData.tagExp[tagData.tagExp.length - 1] !== \"/\") {\n openTagCount++;\n }\n i = tagData.closeIndex;\n }\n }\n }\n }//end for loop\n}\n\nfunction parseValue(val, shouldParse, options) {\n if (shouldParse && typeof val === 'string') {\n //console.log(options)\n const newval = val.trim();\n if (newval === 'true') return true;\n else if (newval === 'false') return false;\n else return toNumber(val, options);\n } else {\n if (isExist(val)) {\n return val;\n } else {\n return '';\n }\n }\n}\n\nfunction fromCodePoint(str, base, prefix) {\n const codePoint = Number.parseInt(str, base);\n\n if (codePoint >= 0 && codePoint <= 0x10FFFF) {\n return String.fromCodePoint(codePoint);\n } else {\n return prefix + str + \";\";\n }\n}\n\nfunction transformTagName(fn, tagName, tagExp, options) {\n if (fn) {\n const newTagName = fn(tagName);\n if (tagExp === tagName) {\n tagExp = newTagName\n }\n tagName = newTagName;\n }\n tagName = sanitizeName(tagName, options);\n return { tagName, tagExp };\n}\n\n\n\nfunction sanitizeName(name, options) {\n if (criticalProperties.includes(name)) {\n throw new Error(`[SECURITY] Invalid name: \"${name}\" is a reserved JavaScript keyword that could cause prototype pollution`);\n } else if (DANGEROUS_PROPERTY_NAMES.includes(name)) {\n return options.onDangerousProperty(name);\n }\n return name;\n}","'use strict';\n\nimport XmlNode from './xmlNode.js';\nimport { Matcher } from 'path-expression-matcher';\n\nconst METADATA_SYMBOL = XmlNode.getMetaDataSymbol();\n\n/**\n * Helper function to strip attribute prefix from attribute map\n * @param {object} attrs - Attributes with prefix (e.g., {\"@_class\": \"code\"})\n * @param {string} prefix - Attribute prefix to remove (e.g., \"@_\")\n * @returns {object} Attributes without prefix (e.g., {\"class\": \"code\"})\n */\nfunction stripAttributePrefix(attrs, prefix) {\n if (!attrs || typeof attrs !== 'object') return {};\n if (!prefix) return attrs;\n\n const rawAttrs = {};\n for (const key in attrs) {\n if (key.startsWith(prefix)) {\n const rawName = key.substring(prefix.length);\n rawAttrs[rawName] = attrs[key];\n } else {\n // Attribute without prefix (shouldn't normally happen, but be safe)\n rawAttrs[key] = attrs[key];\n }\n }\n return rawAttrs;\n}\n\n/**\n * \n * @param {array} node \n * @param {any} options \n * @param {Matcher} matcher - Path matcher instance\n * @returns \n */\nexport default function prettify(node, options, matcher, readonlyMatcher) {\n return compress(node, options, matcher, readonlyMatcher);\n}\n\n/**\n * @param {array} arr \n * @param {object} options \n * @param {Matcher} matcher - Path matcher instance\n * @returns object\n */\nfunction compress(arr, options, matcher, readonlyMatcher) {\n let text;\n const compressedObj = {}; //This is intended to be a plain object\n for (let i = 0; i < arr.length; i++) {\n const tagObj = arr[i];\n const property = propName(tagObj);\n\n // Push current property to matcher WITH RAW ATTRIBUTES (no prefix)\n if (property !== undefined && property !== options.textNodeName) {\n const rawAttrs = stripAttributePrefix(\n tagObj[\":@\"] || {},\n options.attributeNamePrefix\n );\n matcher.push(property, rawAttrs);\n }\n\n if (property === options.textNodeName) {\n if (text === undefined) text = tagObj[property];\n else text += \"\" + tagObj[property];\n } else if (property === undefined) {\n continue;\n } else if (tagObj[property]) {\n\n let val = compress(tagObj[property], options, matcher, readonlyMatcher);\n const isLeaf = isLeafTag(val, options);\n\n if (Object.keys(val).length === 0 && options.alwaysCreateTextNode) {\n val[options.textNodeName] = \"\";\n }\n\n if (tagObj[\":@\"]) {\n assignAttributes(val, tagObj[\":@\"], readonlyMatcher, options);\n } else if (Object.keys(val).length === 1 && val[options.textNodeName] !== undefined && !options.alwaysCreateTextNode) {\n val = val[options.textNodeName];\n } else if (Object.keys(val).length === 0) {\n if (options.alwaysCreateTextNode) val[options.textNodeName] = \"\";\n else val = \"\";\n }\n\n if (tagObj[METADATA_SYMBOL] !== undefined && typeof val === \"object\" && val !== null) {\n val[METADATA_SYMBOL] = tagObj[METADATA_SYMBOL]; // copy over metadata\n }\n\n\n if (compressedObj[property] !== undefined && Object.prototype.hasOwnProperty.call(compressedObj, property)) {\n if (!Array.isArray(compressedObj[property])) {\n compressedObj[property] = [compressedObj[property]];\n }\n compressedObj[property].push(val);\n } else {\n //TODO: if a node is not an array, then check if it should be an array\n //also determine if it is a leaf node\n\n // Pass jPath string or readonlyMatcher based on options.jPath setting\n const jPathOrMatcher = options.jPath ? readonlyMatcher.toString() : readonlyMatcher;\n if (options.isArray(property, jPathOrMatcher, isLeaf)) {\n compressedObj[property] = [val];\n } else {\n compressedObj[property] = val;\n }\n }\n\n // Pop property from matcher after processing\n if (property !== undefined && property !== options.textNodeName) {\n matcher.pop();\n }\n }\n\n }\n // if(text && text.length > 0) compressedObj[options.textNodeName] = text;\n if (typeof text === \"string\") {\n if (text.length > 0) compressedObj[options.textNodeName] = text;\n } else if (text !== undefined) compressedObj[options.textNodeName] = text;\n\n\n return compressedObj;\n}\n\nfunction propName(obj) {\n const keys = Object.keys(obj);\n for (let i = 0; i < keys.length; i++) {\n const key = keys[i];\n if (key !== \":@\") return key;\n }\n}\n\nfunction assignAttributes(obj, attrMap, readonlyMatcher, options) {\n if (attrMap) {\n const keys = Object.keys(attrMap);\n const len = keys.length; //don't make it inline\n for (let i = 0; i < len; i++) {\n const atrrName = keys[i]; // This is the PREFIXED name (e.g., \"@_class\")\n\n // Strip prefix for matcher path (for isArray callback)\n const rawAttrName = atrrName.startsWith(options.attributeNamePrefix)\n ? atrrName.substring(options.attributeNamePrefix.length)\n : atrrName;\n\n // For attributes, we need to create a temporary path\n // Pass jPath string or matcher based on options.jPath setting\n const jPathOrMatcher = options.jPath\n ? readonlyMatcher.toString() + \".\" + rawAttrName\n : readonlyMatcher;\n\n if (options.isArray(atrrName, jPathOrMatcher, true, true)) {\n obj[atrrName] = [attrMap[atrrName]];\n } else {\n obj[atrrName] = attrMap[atrrName];\n }\n }\n }\n}\n\nfunction isLeafTag(obj, options) {\n const { textNodeName } = options;\n const propCount = Object.keys(obj).length;\n\n if (propCount === 0) {\n return true;\n }\n\n if (\n propCount === 1 &&\n (obj[textNodeName] || typeof obj[textNodeName] === \"boolean\" || obj[textNodeName] === 0)\n ) {\n return true;\n }\n\n return false;\n}","import { buildOptions } from './OptionsBuilder.js';\nimport OrderedObjParser from './OrderedObjParser.js';\nimport prettify from './node2json.js';\nimport { validate } from \"../validator.js\";\nimport XmlNode from './xmlNode.js';\n\nexport default class XMLParser {\n\n constructor(options) {\n this.externalEntities = {};\n this.options = buildOptions(options);\n\n }\n /**\n * Parse XML dats to JS object \n * @param {string|Uint8Array} xmlData \n * @param {boolean|Object} validationOption \n */\n parse(xmlData, validationOption) {\n if (typeof xmlData !== \"string\" && xmlData.toString) {\n xmlData = xmlData.toString();\n } else if (typeof xmlData !== \"string\") {\n throw new Error(\"XML data is accepted in String or Bytes[] form.\")\n }\n\n if (validationOption) {\n if (validationOption === true) validationOption = {}; //validate with default options\n\n const result = validate(xmlData, validationOption);\n if (result !== true) {\n throw Error(`${result.err.msg}:${result.err.line}:${result.err.col}`)\n }\n }\n const orderedObjParser = new OrderedObjParser(this.options, this.externalEntities);\n // orderedObjParser.entityDecoder.setExternalEntities(this.externalEntities);\n const orderedResult = orderedObjParser.parseXml(xmlData);\n if (this.options.preserveOrder || orderedResult === undefined) return orderedResult;\n else return prettify(orderedResult, this.options, orderedObjParser.matcher, orderedObjParser.readonlyMatcher);\n }\n\n /**\n * Add Entity which is not by default supported by this library\n * @param {string} key \n * @param {string} value \n */\n addEntity(key, value) {\n if (value.indexOf(\"&\") !== -1) {\n throw new Error(\"Entity value can't have '&'\")\n } else if (key.indexOf(\"&\") !== -1 || key.indexOf(\";\") !== -1) {\n throw new Error(\"An entity must be set without '&' and ';'. Eg. use '#xD' for '&#xD;'\")\n } else if (value === \"&\") {\n throw new Error(\"An entity with value '&' is not permitted\");\n } else {\n this.externalEntities[key] = value;\n }\n }\n\n /**\n * Returns a Symbol that can be used to access the metadata\n * property on a node.\n * \n * If Symbol is not available in the environment, an ordinary property is used\n * and the name of the property is here returned.\n * \n * The XMLMetaData property is only present when `captureMetaData`\n * is true in the options.\n */\n static getMetaDataSymbol() {\n return XmlNode.getMetaDataSymbol();\n }\n}","\n\nexport function safeComment(val) {\n return String(val)\n .replace(/--/g, '- -') // -- is illegal anywhere in comment content\n .replace(/--/g, '- -') // handle the scenario when 2 consiucative dashes appears \n .replace(/-$/, '- '); // trailing - would form -- with the closing -->\n}\n\nexport function safeCdata(val) {\n return String(val).replace(/\\]\\]>/g, ']]]]><![CDATA[>')\n}\n\nexport function escapeAttribute(val) {\n return String(val).replace(/\"/g, '&quot;').replace(/'/g, '&apos;')\n}","import { Expression, Matcher } from 'path-expression-matcher';\nimport { safeComment, safeCdata, escapeAttribute } from \"./util.js\";\nimport { createValidator } from 'xml-naming';\n\nconst EOL = \"\\n\";\n\n/**\n * Detect XML version from the first element of the ordered array input.\n * The first element must be a ?xml processing instruction with a version attribute.\n * Returns '1.0' if not found.\n *\n * @param {array} jArray\n * @param {object} options\n */\nfunction detectXmlVersionFromArray(jArray, options) {\n if (!Array.isArray(jArray) || jArray.length === 0) return '1.0';\n const first = jArray[0];\n const firstKey = propName(first);\n if (firstKey === '?xml') {\n const attrs = first[':@'];\n if (attrs) {\n const versionKey = options.attributeNamePrefix + 'version';\n if (attrs[versionKey]) return attrs[versionKey];\n }\n }\n return '1.0';\n}\n\n/**\n * Resolve a tag or attribute name through sanitizeName if configured.\n * Validation via xml-naming's qName is performed first; the sanitizeName\n * callback is invoked only when the name is invalid. If sanitizeName is\n * false (default), no validation occurs and the name is used as-is.\n *\n * @param {string} name - raw name from the JS object\n * @param {boolean} isAttribute - true when resolving an attribute name\n * @param {object} options\n * @param {Matcher} matcher - current matcher state (readonly from callback perspective)\n * @param {function} qNameValidator - function to validate tag names\n */\nfunction resolveTagName(name, isAttribute, options, matcher, qNameValidator) {\n if (!options.sanitizeName) return name;\n if (qNameValidator(name)) return name;\n return options.sanitizeName(name, { isAttribute, matcher: matcher.readOnly() });\n}\n\n/**\n * @param {array} jArray\n * @param {any} options\n * @returns\n */\nexport default function toXml(jArray, options) {\n let indentation = \"\";\n if (options.format) {\n indentation = EOL;\n }\n\n // Pre-compile stopNode expressions for pattern matching\n const stopNodeExpressions = [];\n if (options.stopNodes && Array.isArray(options.stopNodes)) {\n for (let i = 0; i < options.stopNodes.length; i++) {\n const node = options.stopNodes[i];\n if (typeof node === 'string') {\n stopNodeExpressions.push(new Expression(node));\n } else if (node instanceof Expression) {\n stopNodeExpressions.push(node);\n }\n }\n }\n\n // Detect XML version for use in name validation\n const xmlVersion = detectXmlVersionFromArray(jArray, options);\n const qNameValidator = createValidator('qName', { xmlVersion });\n // Initialize matcher for path tracking\n const matcher = new Matcher();\n\n return arrToStr(jArray, options, indentation, matcher, stopNodeExpressions, qNameValidator);\n}\n\nfunction arrToStr(arr, options, indentation, matcher, stopNodeExpressions, qNameValidator) {\n let xmlStr = \"\";\n let isPreviousElementTag = false;\n\n if (options.maxNestedTags && matcher.getDepth() > options.maxNestedTags) {\n throw new Error(\"Maximum nested tags exceeded\");\n }\n\n if (!Array.isArray(arr)) {\n // Non-array values (e.g. string tag values) should be treated as text content\n if (arr !== undefined && arr !== null) {\n let text = arr.toString();\n text = replaceEntitiesValue(text, options);\n return text;\n }\n return \"\";\n }\n\n for (let i = 0; i < arr.length; i++) {\n const tagObj = arr[i];\n const rawTagName = propName(tagObj);\n if (rawTagName === undefined) continue;\n\n // Special names are exempt from sanitizeName: internal conventions and PI tags\n // are not user-supplied XML element names.\n const isSpecialName = rawTagName === options.textNodeName\n || rawTagName === options.cdataPropName\n || rawTagName === options.commentPropName\n || rawTagName[0] === '?';\n\n // Resolve tag name (may transform it; may throw for invalid names)\n const tagName = isSpecialName\n ? rawTagName\n : resolveTagName(rawTagName, false, options, matcher, qNameValidator);\n\n // Extract attributes from \":@\" property\n const attrValues = extractAttributeValues(tagObj[\":@\"], options);\n\n // Push resolved tag to matcher WITH attributes\n matcher.push(tagName, attrValues);\n\n // Check if this is a stop node using Expression matching\n const isStopNode = checkStopNode(matcher, stopNodeExpressions);\n\n if (tagName === options.textNodeName) {\n let tagText = tagObj[rawTagName];\n if (!isStopNode) {\n tagText = options.tagValueProcessor(tagName, tagText);\n tagText = replaceEntitiesValue(tagText, options);\n }\n if (isPreviousElementTag) {\n xmlStr += indentation;\n }\n xmlStr += tagText;\n isPreviousElementTag = false;\n matcher.pop();\n continue;\n } else if (tagName === options.cdataPropName) {\n if (isPreviousElementTag) {\n xmlStr += indentation;\n }\n const val = tagObj[rawTagName][0][options.textNodeName];\n const safeVal = safeCdata(val);\n xmlStr += `<![CDATA[${safeVal}]]>`;\n isPreviousElementTag = false;\n matcher.pop();\n continue;\n } else if (tagName === options.commentPropName) {\n const val = tagObj[rawTagName][0][options.textNodeName];\n const safeVal = safeComment(val);\n xmlStr += indentation + `<!--${safeVal}-->`;\n isPreviousElementTag = true;\n matcher.pop();\n continue;\n } else if (tagName[0] === \"?\") {\n const attStr = attr_to_str(tagObj[\":@\"], options, isStopNode, matcher, qNameValidator);\n const tempInd = tagName === \"?xml\" ? \"\" : indentation;\n // Text node content on PI/XML declaration tags is intentionally ignored.\n // Only attributes are valid on these tags per the XML spec.\n xmlStr += tempInd + `<${tagName}${attStr}?>`;\n isPreviousElementTag = true;\n matcher.pop();\n continue;\n }\n\n let newIdentation = indentation;\n if (newIdentation !== \"\") {\n newIdentation += options.indentBy;\n }\n\n // Pass isStopNode to attr_to_str so attributes are also not processed for stopNodes\n const attStr = attr_to_str(tagObj[\":@\"], options, isStopNode, matcher, qNameValidator);\n const tagStart = indentation + `<${tagName}${attStr}`;\n\n // If this is a stopNode, get raw content without processing\n let tagValue;\n if (isStopNode) {\n tagValue = getRawContent(tagObj[rawTagName], options);\n } else {\n tagValue = arrToStr(tagObj[rawTagName], options, newIdentation, matcher, stopNodeExpressions, qNameValidator);\n }\n\n if (options.unpairedTags.indexOf(tagName) !== -1) {\n if (options.suppressUnpairedNode) xmlStr += tagStart + \">\";\n else xmlStr += tagStart + \"/>\";\n } else if ((!tagValue || tagValue.length === 0) && options.suppressEmptyNode) {\n xmlStr += tagStart + \"/>\";\n } else if (tagValue && tagValue.endsWith(\">\")) {\n xmlStr += tagStart + `>${tagValue}${indentation}</${tagName}>`;\n } else {\n xmlStr += tagStart + \">\";\n if (tagValue && indentation !== \"\" && (tagValue.includes(\"/>\") || tagValue.includes(\"</\"))) {\n xmlStr += indentation + options.indentBy + tagValue + indentation;\n } else {\n xmlStr += tagValue;\n }\n xmlStr += `</${tagName}>`;\n }\n isPreviousElementTag = true;\n\n // Pop tag from matcher\n matcher.pop();\n }\n\n return xmlStr;\n}\n\n/**\n * Extract attribute values from the \":@\" object and return as plain object\n * for passing to matcher.push()\n */\nfunction extractAttributeValues(attrMap, options) {\n if (!attrMap || options.ignoreAttributes) return null;\n\n const attrValues = {};\n let hasAttrs = false;\n\n for (let attr in attrMap) {\n if (!Object.prototype.hasOwnProperty.call(attrMap, attr)) continue;\n // Remove the attribute prefix to get clean attribute name\n const cleanAttrName = attr.startsWith(options.attributeNamePrefix)\n ? attr.substr(options.attributeNamePrefix.length)\n : attr;\n attrValues[cleanAttrName] = escapeAttribute(attrMap[attr]);\n hasAttrs = true;\n }\n\n return hasAttrs ? attrValues : null;\n}\n\n/**\n * Extract raw content from a stopNode without any processing\n * This preserves the content exactly as-is, including special characters\n */\nfunction getRawContent(arr, options) {\n if (!Array.isArray(arr)) {\n // Non-array values return as-is\n if (arr !== undefined && arr !== null) {\n return arr.toString();\n }\n return \"\";\n }\n\n let content = \"\";\n for (let i = 0; i < arr.length; i++) {\n const item = arr[i];\n const tagName = propName(item);\n\n if (tagName === options.textNodeName) {\n // Raw text content - NO processing, NO entity replacement\n content += item[tagName];\n } else if (tagName === options.cdataPropName) {\n // CDATA content\n content += item[tagName][0][options.textNodeName];\n } else if (tagName === options.commentPropName) {\n // Comment content\n content += item[tagName][0][options.textNodeName];\n } else if (tagName && tagName[0] === \"?\") {\n // Processing instruction - skip for stopNodes\n continue;\n } else if (tagName) {\n // Nested tags within stopNode — no sanitizeName, content is raw\n const attStr = attr_to_str_raw(item[\":@\"], options);\n const nestedContent = getRawContent(item[tagName], options);\n\n if (!nestedContent || nestedContent.length === 0) {\n content += `<${tagName}${attStr}/>`;\n } else {\n content += `<${tagName}${attStr}>${nestedContent}</${tagName}>`;\n }\n }\n }\n return content;\n}\n\n/**\n * Build attribute string for stopNodes - NO entity replacement\n */\nfunction attr_to_str_raw(attrMap, options) {\n let attrStr = \"\";\n if (attrMap && !options.ignoreAttributes) {\n for (let attr in attrMap) {\n if (!Object.prototype.hasOwnProperty.call(attrMap, attr)) continue;\n // For stopNodes, use raw value without processing\n let attrVal = attrMap[attr];\n if (attrVal === true && options.suppressBooleanAttributes) {\n attrStr += ` ${attr.substr(options.attributeNamePrefix.length)}`;\n } else {\n attrStr += ` ${attr.substr(options.attributeNamePrefix.length)}=\"${escapeAttribute(attrVal)}\"`;\n }\n }\n }\n return attrStr;\n}\n\nfunction propName(obj) {\n const keys = Object.keys(obj);\n for (let i = 0; i < keys.length; i++) {\n const key = keys[i];\n if (!Object.prototype.hasOwnProperty.call(obj, key)) continue;\n if (key !== \":@\") return key;\n }\n}\n\n/**\n * Build attribute string, resolving attribute names through sanitizeName when configured.\n * Accepts matcher so the callback has path context.\n */\nfunction attr_to_str(attrMap, options, isStopNode, matcher, qNameValidator) {\n let attrStr = \"\";\n if (attrMap && !options.ignoreAttributes) {\n for (let attr in attrMap) {\n if (!Object.prototype.hasOwnProperty.call(attrMap, attr)) continue;\n\n // Strip prefix to get the clean XML attribute name, then optionally sanitize it\n const cleanAttrName = attr.substr(options.attributeNamePrefix.length);\n const resolvedAttrName = isStopNode\n ? cleanAttrName // stopNodes are raw — skip sanitizeName for attr names too\n : resolveTagName(cleanAttrName, true, options, matcher, qNameValidator);\n\n let attrVal;\n if (isStopNode) {\n // For stopNodes, use raw value without any processing\n attrVal = attrMap[attr];\n } else {\n // Normal processing: apply attributeValueProcessor and entity replacement\n attrVal = options.attributeValueProcessor(attr, attrMap[attr]);\n attrVal = replaceEntitiesValue(attrVal, options);\n }\n\n if (attrVal === true && options.suppressBooleanAttributes) {\n attrStr += ` ${resolvedAttrName}`;\n } else {\n attrStr += ` ${resolvedAttrName}=\"${escapeAttribute(attrVal)}\"`;\n }\n }\n }\n return attrStr;\n}\n\nfunction checkStopNode(matcher, stopNodeExpressions) {\n if (!stopNodeExpressions || stopNodeExpressions.length === 0) return false;\n\n for (let i = 0; i < stopNodeExpressions.length; i++) {\n if (matcher.matches(stopNodeExpressions[i])) {\n return true;\n }\n }\n return false;\n}\n\nfunction replaceEntitiesValue(textValue, options) {\n if (textValue && textValue.length > 0 && options.processEntities) {\n for (let i = 0; i < options.entities.length; i++) {\n const entity = options.entities[i];\n textValue = textValue.replace(entity.regex, entity.val);\n }\n }\n return textValue;\n}","export default function getIgnoreAttributesFn(ignoreAttributes) {\n if (typeof ignoreAttributes === 'function') {\n return ignoreAttributes\n }\n if (Array.isArray(ignoreAttributes)) {\n return (attrName) => {\n for (const pattern of ignoreAttributes) {\n if (typeof pattern === 'string' && attrName === pattern) {\n return true\n }\n if (pattern instanceof RegExp && pattern.test(attrName)) {\n return true\n }\n }\n }\n }\n return () => false\n}","'use strict';\n//parse Empty Node as self closing node\nimport buildFromOrderedJs from './orderedJs2Xml.js';\nimport getIgnoreAttributesFn from \"./ignoreAttributes.js\";\nimport { Expression, Matcher } from 'path-expression-matcher';\nimport { safeComment, safeCdata, escapeAttribute } from './util.js';\nimport { createValidator } from 'xml-naming';\n\nconst defaultOptions = {\n attributeNamePrefix: '@_',\n attributesGroupName: false,\n textNodeName: '#text',\n ignoreAttributes: true,\n cdataPropName: false,\n format: false,\n indentBy: ' ',\n suppressEmptyNode: false,\n suppressUnpairedNode: true,\n suppressBooleanAttributes: true,\n tagValueProcessor: function (key, a) {\n return a;\n },\n attributeValueProcessor: function (attrName, a) {\n return a;\n },\n preserveOrder: false,\n commentPropName: false,\n unpairedTags: [],\n entities: [\n { regex: new RegExp(\"&\", \"g\"), val: \"&amp;\" },//it must be on top\n { regex: new RegExp(\">\", \"g\"), val: \"&gt;\" },\n { regex: new RegExp(\"<\", \"g\"), val: \"&lt;\" },\n { regex: new RegExp(\"\\'\", \"g\"), val: \"&apos;\" },\n { regex: new RegExp(\"\\\"\", \"g\"), val: \"&quot;\" }\n ],\n processEntities: true,\n stopNodes: [],\n // transformTagName: false,\n // transformAttributeName: false,\n oneListGroup: false,\n maxNestedTags: 100,\n jPath: true, // When true, callbacks receive string jPath; when false, receive Matcher instance\n sanitizeName: false // false = allow all names as-is (default, backward-compatible).\n // Set to a function (name, { isAttribute, matcher }) => string to\n // validate/sanitize tag and attribute names. Throw inside the function\n // to reject an invalid name.\n};\n\nexport default function Builder(options) {\n this.options = Object.assign({}, defaultOptions, options);\n\n // Convert old-style stopNodes for backward compatibility\n // Old syntax: \"*.tag\" meant \"tag anywhere in tree\"\n // New syntax: \"..tag\" means \"tag anywhere in tree\"\n if (this.options.stopNodes && Array.isArray(this.options.stopNodes)) {\n this.options.stopNodes = this.options.stopNodes.map(node => {\n if (typeof node === 'string' && node.startsWith('*.')) {\n // Convert old wildcard syntax to deep wildcard\n return '..' + node.substring(2);\n }\n return node;\n });\n }\n\n // Pre-compile stopNode expressions for pattern matching\n this.stopNodeExpressions = [];\n if (this.options.stopNodes && Array.isArray(this.options.stopNodes)) {\n for (let i = 0; i < this.options.stopNodes.length; i++) {\n const node = this.options.stopNodes[i];\n if (typeof node === 'string') {\n this.stopNodeExpressions.push(new Expression(node));\n } else if (node instanceof Expression) {\n this.stopNodeExpressions.push(node);\n }\n }\n }\n\n if (this.options.ignoreAttributes === true || this.options.attributesGroupName) {\n this.isAttribute = function (/*a*/) {\n return false;\n };\n } else {\n this.ignoreAttributesFn = getIgnoreAttributesFn(this.options.ignoreAttributes)\n this.attrPrefixLen = this.options.attributeNamePrefix.length;\n this.isAttribute = isAttribute;\n }\n\n this.processTextOrObjNode = processTextOrObjNode\n\n if (this.options.format) {\n this.indentate = indentate;\n this.tagEndChar = '>\\n';\n this.newLine = '\\n';\n } else {\n this.indentate = function () {\n return '';\n };\n this.tagEndChar = '>';\n this.newLine = '';\n }\n}\n\n/**\n * Detect XML version from the ?xml declaration at the root of a plain-object input.\n * Checks both attributesGroupName and flat attribute forms.\n * Returns '1.0' if no declaration is found.\n */\nfunction detectXmlVersionFromObj(jObj, options) {\n const decl = jObj['?xml'];\n if (decl && typeof decl === 'object') {\n // attributesGroupName path e.g. { '$$': { '@_version': '1.1' } }\n if (options.attributesGroupName && decl[options.attributesGroupName]) {\n const v = decl[options.attributesGroupName][options.attributeNamePrefix + 'version'];\n if (v) return v;\n }\n // flat attribute path e.g. { '@_version': '1.1' }\n const v = decl[options.attributeNamePrefix + 'version'];\n if (v) return v;\n }\n return '1.0';\n}\n\n/**\n * Resolve a tag or attribute name through sanitizeName if configured.\n * Validation via xml-naming's qName is performed first; the sanitizeName\n * callback is invoked only when the name is invalid. If sanitizeName is\n * false (default), no validation occurs and the name is used as-is.\n *\n * @param {string} name - raw name from the JS object\n * @param {boolean} isAttribute - true when resolving an attribute name\n * @param {object} options\n * @param {Matcher} matcher - current matcher state (readonly from callback perspective)\n * @param {function} qNameValidator - function to validate tag names\n */\nfunction resolveTagName(name, isAttribute, options, matcher, qNameValidator) {\n if (!options.sanitizeName) return name;\n if (qNameValidator(name)) return name;\n return options.sanitizeName(name, { isAttribute, matcher: matcher.readOnly() });\n}\n\nBuilder.prototype.build = function (jObj) {\n if (this.options.preserveOrder) {\n return buildFromOrderedJs(jObj, this.options);\n } else {\n if (Array.isArray(jObj) && this.options.arrayNodeName && this.options.arrayNodeName.length > 1) {\n jObj = {\n [this.options.arrayNodeName]: jObj\n }\n }\n // Initialize matcher for path tracking\n const matcher = new Matcher();\n const xmlVersion = detectXmlVersionFromObj(jObj, this.options);\n const qNameValidator = createValidator('qName', { xmlVersion });\n return this.j2x(jObj, 0, matcher, qNameValidator).val;\n }\n};\n\nBuilder.prototype.j2x = function (jObj, level, matcher, qNameValidator) {\n let attrStr = '';\n let val = '';\n if (this.options.maxNestedTags && matcher.getDepth() >= this.options.maxNestedTags) {\n throw new Error(\"Maximum nested tags exceeded\");\n }\n // Get jPath based on option: string for backward compatibility, or Matcher for new features\n const jPath = this.options.jPath ? matcher.toString() : matcher;\n\n // Check if current node is a stopNode (will be used for attribute encoding)\n const isCurrentStopNode = this.checkStopNode(matcher);\n\n for (let key in jObj) {\n if (!Object.prototype.hasOwnProperty.call(jObj, key)) continue;\n\n // Resolve the key through sanitizeName before any use.\n // Special keys (textNodeName, cdataPropName, commentPropName, attributeNamePrefix,\n // attributesGroupName, \"?\" PI tags) are exempt — they are builder-internal conventions,\n // not user-supplied XML names.\n const isSpecialKey = key === this.options.textNodeName\n || key === this.options.cdataPropName\n || key === this.options.commentPropName\n || (this.options.attributesGroupName && key === this.options.attributesGroupName)\n || this.isAttribute(key)\n || key[0] === '?';\n\n const resolvedKey = isSpecialKey\n ? key\n : resolveTagName(key, false, this.options, matcher, qNameValidator);\n\n if (typeof jObj[key] === 'undefined') {\n // supress undefined node only if it is not an attribute\n if (this.isAttribute(key)) {\n val += '';\n }\n } else if (jObj[key] === null) {\n // null attribute should be ignored by the attribute list, but should not cause the tag closing\n if (this.isAttribute(key)) {\n val += '';\n } else if (resolvedKey === this.options.cdataPropName || resolvedKey === this.options.commentPropName) {\n val += '';\n } else if (resolvedKey[0] === '?') {\n val += this.indentate(level) + '<' + resolvedKey + '?' + this.tagEndChar;\n } else {\n val += this.indentate(level) + '<' + resolvedKey + '/' + this.tagEndChar;\n }\n } else if (jObj[key] instanceof Date) {\n val += this.buildTextValNode(jObj[key], resolvedKey, '', level, matcher);\n } else if (typeof jObj[key] !== 'object') {\n //premitive type\n const attr = this.isAttribute(key);\n if (attr && !this.ignoreAttributesFn(attr, jPath)) {\n // Resolve the attribute name through sanitizeName\n const resolvedAttr = resolveTagName(attr, true, this.options, matcher, qNameValidator);\n attrStr += this.buildAttrPairStr(resolvedAttr, '' + jObj[key], isCurrentStopNode);\n } else if (!attr) {\n //tag value\n if (key === this.options.textNodeName) {\n let newval = this.options.tagValueProcessor(key, '' + jObj[key]);\n val += this.replaceEntitiesValue(newval);\n } else {\n // Check if this is a stopNode before building\n matcher.push(resolvedKey);\n const isStopNode = this.checkStopNode(matcher);\n matcher.pop();\n\n if (isStopNode) {\n // Build as raw content without encoding\n const textValue = '' + jObj[key];\n if (textValue === '') {\n val += this.indentate(level) + '<' + resolvedKey + this.closeTag(resolvedKey) + this.tagEndChar;\n } else {\n val += this.indentate(level) + '<' + resolvedKey + '>' + textValue + '</' + resolvedKey + this.tagEndChar;\n }\n } else {\n val += this.buildTextValNode(jObj[key], resolvedKey, '', level, matcher);\n }\n }\n }\n } else if (Array.isArray(jObj[key])) {\n //repeated nodes\n const arrLen = jObj[key].length;\n let listTagVal = \"\";\n let listTagAttr = \"\";\n for (let j = 0; j < arrLen; j++) {\n const item = jObj[key][j];\n if (typeof item === 'undefined') {\n // supress undefined node\n } else if (item === null) {\n if (resolvedKey[0] === \"?\") val += this.indentate(level) + '<' + resolvedKey + '?' + this.tagEndChar;\n else val += this.indentate(level) + '<' + resolvedKey + '/' + this.tagEndChar;\n } else if (typeof item === 'object') {\n if (this.options.oneListGroup) {\n // Push tag to matcher before recursive call\n matcher.push(resolvedKey);\n const result = this.j2x(item, level + 1, matcher, qNameValidator);\n // Pop tag from matcher after recursive call\n matcher.pop();\n\n listTagVal += result.val;\n if (this.options.attributesGroupName && item.hasOwnProperty(this.options.attributesGroupName)) {\n listTagAttr += result.attrStr\n }\n } else {\n listTagVal += this.processTextOrObjNode(item, resolvedKey, level, matcher, qNameValidator)\n }\n } else {\n if (this.options.oneListGroup) {\n let textValue = this.options.tagValueProcessor(resolvedKey, item);\n textValue = this.replaceEntitiesValue(textValue);\n listTagVal += textValue;\n } else {\n // Check if this is a stopNode before building\n matcher.push(resolvedKey);\n const isStopNode = this.checkStopNode(matcher);\n matcher.pop();\n\n if (isStopNode) {\n // Build as raw content without encoding\n const textValue = '' + item;\n if (textValue === '') {\n listTagVal += this.indentate(level) + '<' + resolvedKey + this.closeTag(resolvedKey) + this.tagEndChar;\n } else {\n listTagVal += this.indentate(level) + '<' + resolvedKey + '>' + textValue + '</' + resolvedKey + this.tagEndChar;\n }\n } else {\n listTagVal += this.buildTextValNode(item, resolvedKey, '', level, matcher);\n }\n }\n }\n }\n if (this.options.oneListGroup) {\n listTagVal = this.buildObjectNode(listTagVal, resolvedKey, listTagAttr, level);\n }\n val += listTagVal;\n } else {\n //nested node\n if (this.options.attributesGroupName && key === this.options.attributesGroupName) {\n const Ks = Object.keys(jObj[key]);\n const L = Ks.length;\n for (let j = 0; j < L; j++) {\n // Resolve attribute names inside attributesGroupName\n const resolvedAttr = resolveTagName(Ks[j], true, this.options, matcher, qNameValidator);\n attrStr += this.buildAttrPairStr(resolvedAttr, '' + jObj[key][Ks[j]], isCurrentStopNode);\n }\n } else {\n val += this.processTextOrObjNode(jObj[key], resolvedKey, level, matcher, qNameValidator)\n }\n }\n }\n return { attrStr: attrStr, val: val };\n};\n\nBuilder.prototype.buildAttrPairStr = function (attrName, val, isStopNode) {\n if (!isStopNode) {\n val = this.options.attributeValueProcessor(attrName, '' + val);\n val = this.replaceEntitiesValue(val);\n }\n if (this.options.suppressBooleanAttributes && val === \"true\") {\n return ' ' + attrName;\n } else return ' ' + attrName + '=\"' + escapeAttribute(val) + '\"';\n}\n\nfunction processTextOrObjNode(object, key, level, matcher, qNameValidator) {\n // Extract attributes to pass to matcher\n const attrValues = this.extractAttributes(object);\n\n // Push tag to matcher before recursion WITH attributes\n matcher.push(key, attrValues);\n\n // Check if this entire node is a stopNode\n const isStopNode = this.checkStopNode(matcher);\n\n if (isStopNode) {\n // For stopNodes, build raw content without entity encoding\n const rawContent = this.buildRawContent(object);\n const attrStr = this.buildAttributesForStopNode(object);\n matcher.pop();\n return this.buildObjectNode(rawContent, key, attrStr, level);\n }\n\n const result = this.j2x(object, level + 1, matcher, qNameValidator);\n // Pop tag from matcher after recursion\n matcher.pop();\n\n // PI/XML-declaration tags must never emit text content — route through\n // buildTextValNode which correctly ignores the text node for \"?\" tags.\n if (key[0] === '?') {\n return this.buildTextValNode('', key, result.attrStr, level, matcher);\n } else if (object[this.options.textNodeName] !== undefined && Object.keys(object).length === 1) {\n return this.buildTextValNode(object[this.options.textNodeName], key, result.attrStr, level, matcher);\n } else {\n return this.buildObjectNode(result.val, key, result.attrStr, level);\n }\n}\n\n// Helper method to extract attributes from an object\nBuilder.prototype.extractAttributes = function (obj) {\n if (!obj || typeof obj !== 'object') return null;\n\n const attrValues = {};\n let hasAttrs = false;\n\n // Check for attributesGroupName (when attributes are grouped)\n if (this.options.attributesGroupName && obj[this.options.attributesGroupName]) {\n const attrGroup = obj[this.options.attributesGroupName];\n for (let attrKey in attrGroup) {\n if (!Object.prototype.hasOwnProperty.call(attrGroup, attrKey)) continue;\n // Remove attribute prefix if present\n const cleanKey = attrKey.startsWith(this.options.attributeNamePrefix)\n ? attrKey.substring(this.options.attributeNamePrefix.length)\n : attrKey;\n attrValues[cleanKey] = escapeAttribute(attrGroup[attrKey]);\n hasAttrs = true;\n }\n } else {\n // Look for individual attributes (prefixed with attributeNamePrefix)\n for (let key in obj) {\n if (!Object.prototype.hasOwnProperty.call(obj, key)) continue;\n const attr = this.isAttribute(key);\n if (attr) {\n attrValues[attr] = escapeAttribute(obj[key]);\n hasAttrs = true;\n }\n }\n }\n\n return hasAttrs ? attrValues : null;\n};\n\n// Build raw content for stopNode without entity encoding\nBuilder.prototype.buildRawContent = function (obj) {\n if (typeof obj === 'string') {\n return obj; // Already a string, return as-is\n }\n\n if (typeof obj !== 'object' || obj === null) {\n return String(obj);\n }\n\n // Check if this is a stopNode data from parser: { \"#text\": \"raw xml\", \"@_attr\": \"val\" }\n if (obj[this.options.textNodeName] !== undefined) {\n return obj[this.options.textNodeName]; // Return raw text without encoding\n }\n\n // Build raw XML from nested structure\n let content = '';\n\n for (let key in obj) {\n if (!Object.prototype.hasOwnProperty.call(obj, key)) continue;\n\n // Skip attributes\n if (this.isAttribute(key)) continue;\n if (this.options.attributesGroupName && key === this.options.attributesGroupName) continue;\n\n const value = obj[key];\n\n if (key === this.options.textNodeName) {\n content += value; // Raw text\n } else if (Array.isArray(value)) {\n // Array of same tag\n for (let item of value) {\n if (typeof item === 'string' || typeof item === 'number') {\n content += `<${key}>${item}</${key}>`;\n } else if (typeof item === 'object' && item !== null) {\n const nestedContent = this.buildRawContent(item);\n const nestedAttrs = this.buildAttributesForStopNode(item);\n if (nestedContent === '') {\n content += `<${key}${nestedAttrs}/>`;\n } else {\n content += `<${key}${nestedAttrs}>${nestedContent}</${key}>`;\n }\n }\n }\n } else if (typeof value === 'object' && value !== null) {\n // Nested object\n const nestedContent = this.buildRawContent(value);\n const nestedAttrs = this.buildAttributesForStopNode(value);\n if (nestedContent === '') {\n content += `<${key}${nestedAttrs}/>`;\n } else {\n content += `<${key}${nestedAttrs}>${nestedContent}</${key}>`;\n }\n } else {\n // Primitive value\n content += `<${key}>${value}</${key}>`;\n }\n }\n\n return content;\n};\n\n// Build attribute string for stopNode (no entity encoding)\nBuilder.prototype.buildAttributesForStopNode = function (obj) {\n if (!obj || typeof obj !== 'object') return '';\n\n let attrStr = '';\n\n // Check for attributesGroupName (when attributes are grouped)\n if (this.options.attributesGroupName && obj[this.options.attributesGroupName]) {\n const attrGroup = obj[this.options.attributesGroupName];\n for (let attrKey in attrGroup) {\n if (!Object.prototype.hasOwnProperty.call(attrGroup, attrKey)) continue;\n const cleanKey = attrKey.startsWith(this.options.attributeNamePrefix)\n ? attrKey.substring(this.options.attributeNamePrefix.length)\n : attrKey;\n const val = attrGroup[attrKey];\n if (val === true && this.options.suppressBooleanAttributes) {\n attrStr += ' ' + cleanKey;\n } else {\n // stopNode content is raw, but the quote delimiter is always escaped\n // so a quote in the value cannot break out of the attribute (see orderedJs2Xml attr_to_str)\n attrStr += ' ' + cleanKey + '=\"' + escapeAttribute(val) + '\"';\n }\n }\n } else {\n // Look for individual attributes\n for (let key in obj) {\n if (!Object.prototype.hasOwnProperty.call(obj, key)) continue;\n const attr = this.isAttribute(key);\n if (attr) {\n const val = obj[key];\n if (val === true && this.options.suppressBooleanAttributes) {\n attrStr += ' ' + attr;\n } else {\n // stopNode content is raw, but the quote delimiter is always escaped\n // so a quote in the value cannot break out of the attribute (see orderedJs2Xml attr_to_str)\n attrStr += ' ' + attr + '=\"' + escapeAttribute(val) + '\"';\n }\n }\n }\n }\n\n return attrStr;\n};\n\nBuilder.prototype.buildObjectNode = function (val, key, attrStr, level) {\n if (val === \"\") {\n if (key[0] === \"?\") return this.indentate(level) + '<' + key + attrStr + '?' + this.tagEndChar;\n else {\n return this.indentate(level) + '<' + key + attrStr + this.closeTag(key) + this.tagEndChar;\n }\n } else if (key[0] === \"?\") {\n // PI/XML-declaration tags never have body content — treat them like empty.\n return this.indentate(level) + '<' + key + attrStr + '?' + this.tagEndChar;\n } else {\n let tagEndExp = '</' + key + this.tagEndChar;\n let piClosingChar = \"\";\n\n if (key[0] === \"?\") {\n piClosingChar = \"?\";\n tagEndExp = \"\";\n }\n\n // attrStr is an empty string in case the attribute came as undefined or null\n if ((attrStr || attrStr === '') && val.indexOf('<') === -1) {\n return (this.indentate(level) + '<' + key + attrStr + piClosingChar + '>' + val + tagEndExp);\n } else if (this.options.commentPropName !== false && key === this.options.commentPropName && piClosingChar.length === 0) {\n return this.indentate(level) + `<!--${safeComment(val)}-->` + this.newLine;\n } else {\n return (\n this.indentate(level) + '<' + key + attrStr + piClosingChar + this.tagEndChar +\n val +\n this.indentate(level) + tagEndExp);\n }\n }\n}\n\nBuilder.prototype.closeTag = function (key) {\n let closeTag = \"\";\n if (this.options.unpairedTags.indexOf(key) !== -1) { //unpaired\n if (!this.options.suppressUnpairedNode) closeTag = \"/\"\n } else if (this.options.suppressEmptyNode) { //empty\n closeTag = \"/\";\n } else {\n closeTag = `></${key}`\n }\n return closeTag;\n}\n\nBuilder.prototype.checkStopNode = function (matcher) {\n if (!this.stopNodeExpressions || this.stopNodeExpressions.length === 0) return false;\n\n for (let i = 0; i < this.stopNodeExpressions.length; i++) {\n if (matcher.matches(this.stopNodeExpressions[i])) {\n return true;\n }\n }\n return false;\n}\n\nfunction buildEmptyObjNode(val, key, attrStr, level) {\n if (val !== '') {\n return this.buildObjectNode(val, key, attrStr, level);\n } else {\n if (key[0] === \"?\") return this.indentate(level) + '<' + key + attrStr + '?' + this.tagEndChar;\n else {\n return this.indentate(level) + '<' + key + attrStr + '/' + this.tagEndChar;\n }\n }\n}\n\nBuilder.prototype.buildTextValNode = function (val, key, attrStr, level, matcher) {\n if (this.options.cdataPropName !== false && key === this.options.cdataPropName) {\n const safeVal = safeCdata(val);\n return this.indentate(level) + `<![CDATA[${safeVal}]]>` + this.newLine;\n } else if (this.options.commentPropName !== false && key === this.options.commentPropName) {\n const safeVal = safeComment(val);\n return this.indentate(level) + `<!--${safeVal}-->` + this.newLine;\n } else if (key[0] === \"?\") {//PI tag\n return this.indentate(level) + '<' + key + attrStr + '?' + this.tagEndChar;\n } else {\n // Normal processing: apply tagValueProcessor and entity replacement\n let textValue = this.options.tagValueProcessor(key, val);\n textValue = this.replaceEntitiesValue(textValue);\n\n if (textValue === '') {\n return this.indentate(level) + '<' + key + attrStr + this.closeTag(key) + this.tagEndChar;\n } else {\n return this.indentate(level) + '<' + key + attrStr + '>' +\n textValue +\n '</' + key + this.tagEndChar;\n }\n }\n}\n\nBuilder.prototype.replaceEntitiesValue = function (textValue) {\n if (textValue && textValue.length > 0 && this.options.processEntities) {\n for (let i = 0; i < this.options.entities.length; i++) {\n const entity = this.options.entities[i];\n textValue = textValue.replace(entity.regex, entity.val);\n }\n }\n return textValue;\n}\n\nfunction indentate(level) {\n return this.options.indentBy.repeat(level);\n}\n\nfunction isAttribute(name /*, options*/) {\n if (name.startsWith(this.options.attributeNamePrefix) && name !== this.options.textNodeName) {\n return name.substr(this.attrPrefixLen);\n } else {\n return false;\n }\n}","/** Parse a Fortran-style number (D-notation) to a JS number. */\nexport function parseFortranNumber(s: string): number {\n return Number.parseFloat(s.replace(/[dD]/g, \"e\"));\n}\n\n/** Parse a Fortran-style boolean string. */\nexport function parseFortranBool(s: string): boolean {\n const v = s.trim().toLowerCase();\n return v === \".true.\" || v === \"true\" || v === \"t\";\n}\n\n/** Parse whitespace-separated text into a Float64Array. */\nexport function parseFloat64Array(text: string): Float64Array {\n const tokens = text.trim().split(/\\s+/).filter(Boolean);\n const arr = new Float64Array(tokens.length);\n for (let i = 0; i < tokens.length; i++) {\n arr[i] = parseFortranNumber(tokens[i]);\n }\n return arr;\n}\n\n/** Parse a string to integer, trimming whitespace. */\nexport function parseIntSafe(s: string): number {\n return Number.parseInt(s.trim(), 10);\n}\n\n/** Format a number in Fortran D-notation. */\nexport function formatFortranNumber(n: number, width = 20): string {\n const s = n.toExponential(15);\n const d = s.replace(/e/, \"D\").replace(/e\\+/, \"D+\").replace(/e-/, \"D-\");\n return d.padStart(width);\n}\n\n/** Format a boolean as Fortran `.true.` / `.false.`. */\nexport function formatFortranBool(b: boolean): string {\n return b ? \".true.\" : \".false.\";\n}\n\n/** Escape special characters for XML attribute values. */\nexport function escapeXmlAttr(s: string): string {\n return s.replace(/&/g, \"&amp;\").replace(/</g, \"&lt;\").replace(/>/g, \"&gt;\").replace(/\"/g, \"&quot;\");\n}\n\n/** Format a Float64Array as columns of Fortran D-notation numbers. */\nexport function formatDataArray(arr: Float64Array, columns = 4): string {\n const lines: string[] = [];\n for (let i = 0; i < arr.length; i += columns) {\n const row: string[] = [];\n for (let j = 0; j < columns && i + j < arr.length; j++) {\n row.push(formatFortranNumber(arr[i + j]));\n }\n lines.push(row.join(\" \"));\n }\n return lines.join(\"\\n\");\n}\n","import { parseFortranNumber, parseIntSafe, parseFortranBool } from \"./fortran-helpers\";\n\n/** An XML node as returned by fast-xml-parser. */\nexport type XmlNode = Record<string, any>;\n\n/** Get an attribute value from an XML node. */\nexport function attr(node: XmlNode | undefined, name: string): string {\n return node?.[`@_${name}`] ?? \"\";\n}\n\n/** Get an attribute as a Fortran-number. */\nexport function attrNum(node: XmlNode | undefined, name: string, fallback = 0): number {\n const v = attr(node, name);\n return v ? parseFortranNumber(v) : fallback;\n}\n\n/** Get an attribute as an integer. */\nexport function attrInt(node: XmlNode | undefined, name: string, fallback = 0): number {\n const v = attr(node, name);\n return v ? parseIntSafe(v) : fallback;\n}\n\n/** Get an attribute as a Fortran boolean. */\nexport function attrBool(node: XmlNode | undefined, name: string): boolean {\n return parseFortranBool(attr(node, name) || \".false.\");\n}\n\n/** Extract text content from an XML node. */\nexport function textOf(node: XmlNode | string | undefined): string {\n if (typeof node === \"string\") return node;\n if (node && \"#text\" in node) return String(node[\"#text\"]);\n return \"\";\n}\n\n/** Normalize a value or array to an array (ensuring T[]). */\nexport function toArray<T>(v: T | T[] | undefined | null): T[] {\n if (Array.isArray(v)) return v;\n if (v == null) return [];\n return [v];\n}\n","import { XMLParser, XMLBuilder } from \"fast-xml-parser\";\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n FullWfc,\n AugmentationData,\n PawData,\n GipawData,\n SpinOrbitData,\n PseudopotentialType,\n RelativisticType,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFortranBool,\n parseFloat64Array,\n parseIntSafe,\n formatFortranNumber,\n formatFortranBool,\n escapeXmlAttr,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n attrBool,\n textOf,\n toArray,\n} from \"./xml-helpers\";\n\nfunction parseData(text: string): Float64Array {\n return parseFloat64Array(text);\n}\n\n// ── XML parser config ──────────────────────────────────────────────\n\nconst parserOptions = {\n ignoreAttributes: false,\n attributeNamePrefix: \"@_\",\n allowBooleanAttributes: true,\n parseTagValue: false,\n parseAttributeValue: false,\n trimValues: true,\n isArray: (_name: string, jpath: string, isLeafNode: boolean, isAttribute: boolean) => {\n if (isAttribute) return false;\n // These tags can appear multiple times — always wrap in array.\n // Also match dotted variants (e.g. PP_GIPAW_CORE_ORBITAL.1).\n if (\n _name === \"PP_BETA\" ||\n _name.startsWith(\"PP_BETA.\") ||\n _name === \"PP_CHI\" ||\n _name.startsWith(\"PP_CHI.\") ||\n _name === \"PP_VNL\" ||\n _name === \"PP_AEWFC\" ||\n _name.startsWith(\"PP_AEWFC.\") ||\n _name.startsWith(\"PP_GIPAW_CORE_ORBITAL.\") ||\n _name.startsWith(\"PP_GIPAW_ORBITAL.\") ||\n _name === \"PP_RELWFC\" ||\n _name === \"PP_RELBETA\"\n ) {\n return true;\n }\n return false;\n },\n};\n\n// ── Section parsers ────────────────────────────────────────────────\n\nfunction parseHeader(node: XmlNode): PseudopotentialHeader {\n return {\n generated: attr(node, \"generated\") || undefined,\n author: attr(node, \"author\") || undefined,\n date: attr(node, \"date\") || undefined,\n comment: attr(node, \"comment\") || undefined,\n element: attr(node, \"element\").trim(),\n pseudoType: (attr(node, \"pseudo_type\") as PseudopotentialType) || \"NC\",\n relativistic: (attr(node, \"relativistic\") as RelativisticType) || \"scalar\",\n isUltrasoft: attrBool(node, \"is_ultrasoft\"),\n isPaw: attrBool(node, \"is_paw\"),\n isCoulomb: attrBool(node, \"is_coulomb\"),\n hasSo: attrBool(node, \"has_so\"),\n hasWfc: attrBool(node, \"has_wfc\"),\n hasGipaw: attrBool(node, \"has_gipaw\"),\n pawAsGipaw: attrBool(node, \"paw_as_gipaw\"),\n coreCorrection: attrBool(node, \"core_correction\"),\n functional: attr(node, \"functional\"),\n zValence: attrNum(node, \"z_valence\"),\n totalPsenergy: attrNum(node, \"total_psenergy\"),\n wfcCutoff: attrNum(node, \"wfc_cutoff\"),\n rhoCutoff: attrNum(node, \"rho_cutoff\"),\n lMax: attrInt(node, \"l_max\"),\n lMaxRho: attrInt(node, \"l_max_rho\"),\n lLocal: attrInt(node, \"l_local\", -1),\n meshSize: attrInt(node, \"mesh_size\"),\n numberOfWfc: attrInt(node, \"number_of_wfc\"),\n numberOfProj: attrInt(node, \"number_of_proj\"),\n };\n}\n\nfunction parseMesh(node: XmlNode): PseudopotentialMesh {\n return {\n dx: attr(node, \"dx\") ? attrNum(node, \"dx\") : undefined,\n mesh: attr(node, \"mesh\") ? attrInt(node, \"mesh\") : undefined,\n xmin: attr(node, \"xmin\") ? attrNum(node, \"xmin\") : undefined,\n rmax: attrNum(node, \"rmax\"),\n zmesh: attr(node, \"zmesh\") ? attrNum(node, \"zmesh\") : undefined,\n r: parseData(textOf(node[\"PP_R\"])),\n rab: parseData(textOf(node[\"PP_RAB\"])),\n };\n}\n\nfunction parseLocal(node: XmlNode): PseudopotentialLocal {\n return { vloc: parseData(textOf(node)) };\n}\n\nfunction parseBeta(node: XmlNode): BetaProjector {\n return {\n angularMomentum: attrInt(node, \"angular_momentum\"),\n cutoffRadiusIndex: attr(node, \"cutoff_radius_index\")\n ? attrInt(node, \"cutoff_radius_index\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n normConservingRadius: attr(node, \"norm_conserving_radius\")\n ? attrNum(node, \"norm_conserving_radius\")\n : undefined,\n ultrasoftCutoffRadius: attrNum(node, \"ultrasoft_cutoff_radius\"),\n label: attr(node, \"label\"),\n beta: parseData(textOf(node)),\n };\n}\n\nfunction parseNonlocal(node: XmlNode): PseudopotentialNonlocal {\n const betas: BetaProjector[] = [];\n for (const [key, val] of Object.entries(node)) {\n if (key === \"PP_BETA\" || key.startsWith(\"PP_BETA.\")) {\n betas.push(...toArray(val).map(parseBeta));\n }\n }\n\n const dijText = textOf(node[\"PP_DIJ\"]);\n const tokens = dijText.trim().split(/\\s+/).filter(Boolean).map(parseFortranNumber);\n const dij: Array<[number, number, number]> = [];\n\n if (tokens.length > 0) {\n const nProj = betas.length;\n\n // Flat matrix format: tokens.length == nProj^2, row-major\n if (nProj > 0 && tokens.length === nProj * nProj) {\n for (let i = 0; i < nProj; i++) {\n for (let j = 0; j < nProj; j++) {\n dij.push([i + 1, j + 1, tokens[i * nProj + j]]);\n }\n }\n }\n // Triplet format: tokens.length % 3 == 0, each triplet is (i, j, value)\n else if (tokens.length % 3 === 0) {\n for (let k = 0; k < tokens.length; k += 3) {\n dij.push([tokens[k], tokens[k + 1], tokens[k + 2]]);\n }\n }\n }\n\n // PP_AUGMENTATION (optional, child of PP_NONLOCAL)\n const augmentation = node[\"PP_AUGMENTATION\"]\n ? parseAugmentation(node[\"PP_AUGMENTATION\"])\n : undefined;\n\n // nqf from PP_NONLOCAL or PP_AUGMENTATION attributes\n const nqf = augmentation?.nqf ?? undefined;\n\n return { betas, dij, nqf, augmentation };\n}\n\nfunction parseAugmentation(node: XmlNode): AugmentationData {\n return {\n qWithL: attr(node, \"q_with_l\") ? attrBool(node, \"q_with_l\") : undefined,\n nqf: attr(node, \"nqf\") ? attrInt(node, \"nqf\") : undefined,\n shape: attr(node, \"shape\") || undefined,\n rMatchAugfun: attr(node, \"r_match_augfun\")\n ? attrNum(node, \"r_match_augfun\")\n : undefined,\n irc: attr(node, \"irc\") ? attrInt(node, \"irc\") : undefined,\n lmaxAug: attr(node, \"l_max_aug\") ? attrInt(node, \"l_max_aug\") : undefined,\n q: node[\"PP_Q\"] ? parseData(textOf(node[\"PP_Q\"])) : undefined,\n multipoles: node[\"PP_MULTIPOLES\"]\n ? parseData(textOf(node[\"PP_MULTIPOLES\"]))\n : undefined,\n qfcoeff: node[\"PP_QFCOEFF\"]\n ? parseData(textOf(node[\"PP_QFCOEFF\"]))\n : undefined,\n rinner: node[\"PP_RINNER\"]\n ? parseData(textOf(node[\"PP_RINNER\"]))\n : undefined,\n };\n}\n\nfunction parsePswfcNode(node: XmlNode): PseudopotentialWfc {\n return {\n l: attrInt(node, \"l\"),\n occupation: attrNum(node, \"occupation\"),\n label: attr(node, \"label\"),\n n: attr(node, \"n\") ? attrInt(node, \"n\") : undefined,\n pseudoEnergy: attr(node, \"pseudo_energy\")\n ? attrNum(node, \"pseudo_energy\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n ultrasoftCutoffRadius: attr(node, \"ultrasoft_cutoff_radius\")\n ? attrNum(node, \"ultrasoft_cutoff_radius\")\n : undefined,\n chi: parseData(textOf(node)),\n };\n}\n\nfunction parseFullWfcNode(node: XmlNode): FullWfc {\n return {\n l: attrInt(node, \"l\"),\n label: attr(node, \"label\"),\n aewfc: parseData(textOf(node)),\n };\n}\n\nfunction parsePaw(node: XmlNode): PawData {\n return {\n pawDataFormat: attrInt(node, \"paw_data_format\"),\n coreEnergy: attrNum(node, \"core_energy\"),\n occupations: node[\"PP_OCCUPATIONS\"]\n ? parseData(textOf(node[\"PP_OCCUPATIONS\"]))\n : new Float64Array(0),\n aeNlcc: node[\"PP_AE_NLCC\"]\n ? parseData(textOf(node[\"PP_AE_NLCC\"]))\n : new Float64Array(0),\n aeVloc: node[\"PP_AE_VLOC\"]\n ? parseData(textOf(node[\"PP_AE_VLOC\"]))\n : new Float64Array(0),\n aeWfcs: [],\n psWfcs: [],\n };\n}\n\nfunction parseGipaw(node: XmlNode): GipawData {\n const coreOrbitals: GipawData[\"coreOrbitals\"] = [];\n const coreOrbsSection = node[\"PP_GIPAW_CORE_ORBITALS\"];\n if (coreOrbsSection) {\n for (const [key, val] of Object.entries(coreOrbsSection)) {\n if (key.startsWith(\"PP_GIPAW_CORE_ORBITAL.\")) {\n for (const co of toArray(val)) {\n coreOrbitals.push({\n n: attrInt(co, \"n\"),\n l: attrInt(co, \"l\"),\n orbital: parseData(textOf(co)),\n });\n }\n }\n }\n }\n\n const orbitals: GipawData[\"orbitals\"] = [];\n const orbsSection = node[\"PP_GIPAW_ORBITALS\"];\n if (orbsSection) {\n for (const [key, val] of Object.entries(orbsSection)) {\n if (key.startsWith(\"PP_GIPAW_ORBITAL.\")) {\n for (const orb of toArray(val)) {\n orbitals.push({\n l: attrInt(orb, \"l\"),\n label: attr(orb, \"label\"),\n aeOrbital: orb[\"PP_GIPAW_ORBITAL_AE\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_AE\"]))\n : new Float64Array(0),\n psOrbital: orb[\"PP_GIPAW_ORBITAL_PS\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_PS\"]))\n : new Float64Array(0),\n });\n }\n }\n }\n }\n\n let vlocAe = new Float64Array(0);\n let vlocPs = new Float64Array(0);\n const vlocalSection = node[\"PP_GIPAW_VLOCAL\"];\n if (vlocalSection) {\n vlocAe = vlocalSection[\"GIPAW_VLOCAL_AE\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_AE\"]))\n : vlocAe;\n vlocPs = vlocalSection[\"GIPAW_VLOCAL_PS\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_PS\"]))\n : vlocPs;\n }\n\n return {\n gipawDataFormat: attrInt(node, \"gipaw_data_format\"),\n coreOrbitals,\n orbitals,\n vlocAe,\n vlocPs,\n };\n}\n\nfunction parseSpinOrbit(node: XmlNode): SpinOrbitData {\n const relWfcs: SpinOrbitData[\"relWfcs\"] = [];\n for (const wfc of toArray(node[\"PP_RELWFC\"])) {\n relWfcs.push({\n jchi: attrNum(wfc, \"jchi\"),\n index: attr(wfc, \"index\") ? attrInt(wfc, \"index\") : undefined,\n els: attr(wfc, \"els\") || undefined,\n nn: attr(wfc, \"nn\") ? attrInt(wfc, \"nn\") : undefined,\n lchi: attr(wfc, \"lchi\") ? attrInt(wfc, \"lchi\") : undefined,\n oc: attr(wfc, \"oc\") ? attrNum(wfc, \"oc\") : undefined,\n });\n }\n\n const relBetas: SpinOrbitData[\"relBetas\"] = [];\n for (const beta of toArray(node[\"PP_RELBETA\"])) {\n relBetas.push({\n jjj: attrNum(beta, \"jjj\"),\n index: attr(beta, \"index\") ? attrInt(beta, \"index\") : undefined,\n lll: attr(beta, \"lll\") ? attrInt(beta, \"lll\") : undefined,\n });\n }\n\n return { relWfcs, relBetas };\n}\n\n// ── Main parser ────────────────────────────────────────────────────\n\n/**\n * Parse a UPF v2.0.1 pseudopotential string into a Pseudopotential object.\n *\n * @param text - The complete UPF file content as a string.\n * @returns A parsed Pseudopotential object.\n * @throws If the text is not valid UPF v2.0.1 format.\n */\nexport function fromUPF(text: string): Pseudopotential {\n const parser = new XMLParser(parserOptions);\n const doc = parser.parse(text);\n\n const upf: XmlNode = doc?.UPF;\n if (!upf) {\n throw new Error(\"Not a UPF file: missing <UPF> root element\");\n }\n\n const version = (attr(upf, \"version\") || \"2.0.1\") as \"2.0.1\";\n\n // PP_INFO (optional, plain text)\n const info = upf[\"PP_INFO\"] ? textOf(upf[\"PP_INFO\"]).trim() || undefined : undefined;\n\n // PP_HEADER (required, self-closing tag with attributes)\n if (!upf[\"PP_HEADER\"]) {\n throw new Error(\"Missing PP_HEADER section\");\n }\n const header = parseHeader(upf[\"PP_HEADER\"]);\n\n // PP_MESH (required)\n if (!upf[\"PP_MESH\"]) {\n throw new Error(\"Missing PP_MESH section\");\n }\n const mesh = parseMesh(upf[\"PP_MESH\"]);\n\n // PP_NLCC (optional)\n const nlcc = upf[\"PP_NLCC\"] ? parseData(textOf(upf[\"PP_NLCC\"])) : undefined;\n\n // PP_LOCAL (required)\n if (!upf[\"PP_LOCAL\"]) {\n throw new Error(\"Missing PP_LOCAL section\");\n }\n const local = parseLocal(upf[\"PP_LOCAL\"]);\n\n // PP_SEMILOCAL (optional)\n let semilocal: Pseudopotential[\"semilocal\"] | undefined;\n if (upf[\"PP_SEMILOCAL\"]) {\n semilocal = toArray(upf[\"PP_SEMILOCAL\"][\"PP_VNL\"]).map((vnl: XmlNode) => ({\n l: attrInt(vnl, \"L\"),\n j: attr(vnl, \"J\") ? attrNum(vnl, \"J\") : undefined,\n vnl: parseData(textOf(vnl)),\n }));\n }\n\n // PP_NONLOCAL (required)\n if (!upf[\"PP_NONLOCAL\"]) {\n throw new Error(\"Missing PP_NONLOCAL section\");\n }\n const nonlocal = parseNonlocal(upf[\"PP_NONLOCAL\"]);\n\n // PP_PSWFC (optional)\n const pswfcRaw = upf[\"PP_PSWFC\"];\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcRaw) {\n for (const [key, val] of Object.entries(pswfcRaw)) {\n if (key === \"PP_CHI\" || key.startsWith(\"PP_CHI.\")) {\n for (const chi of toArray(val)) {\n pswfc.push(parsePswfcNode(chi));\n }\n }\n }\n }\n\n // PP_FULL_WFC (optional, PAW only)\n let fullWfc: FullWfc[] | undefined;\n if (upf[\"PP_FULL_WFC\"]) {\n const wfcs: FullWfc[] = [];\n for (const [key, val] of Object.entries(upf[\"PP_FULL_WFC\"])) {\n if (key.startsWith(\"PP_AEWFC\")) {\n for (const wfc of toArray(val)) {\n wfcs.push(parseFullWfcNode(wfc));\n }\n }\n }\n fullWfc = wfcs.length > 0 ? wfcs : undefined;\n }\n\n // PP_RHOATOM (required)\n if (!upf[\"PP_RHOATOM\"]) {\n throw new Error(\"Missing PP_RHOATOM section\");\n }\n const rhoatom = parseData(textOf(upf[\"PP_RHOATOM\"]));\n\n // PP_PAW (optional)\n const paw = upf[\"PP_PAW\"] ? parsePaw(upf[\"PP_PAW\"]) : undefined;\n\n // PP_GIPAW (optional — tag may be PP_GIPAW or PP_GIPAW_RECONSTRUCTION)\n const gipaw = upf[\"PP_GIPAW\"]\n ? parseGipaw(upf[\"PP_GIPAW\"])\n : upf[\"PP_GIPAW_RECONSTRUCTION\"]\n ? parseGipaw(upf[\"PP_GIPAW_RECONSTRUCTION\"])\n : undefined;\n\n // PP_SPIN_ORB (optional)\n const spinOrbit = upf[\"PP_SPIN_ORB\"]\n ? parseSpinOrbit(upf[\"PP_SPIN_ORB\"])\n : undefined;\n\n // Populate paw.aeWfcs/psWfcs from top-level sections (UPF v2.0.1 spec:\n // PP_FULL_WFC and PP_PSWFC are siblings of PP_PAW, not children).\n if (paw && fullWfc && fullWfc.length > 0) {\n paw.aeWfcs = fullWfc;\n }\n if (paw && pswfc.length > 0) {\n paw.psWfcs = pswfc.map((w) => ({\n l: w.l,\n label: w.label ?? \"\",\n aewfc: w.chi,\n }));\n }\n\n return {\n version,\n info,\n header,\n mesh,\n nlcc,\n local,\n semilocal,\n nonlocal,\n pswfc,\n fullWfc,\n rhoatom,\n paw,\n gipaw,\n spinOrbit,\n };\n}\n\n// ── Serializer ─────────────────────────────────────────────────────\n\n/**\n * Serialize a Pseudopotential object back to UPF v2.0.1 format.\n *\n * @param pp - The pseudopotential to serialize.\n * @returns The UPF file content as a string.\n */\nexport function toUPF(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n lines.push(`<UPF version=\"${pp.version}\">`);\n lines.push(\"\");\n\n // PP_INFO\n if (pp.info) {\n lines.push(\"<PP_INFO>\");\n lines.push(pp.info);\n lines.push(\"</PP_INFO>\");\n lines.push(\"\");\n }\n\n // PP_HEADER\n lines.push(\"<PP_HEADER\");\n lines.push(` generated=\"${escapeXmlAttr(pp.header.generated ?? \"\")}\"`);\n lines.push(` author=\"${escapeXmlAttr(pp.header.author ?? \"\")}\"`);\n lines.push(` date=\"${escapeXmlAttr(pp.header.date ?? \"\")}\"`);\n lines.push(` comment=\"${escapeXmlAttr(pp.header.comment ?? \"\")}\"`);\n lines.push(` element=\"${pp.header.element}\"`);\n lines.push(` pseudo_type=\"${pp.header.pseudoType}\"`);\n lines.push(` relativistic=\"${pp.header.relativistic}\"`);\n lines.push(` is_ultrasoft=\"${formatFortranBool(pp.header.isUltrasoft)}\"`);\n lines.push(` is_paw=\"${formatFortranBool(pp.header.isPaw)}\"`);\n lines.push(` is_coulomb=\"${formatFortranBool(pp.header.isCoulomb)}\"`);\n lines.push(` has_so=\"${formatFortranBool(pp.header.hasSo)}\"`);\n lines.push(` has_wfc=\"${formatFortranBool(pp.header.hasWfc)}\"`);\n lines.push(` has_gipaw=\"${formatFortranBool(pp.header.hasGipaw)}\"`);\n lines.push(` paw_as_gipaw=\"${formatFortranBool(pp.header.pawAsGipaw)}\"`);\n lines.push(` core_correction=\"${formatFortranBool(pp.header.coreCorrection)}\"`);\n lines.push(` functional=\"${pp.header.functional}\"`);\n lines.push(` z_valence=\"${formatFortranNumber(pp.header.zValence)}\"`);\n lines.push(` total_psenergy=\"${formatFortranNumber(pp.header.totalPsenergy)}\"`);\n lines.push(` wfc_cutoff=\"${formatFortranNumber(pp.header.wfcCutoff)}\"`);\n lines.push(` rho_cutoff=\"${formatFortranNumber(pp.header.rhoCutoff)}\"`);\n lines.push(` l_max=\"${pp.header.lMax}\"`);\n lines.push(` l_max_rho=\"${pp.header.lMaxRho}\"`);\n lines.push(` l_local=\"${pp.header.lLocal}\"`);\n lines.push(` mesh_size=\"${pp.header.meshSize}\"`);\n lines.push(` number_of_wfc=\"${pp.header.numberOfWfc}\"`);\n lines.push(` number_of_proj=\"${pp.header.numberOfProj}\"/>`);\n lines.push(\"\");\n\n // PP_MESH\n const meshAttrs: string[] = [];\n if (pp.mesh.dx != null) meshAttrs.push(`dx=\"${pp.mesh.dx}\"`);\n if (pp.mesh.mesh != null) meshAttrs.push(`mesh=\"${pp.mesh.mesh}\"`);\n if (pp.mesh.xmin != null) meshAttrs.push(`xmin=\"${pp.mesh.xmin}\"`);\n meshAttrs.push(`rmax=\"${pp.mesh.rmax}\"`);\n if (pp.mesh.zmesh != null) meshAttrs.push(`zmesh=\"${pp.mesh.zmesh}\"`);\n lines.push(`<PP_MESH ${meshAttrs.join(\" \")}>`);\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n lines.push(\"\");\n\n // PP_NLCC (optional)\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n lines.push(\"\");\n }\n\n // PP_LOCAL\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n lines.push(\"\");\n\n // PP_SEMILOCAL (optional)\n if (pp.semilocal) {\n lines.push(\"<PP_SEMILOCAL>\");\n for (const vnl of pp.semilocal) {\n lines.push(`<PP_VNL L=\"${vnl.l}\"${vnl.j !== undefined ? ` J=\"${vnl.j}\"` : \"\"}>`);\n lines.push(formatDataArray(vnl.vnl));\n lines.push(\"</PP_VNL>\");\n }\n lines.push(\"</PP_SEMILOCAL>\");\n lines.push(\"\");\n }\n\n // PP_NONLOCAL\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n const betaAttrs = [\n `index=\"${i + 1}\"`,\n `angular_momentum=\"${beta.angularMomentum}\"`,\n `label=\"${beta.label}\"`,\n ];\n if (beta.cutoffRadiusIndex != null) betaAttrs.push(`cutoff_radius_index=\"${beta.cutoffRadiusIndex}\"`);\n if (beta.cutoffRadius != null) betaAttrs.push(`cutoff_radius=\"${formatFortranNumber(beta.cutoffRadius)}\"`);\n betaAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(beta.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_BETA ${betaAttrs.join(\" \")}>`);\n lines.push(formatDataArray(beta.beta));\n lines.push(\"</PP_BETA>\");\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(`${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n\n // PP_AUGMENTATION (optional, USPP/PAW)\n if (pp.nonlocal.augmentation) {\n const aug = pp.nonlocal.augmentation;\n const augAttrs: string[] = [];\n if (aug.qWithL != null) augAttrs.push(`q_with_l=\"${aug.qWithL ? \"T\" : \"F\"}\"`);\n if (aug.nqf != null) augAttrs.push(`nqf=\"${aug.nqf}\"`);\n if (aug.shape != null) augAttrs.push(`shape=\"${aug.shape}\"`);\n if (aug.rMatchAugfun != null) augAttrs.push(`r_match_augfun=\"${formatFortranNumber(aug.rMatchAugfun)}\"`);\n if (aug.irc != null) augAttrs.push(`irc=\"${aug.irc}\"`);\n if (aug.lmaxAug != null) augAttrs.push(`l_max_aug=\"${aug.lmaxAug}\"`);\n lines.push(`<PP_AUGMENTATION ${augAttrs.join(\" \")}>`);\n if (aug.q) {\n lines.push(\"<PP_Q>\");\n lines.push(formatDataArray(aug.q));\n lines.push(\"</PP_Q>\");\n }\n if (aug.multipoles) {\n lines.push(\"<PP_MULTIPOLES>\");\n lines.push(formatDataArray(aug.multipoles));\n lines.push(\"</PP_MULTIPOLES>\");\n }\n if (aug.qfcoeff) {\n lines.push(\"<PP_QFCOEFF>\");\n lines.push(formatDataArray(aug.qfcoeff));\n lines.push(\"</PP_QFCOEFF>\");\n }\n if (aug.rinner) {\n lines.push(\"<PP_RINNER>\");\n lines.push(formatDataArray(aug.rinner));\n lines.push(\"</PP_RINNER>\");\n }\n lines.push(\"</PP_AUGMENTATION>\");\n }\n\n lines.push(\"</PP_NONLOCAL>\");\n lines.push(\"\");\n\n // PP_PSWFC\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (let i = 0; i < pp.pswfc.length; i++) {\n const wfc = pp.pswfc[i];\n const chiAttrs = [\n `index=\"${i + 1}\"`,\n `l=\"${wfc.l}\"`,\n `occupation=\"${formatFortranNumber(wfc.occupation)}\"`,\n `label=\"${wfc.label ?? \"\"}\"`,\n ];\n if (wfc.n != null) chiAttrs.push(`n=\"${wfc.n}\"`);\n if (wfc.pseudoEnergy != null) chiAttrs.push(`pseudo_energy=\"${formatFortranNumber(wfc.pseudoEnergy)}\"`);\n if (wfc.cutoffRadius != null) chiAttrs.push(`cutoff_radius=\"${formatFortranNumber(wfc.cutoffRadius)}\"`);\n if (wfc.ultrasoftCutoffRadius != null) chiAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(wfc.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_CHI ${chiAttrs.join(\" \")}>`);\n lines.push(formatDataArray(wfc.chi));\n lines.push(\"</PP_CHI>\");\n }\n lines.push(\"</PP_PSWFC>\");\n lines.push(\"\");\n }\n\n // PP_FULL_WFC (optional)\n if (pp.fullWfc && pp.fullWfc.length > 0) {\n lines.push(\"<PP_FULL_WFC>\");\n for (const wfc of pp.fullWfc) {\n lines.push(`<PP_AEWFC l=\"${wfc.l}\" label=\"${wfc.label}\">`);\n lines.push(formatDataArray(wfc.aewfc));\n lines.push(\"</PP_AEWFC>\");\n }\n lines.push(\"</PP_FULL_WFC>\");\n lines.push(\"\");\n }\n\n // PP_RHOATOM\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n lines.push(\"\");\n\n // PP_PAW (optional)\n if (pp.paw) {\n lines.push(`<PP_PAW paw_data_format=\"${pp.paw.pawDataFormat}\" core_energy=\"${formatFortranNumber(pp.paw.coreEnergy)}\">`);\n if (pp.paw.occupations.length > 0) {\n lines.push(\"<PP_OCCUPATIONS>\");\n lines.push(formatDataArray(pp.paw.occupations));\n lines.push(\"</PP_OCCUPATIONS>\");\n }\n if (pp.paw.aeNlcc.length > 0) {\n lines.push(\"<PP_AE_NLCC>\");\n lines.push(formatDataArray(pp.paw.aeNlcc));\n lines.push(\"</PP_AE_NLCC>\");\n }\n if (pp.paw.aeVloc.length > 0) {\n lines.push(\"<PP_AE_VLOC>\");\n lines.push(formatDataArray(pp.paw.aeVloc));\n lines.push(\"</PP_AE_VLOC>\");\n }\n if (pp.paw.aeWfcs.length > 0) {\n for (const wfc of pp.paw.aeWfcs) {\n lines.push(`<PP_AEWFC l=\"${wfc.l}\" label=\"${wfc.label}\">`);\n lines.push(formatDataArray(wfc.aewfc));\n lines.push(\"</PP_AEWFC>\");\n }\n }\n if (pp.paw.psWfcs.length > 0) {\n for (const wfc of pp.paw.psWfcs) {\n lines.push(`<PP_PSWFC l=\"${wfc.l}\" label=\"${wfc.label}\">`);\n lines.push(formatDataArray(wfc.aewfc));\n lines.push(\"</PP_PSWFC>\");\n }\n }\n lines.push(\"</PP_PAW>\");\n lines.push(\"\");\n }\n\n // PP_GIPAW (optional)\n if (pp.gipaw) {\n lines.push(`<PP_GIPAW gipaw_data_format=\"${pp.gipaw.gipawDataFormat}\">`);\n if (pp.gipaw.coreOrbitals.length > 0) {\n lines.push(`<PP_GIPAW_CORE_ORBITALS number_of_core_orbitals=\"${pp.gipaw.coreOrbitals.length}\">`);\n for (let i = 0; i < pp.gipaw.coreOrbitals.length; i++) {\n const co = pp.gipaw.coreOrbitals[i];\n lines.push(`<PP_GIPAW_CORE_ORBITAL.${i + 1} n=\"${co.n}\" l=\"${co.l}\">`);\n if (co.orbital.length > 0) lines.push(formatDataArray(co.orbital));\n lines.push(`</PP_GIPAW_CORE_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_CORE_ORBITALS>\");\n }\n if (pp.gipaw.orbitals.length > 0) {\n lines.push(\"<PP_GIPAW_ORBITALS>\");\n for (let i = 0; i < pp.gipaw.orbitals.length; i++) {\n const orb = pp.gipaw.orbitals[i];\n lines.push(`<PP_GIPAW_ORBITAL.${i + 1} l=\"${orb.l}\" label=\"${escapeXmlAttr(orb.label)}\">`);\n lines.push(\"<PP_GIPAW_ORBITAL_AE>\");\n lines.push(formatDataArray(orb.aeOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_AE>\");\n lines.push(\"<PP_GIPAW_ORBITAL_PS>\");\n lines.push(formatDataArray(orb.psOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_PS>\");\n lines.push(`</PP_GIPAW_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_ORBITALS>\");\n }\n if (pp.gipaw.vlocAe.length > 0 || pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<PP_GIPAW_VLOCAL>\");\n if (pp.gipaw.vlocAe.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_AE>\");\n lines.push(formatDataArray(pp.gipaw.vlocAe));\n lines.push(\"</GIPAW_VLOCAL_AE>\");\n }\n if (pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_PS>\");\n lines.push(formatDataArray(pp.gipaw.vlocPs));\n lines.push(\"</GIPAW_VLOCAL_PS>\");\n }\n lines.push(\"</PP_GIPAW_VLOCAL>\");\n }\n lines.push(\"</PP_GIPAW>\");\n lines.push(\"\");\n }\n\n lines.push(\"</UPF>\");\n\n return lines.join(\"\\n\");\n}\n","/**\n * UPF v1 pseudopotential parser and serializer.\n *\n * UPF v1 is the legacy Quantum ESPRESSO format with fixed-width headers\n * and `<SECTION>`/`</SECTION>` delimiters (not XML attributes).\n * Units: Rydberg (energy), Bohr (length) — same as UPF v2.\n */\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nfunction extractSection(text: string, tag: string): string | null {\n const open = `<${tag}>`;\n const close = `</${tag}>`;\n const start = text.indexOf(open);\n if (start === -1) return null;\n const end = text.indexOf(close, start);\n if (end === -1) return null;\n return text.substring(start + open.length, end);\n}\n\nfunction extractSubSection(text: string, tag: string): string | null {\n return extractSection(text, tag);\n}\n\nfunction lines(text: string): string[] {\n return text.split(\"\\n\").filter((l) => l.trim().length > 0);\n}\n\n/**\n * Parse a UPF v1 pseudopotential string.\n *\n * UPF v1 format:\n * - First line: version number (0 or 1)\n * - Header: element, type, functional, z_valence, etc.\n * - `<PP_MESH>`: radial grid\n * - `<PP_LOCAL>`: local potential\n * - `<PP_NONLOCAL>`: projectors and D_ij\n * - `<PP_PSWFC>`: pseudo wavefunctions\n * - `<PP_RHOATOM>`: atomic charge density\n */\nexport function fromUPFv1(text: string): Pseudopotential {\n // Detect UPF v1: first non-empty line should be a number\n const firstLine = text.trim().split(\"\\n\")[0].trim();\n const versionMatch = firstLine.match(/^(\\d+)/);\n if (!versionMatch) {\n throw new Error(\"Not a UPF v1 file: first line is not a version number\");\n }\n\n // Extract header section\n const headerSection = extractSection(text, \"PP_HEADER\");\n if (!headerSection) throw new Error(\"Missing PP_HEADER section\");\n\n const headerLines = lines(headerSection);\n\n // Parse header fields (UPF v1 uses free-format Fortran reads)\n // Line format varies; we parse what we can find\n let element = \"X\";\n let pseudoType: PseudopotentialHeader[\"pseudoType\"] = \"NC\";\n let functional = \"\";\n let zValence = 0;\n let lMax = 0;\n let meshSize = 0;\n let numberOfWfc = 0;\n let numberOfProj = 0;\n let coreCorrection = false;\n\n for (const line of headerLines) {\n const trimmed = line.trim();\n // Try to extract element from first meaningful line\n // Handle quoted element names like 'H' or unquoted like H\n const elemMatch = trimmed.match(/^['\"]?([A-Z][a-z]?)['\"]?(?:\\s|$)/);\n if (elemMatch) {\n element = elemMatch[1];\n }\n // Look for pseudo type indicators\n if (trimmed.includes(\"'NC'\") || trimmed.includes('\"NC\"') || trimmed.includes(\"NC\")) {\n pseudoType = \"NC\";\n }\n if (trimmed.includes(\"'US'\") || trimmed.includes('\"US\"') || trimmed.includes(\"US\")) {\n pseudoType = \"US\";\n }\n if (trimmed.includes(\"'PAW'\") || trimmed.includes('\"PAW\"') || trimmed.includes(\"PAW\")) {\n pseudoType = \"PAW\";\n }\n // Look for functional (quoted string like 'SLA-PW-PBE-PBE')\n const funcMatch = trimmed.match(/^['\"]([^'\"]+)['\"]/);\n if (funcMatch && (funcMatch[1].includes(\"SLA\") || funcMatch[1].includes(\"PBE\") || funcMatch[1].includes(\"LDA\"))) {\n functional = funcMatch[1];\n }\n // Look for z_valence\n const zMatch = trimmed.match(/(\\d+\\.?\\d*)\\s*(?:zp|z_valence|z_p)/i);\n if (zMatch) zValence = parseFloat(zMatch[1]);\n // Look for lmax\n const lmaxMatch = trimmed.match(/lmax\\s*=\\s*(\\d+)/i);\n if (lmaxMatch) lMax = parseInt(lmaxMatch[1]);\n // Look for mesh size\n const meshMatch = trimmed.match(/mesh\\s*=\\s*(\\d+)/i);\n if (meshMatch) meshSize = parseInt(meshMatch[1]);\n // Look for number of wavefunctions and projectors\n const nwfcMatch = trimmed.match(/(\\d+)\\s+(\\d+)\\s+(?:nwfc|nbeta)/i);\n if (nwfcMatch) {\n numberOfWfc = parseInt(nwfcMatch[1]);\n numberOfProj = parseInt(nwfcMatch[2]);\n }\n // Core correction\n if (trimmed.includes(\".true.\") || trimmed.includes(\"T\")) {\n coreCorrection = true;\n }\n }\n\n // Parse PP_MESH section\n const meshSection = extractSection(text, \"PP_MESH\");\n let r = new Float64Array(0);\n let rab = new Float64Array(0);\n\n if (meshSection) {\n const rSection = extractSubSection(meshSection, \"PP_R\");\n const rabSection = extractSubSection(meshSection, \"PP_RAB\");\n if (rSection) r = parseFloat64Array(rSection);\n if (rabSection) rab = parseFloat64Array(rabSection);\n }\n\n if (r.length === 0) throw new Error(\"Empty or missing PP_R section\");\n meshSize = r.length;\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Parse PP_LOCAL section\n const localSection = extractSection(text, \"PP_LOCAL\");\n if (!localSection) throw new Error(\"Missing PP_LOCAL section\");\n const local: PseudopotentialLocal = { vloc: parseFloat64Array(localSection) };\n\n // Parse PP_NONLOCAL section\n const nonlocalSection = extractSection(text, \"PP_NONLOCAL\");\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n\n if (nonlocalSection) {\n // Parse beta projectors\n const betaMatches = nonlocalSection.match(/<PP_BETA[^>]*>([\\s\\S]*?)<\\/PP_BETA>/g);\n if (betaMatches) {\n for (const betaBlock of betaMatches) {\n const inner = betaBlock.replace(/<\\/?PP_BETA[^>]*>/g, \"\");\n const innerLines = lines(inner);\n if (innerLines.length >= 2) {\n // First line: nbeta, lll, label\n const metaParts = innerLines[0].trim().split(/\\s+/);\n const l = metaParts.length >= 2 ? parseInt(metaParts[1]) : 0;\n const label = metaParts.length >= 3 ? metaParts[2].replace(/['\"]/g, \"\") : `l=${l}`;\n\n // Second line: kkbeta (cutoff index)\n const cutoffLine = innerLines[1].trim().split(/\\s+/);\n const cutoffIndex = cutoffLine.length >= 1 ? parseInt(cutoffLine[0]) : 0;\n\n // Remaining lines: projector data\n const dataText = innerLines.slice(1).join(\"\\n\");\n const betaData = parseFloat64Array(dataText.replace(/^\\s*\\d+\\s+/gm, \"\"));\n\n betas.push({\n angularMomentum: l,\n cutoffRadiusIndex: cutoffIndex,\n ultrasoftCutoffRadius: 0,\n label,\n beta: betaData,\n });\n }\n }\n }\n\n // Parse D_ij\n const dijSection = extractSection(nonlocalSection, \"PP_DIJ\");\n if (dijSection) {\n const dijLines = lines(dijSection);\n for (const line of dijLines) {\n const parts = line.trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 3) {\n const nb = parseInt(parts[0]);\n const mb = parseInt(parts[1]);\n const val = parseFortranNumber(parts[2]);\n if (!isNaN(nb) && !isNaN(mb) && !isNaN(val)) {\n dij.push([nb, mb, val]);\n }\n }\n }\n }\n }\n\n const nonlocal: PseudopotentialNonlocal = { betas, dij };\n\n // Parse PP_PSWFC section\n const pswfcSection = extractSection(text, \"PP_PSWFC\");\n const pswfc: PseudopotentialWfc[] = [];\n\n if (pswfcSection) {\n const pswfcLines = lines(pswfcSection);\n let i = 0;\n while (i < pswfcLines.length) {\n const line = pswfcLines[i].trim();\n // Wavefunction header: label l oc\n const wfcMatch = line.match(/['\"]?(\\w+)['\"]?\\s+(\\d+)\\s+([\\d.]+)/);\n if (wfcMatch) {\n const label = wfcMatch[1];\n const l = parseInt(wfcMatch[2]);\n const occupation = parseFloat(wfcMatch[3]);\n i++;\n // Collect data lines until next header or end\n const dataLines: string[] = [];\n while (i < pswfcLines.length && !pswfcLines[i].trim().match(/['\"]?\\w+['\"]?\\s+\\d+\\s+[\\d.]+/)) {\n dataLines.push(pswfcLines[i]);\n i++;\n }\n const chi = parseFloat64Array(dataLines.join(\"\\n\"));\n pswfc.push({ l, occupation, label, chi });\n } else {\n i++;\n }\n }\n }\n\n // Parse PP_RHOATOM section\n const rhoatomSection = extractSection(text, \"PP_RHOATOM\");\n const rhoatom = rhoatomSection ? parseFloat64Array(rhoatomSection) : new Float64Array(meshSize);\n\n return {\n format: \"UPF1\",\n version: \"1.0.0\",\n header: {\n element,\n pseudoType,\n relativistic: \"scalar\",\n isUltrasoft: pseudoType === \"US\",\n isPaw: pseudoType === \"PAW\",\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize,\n numberOfWfc,\n numberOfProj,\n },\n mesh,\n local,\n nonlocal,\n pswfc,\n rhoatom,\n };\n}\n\n/**\n * Serialize a Pseudopotential to UPF v1 format.\n *\n * NOTE: UPF v1 is a legacy format. This serializer produces valid UPF v1\n * but UPF v2 is preferred for new files.\n */\nexport function toUPFv1(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n // Version line\n lines.push(\" 0\");\n lines.push(\"<PP_HEADER>\");\n lines.push(` '${pp.header.element}'`);\n lines.push(` '${pp.header.pseudoType}'`);\n lines.push(` ${pp.header.coreCorrection ? \".true.\" : \".false.\"} nlcc`);\n lines.push(` '${pp.header.functional}' dft`);\n lines.push(` ${pp.header.zValence.toFixed(8)} zp`);\n lines.push(` ${pp.header.totalPsenergy.toFixed(8)} etotps`);\n lines.push(` ${pp.header.wfcCutoff.toFixed(2)} ${pp.header.rhoCutoff.toFixed(2)} ecutwfc,ecutrho`);\n lines.push(` ${pp.header.lMax} 'lmax'`);\n lines.push(` ${pp.mesh.r.length} 'mesh'`);\n lines.push(` ${pp.pswfc.length} ${pp.nonlocal.betas.length} 'nwfc nbeta'`);\n\n // Wavefunction labels\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(4)}`);\n }\n\n lines.push(\"</PP_HEADER>\");\n\n lines.push(\"<PP_MESH>\");\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n }\n\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n lines.push(`<PP_BETA>`);\n lines.push(` ${i + 1} ${beta.angularMomentum} '${beta.label}'`);\n lines.push(` ${pp.mesh.r.length}`);\n lines.push(formatDataArray(beta.beta));\n lines.push(`</PP_BETA>`);\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(` ${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n lines.push(\"</PP_NONLOCAL>\");\n\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(8)}`);\n lines.push(formatDataArray(wfc.chi));\n }\n lines.push(\"</PP_PSWFC>\");\n }\n\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n\n return lines.join(\"\\n\");\n}\n","import { PeriodicTable } from \"../../data/periodictable/atomicData\";\n\n/** Reverse lookup: element symbol → atomic number. */\nconst SymbolToZ = new Map<string, number>();\nfor (const [z, info] of Object.entries(PeriodicTable)) {\n SymbolToZ.set(info.symbol, Number(z));\n}\n\n/** Return the element symbol for a given atomic number (1-based). Returns \"X\" if unknown. */\nexport function guessElement(z: number): string {\n const info = PeriodicTable[Math.round(z)];\n return info?.symbol ?? \"X\";\n}\n\n/** Return the atomic number for a given element symbol. Returns 0 if unknown. */\nexport function elementToZ(element: string): number {\n return SymbolToZ.get(element) ?? 0;\n}\n","/**\n * FHI98PP (.cpi / .fhi) pseudopotential parser and serializer.\n *\n * The FHI format stores norm-conserving pseudopotentials in semilocal form\n * on a logarithmic radial grid. Units: Hartree (energy), Bohr (length).\n *\n * Grid formula: r(i) = (exp(dx * i) - 1) / Z_eff\n * Stored data: V_l(r) = r * [V_nl(r) + Z_ion/r] (semilocal with Coulomb tail)\n *\n * References:\n * - Fuchs & Scheffler, Comput. Phys. Commun. 119, 67 (1999)\n * - ABINIT format 6: .fhi = ABINIT header + .cpi content\n */\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement } from \"./elements\";\n\n/**\n * Parse an FHI98PP pseudopotential file — auto-detects format.\n *\n * - `.fhi` format (ABINIT format 6): 7 ABINIT header lines + .cpi content\n * - `.cpi` format: starts directly with valence data\n *\n * Detection: if the first non-empty line starts with a digit → `.cpi`;\n * otherwise → `.fhi`.\n */\nexport function fromFHI(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\");\n const firstNonEmpty = allLines.find((l) => l.trim().length > 0);\n if (!firstNonEmpty) throw new Error(\"FHI file too short to parse\");\n\n // .fhi format (ABINIT format 6) starts with a text description.\n // .cpi format starts with a number (Z_val).\n if (/^\\s*\\d/.test(firstNonEmpty)) {\n return parseCpi(text);\n }\n return parseFhiHeader(text);\n}\n\n/**\n * Parse a raw .cpi body (without ABINIT header).\n *\n * Format:\n * Line 1: Z_val n_components\n * Lines 2+: legacy zero-header (variable length, scanned for the mesh line)\n * Then: index r(i) V_0(i) V_1(i) ... V_{lmax}(i) [f_core f_core' f_core'']\n */\nfunction parseCpi(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 4) {\n throw new Error(\"FHI file too short to parse\");\n }\n\n // Line 1: Z_val, n_components\n const line1 = allLines[0].trim().split(/\\s+/);\n const zValence = parseFortranNumber(line1[0]);\n const nComponents = parseIntSafe(line1[1]);\n const lMax = nComponents - 1;\n\n // Lines 2+: legacy header (variable number of zero lines).\n // Scan for the mesh line: first token is a positive integer (mesh_max),\n // second token is a floating-point number (dx).\n let meshLineIdx = 1;\n for (; meshLineIdx < allLines.length; meshLineIdx++) {\n const parts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 2) {\n const firstInt = parseIntSafe(parts[0]);\n if (firstInt > 0) break;\n }\n }\n const meshParts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n const meshMax = parseIntSafe(meshParts[0]);\n const dx = parseFortranNumber(meshParts[1]);\n\n // Parse data block (lines after mesh line)\n // Columns: index, r(i), V_0(i), V_1(i), ... [, f_core, f_core', f_core'']\n const rValues: number[] = [];\n const semilocal: Float64Array[] = [];\n for (let l = 0; l <= lMax; l++) {\n semilocal.push(new Float64Array(meshMax));\n }\n let hasNlcc = false;\n const nlccData: number[] = [];\n\n for (let i = meshLineIdx + 1; i < allLines.length && rValues.length < meshMax; i++) {\n const parts = allLines[i].trim().split(/\\s+/).filter(Boolean);\n if (parts.length < 3) continue;\n\n const idx = parseIntSafe(parts[0]);\n const r = parseFortranNumber(parts[1]);\n\n // Semilocal potentials\n for (let l = 0; l <= lMax && l + 2 < parts.length; l++) {\n semilocal[l][rValues.length] = parseFortranNumber(parts[l + 2]);\n }\n\n // NLCC data (columns after semilocal potentials)\n const nlccStart = nComponents + 2;\n if (parts.length > nlccStart) {\n hasNlcc = true;\n nlccData.push(parseFortranNumber(parts[nlccStart]));\n }\n\n rValues.push(r);\n }\n\n // Build mesh\n const r = new Float64Array(rValues);\n const rmax = r[r.length - 1];\n\n // Compute rab (dr/di) from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n dx,\n rmax,\n r,\n rab,\n };\n\n // Convert semilocal to local potential (l=0 channel is typically the local part)\n // For FHI format, V_0 is the l=0 semilocal potential which includes the local part\n const local: PseudopotentialLocal = {\n vloc: semilocal.length > 0 ? semilocal[0] : new Float64Array(r.length),\n };\n\n // Store semilocal potentials\n const semilocalPotentials = semilocal.map((vnl, l) => ({\n l,\n vnl,\n }));\n\n // No KB projectors from FHI format — store as semilocal\n const nonlocal: PseudopotentialNonlocal = {\n betas: [],\n dij: [],\n };\n\n // Build rhoatom (approximate from semilocal if available)\n const rhoatom = new Float64Array(r.length);\n\n return {\n format: \"CPI\",\n version: \"2.0.1\",\n header: {\n element: \"\",\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: hasNlcc,\n functional: \"\",\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: 0,\n numberOfProj: 0,\n },\n mesh,\n local,\n semilocal: semilocalPotentials,\n nonlocal,\n pswfc: [],\n rhoatom,\n nlcc: hasNlcc ? new Float64Array(nlccData) : undefined,\n };\n}\n\n/**\n * Parse an FHI .fhi file (ABINIT format 6).\n * Skips the 7 ABINIT header lines, then parses the .cpi body.\n */\nfunction parseFhiHeader(text: string): Pseudopotential {\n // Skip 7 ABINIT header lines, then parse as .cpi\n const allLines = text.split(\"\\n\");\n const cpiContent = allLines.slice(7).join(\"\\n\");\n const pp = parseCpi(cpiContent);\n\n // Extract metadata from ABINIT header\n if (allLines.length >= 3) {\n const line2 = allLines[1].trim().split(/\\s+/);\n if (line2.length >= 1) {\n const zatom = parseFloat(line2[0]);\n if (zatom > 0) pp.header.element = guessElement(zatom);\n }\n if (line2.length >= 2) {\n pp.header.zValence = parseFloat(line2[1]);\n }\n\n const line3 = allLines[2].trim().split(/\\s+/);\n if (line3.length >= 3) {\n // pspcod should be 6 for FHI\n const pspxc = parseIntSafe(line3[1]);\n pp.header.xcCode = pspxc;\n }\n }\n\n return pp;\n}\n\n/**\n * Serialize a Pseudopotential to FHI .cpi format.\n */\nexport function toFHI(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const nComponents = pp.header.lMax + 1;\n const r = pp.mesh.r;\n\n // Line 1: Z_val, n_components\n lines.push(`${formatFortranNumber(pp.header.zValence, 20)} ${nComponents}`);\n\n // Lines 2-10: legacy header (zeros)\n for (let i = 0; i < 9; i++) {\n lines.push(\" 0.0000 0.0000 0.0000 0.0000\");\n }\n\n // Line 11: mesh_max, dx\n const dx = pp.mesh.dx ?? 0.01;\n lines.push(`${r.length.toString().padStart(6)} ${formatFortranNumber(dx, 20)}`);\n\n // Data block\n for (let i = 0; i < r.length; i++) {\n const parts: string[] = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(r[i], 20),\n ];\n\n // Semilocal potentials or local potential\n if (pp.semilocal && pp.semilocal.length > 0) {\n for (let l = 0; l <= pp.header.lMax; l++) {\n const sl = pp.semilocal.find((s) => s.l === l);\n parts.push(formatFortranNumber(sl ? sl.vnl[i] : 0, 20));\n }\n } else {\n // Use local potential for all channels\n for (let l = 0; l <= pp.header.lMax; l++) {\n parts.push(formatFortranNumber(pp.local.vloc[i], 20));\n }\n }\n\n // NLCC data\n if (pp.nlcc && i < pp.nlcc.length) {\n parts.push(formatFortranNumber(pp.nlcc[i], 20));\n }\n\n lines.push(parts.join(\" \"));\n }\n\n return lines.join(\"\\n\");\n}\n\n\n","/**\n * PSP8 (ABINIT format 8) pseudopotential parser and serializer.\n *\n * PSP8 is a norm-conserving pseudopotential format produced by ONCVPSP\n * and used widely in the ABINIT/PseudoDojo ecosystem.\n *\n * Units: Hartree (energy), Bohr (length).\n * Grid: Linear, r(i) = (i-1) * dr, starting at r=0.\n *\n * Reference: https://docs.abinit.org/developers/psp8_info/\n */\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement, elementToZ } from \"./elements\";\n\n/**\n * Parse a PSP8 pseudopotential file.\n *\n * Structure:\n * Header (6-7 lines):\n * Line 1: title\n * Line 2: zatom, zion, pspd\n * Line 3: pspcod(=8), pspxc, lmax, lloc, mmax, r2well\n * Line 4: rchrg, fchrg, qchrg\n * Line 5: nproj(0..lmax)\n * Line 6: extension_switch\n * Line 7 (if extension_switch=2 or 3): nprojso(1..lmax)\n *\n * Data blocks:\n * For each l with nproj(l) > 0: projector block\n * Local potential block\n * If extension_switch=2 or 3: SO projector blocks\n * If fchrg > 0: NLCC block\n */\nexport function fromPSP8(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 6) {\n throw new Error(\"PSP8 file too short to parse\");\n }\n\n let lineIdx = 0;\n\n // Line 1: title\n const title = allLines[lineIdx++].trim();\n\n // Line 2: zatom, zion, pspd\n const line2 = allLines[lineIdx++].trim().split(/\\s+/);\n const zatom = parseFortranNumber(line2[0]);\n const zion = parseFortranNumber(line2[1]);\n const pspd = line2.length > 2 ? line2[2] : \"\";\n\n // Line 3: pspcod, pspxc, lmax, lloc, mmax, r2well\n const line3 = allLines[lineIdx++].trim().split(/\\s+/);\n const pspcod = parseIntSafe(line3[0]);\n if (pspcod !== 8) {\n throw new Error(`Expected pspcod=8 for PSP8 format, got ${pspcod}`);\n }\n const pspxc = parseIntSafe(line3[1]);\n const lmax = parseIntSafe(line3[2]);\n const lloc = parseIntSafe(line3[3]);\n const mmax = parseIntSafe(line3[4]);\n\n // Line 4: rchrg, fchrg, qchrg\n const line4 = allLines[lineIdx++].trim().split(/\\s+/);\n const rchrg = parseFortranNumber(line4[0]);\n const fchrg = parseFortranNumber(line4[1]);\n const qchrg = line4.length > 2 ? parseFortranNumber(line4[2]) : 0;\n\n // Line 5: nproj(0..lmax)\n const line5 = allLines[lineIdx++].trim().split(/\\s+/);\n const nproj: number[] = [];\n for (let l = 0; l <= lmax; l++) {\n nproj.push(l < line5.length ? parseIntSafe(line5[l]) : 0);\n }\n\n // Line 6: extension_switch\n const extensionSwitch = parseIntSafe(allLines[lineIdx++].trim());\n\n // Line 7 (if SO): nprojso(1..lmax)\n const nprojso: number[] = [];\n if (extensionSwitch === 2 || extensionSwitch === 3) {\n const line7 = allLines[lineIdx++].trim().split(/\\s+/);\n for (let l = 1; l <= lmax; l++) {\n nprojso.push(l - 1 < line7.length ? parseIntSafe(line7[l - 1]) : 0);\n }\n }\n\n // Build linear radial grid\n const rValues = new Float64Array(mmax);\n for (let i = 0; i < mmax; i++) {\n rValues[i] = i * (mmax > 1 ? (rValues[mmax - 1] || 1.0) / (mmax - 1) : 0);\n }\n // We'll fill in actual r values from data blocks\n\n // Parse projector blocks and local potential\n const betas: BetaProjector[] = [];\n let localVloc = new Float64Array(mmax);\n const ekbValues: number[][] = [];\n\n // Data blocks appear in l order. If lloc <= lmax, the local potential\n // replaces the projector block at position lloc.\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) {\n // This is the local potential block\n // Header line: just the l value\n const headerLine = allLines[lineIdx++].trim();\n // Data: mmax lines of (index, r, vloc)\n const vlocValues = new Float64Array(mmax);\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 3) {\n const idx = parseIntSafe(parts[0]);\n if (i === 0) rValues[i] = parseFortranNumber(parts[1]);\n if (i > 0) rValues[i] = parseFortranNumber(parts[1]);\n vlocValues[i] = parseFortranNumber(parts[2]);\n }\n }\n localVloc = vlocValues;\n } else if (nproj[l] > 0) {\n // Projector block\n // Header line: l ekb(1) ekb(2) ...\n const headerParts = allLines[lineIdx++].trim().split(/\\s+/);\n const blockL = parseIntSafe(headerParts[0]);\n const ekb: number[] = [];\n for (let p = 1; p < headerParts.length; p++) {\n ekb.push(parseFortranNumber(headerParts[p]));\n }\n ekbValues.push(ekb);\n\n // Data: mmax lines of (index, r, projector_1, projector_2, ...)\n const projectorData: Float64Array[] = [];\n for (let p = 0; p < nproj[l]; p++) {\n projectorData.push(new Float64Array(mmax));\n }\n\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 3) {\n if (i === 0) rValues[i] = parseFortranNumber(parts[1]);\n if (i > 0) rValues[i] = parseFortranNumber(parts[1]);\n for (let p = 0; p < nproj[l] && p + 2 < parts.length; p++) {\n projectorData[p][i] = parseFortranNumber(parts[p + 2]);\n }\n }\n }\n\n // Create one beta projector per ekb value\n for (let p = 0; p < nproj[l]; p++) {\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}`,\n beta: projectorData[p],\n });\n }\n } else {\n // No projectors for this l, and not local channel — skip (shouldn't happen)\n }\n }\n\n // If lloc > lmax, local potential comes after all projector blocks\n if (lloc > lmax) {\n // Header line\n const headerLine = allLines[lineIdx++].trim();\n const vlocValues = new Float64Array(mmax);\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 3) {\n if (i === 0) rValues[i] = parseFortranNumber(parts[1]);\n if (i > 0) rValues[i] = parseFortranNumber(parts[1]);\n vlocValues[i] = parseFortranNumber(parts[2]);\n }\n }\n localVloc = vlocValues;\n }\n\n // Parse SO projector blocks (extension_switch == 2 or 3)\n if (extensionSwitch === 2 || extensionSwitch === 3) {\n for (let l = 1; l <= lmax; l++) {\n if (nprojso[l - 1] > 0) {\n // Header line: l ekbso(1) ekbso(2) ...\n const soHeaderParts = allLines[lineIdx++].trim().split(/\\s+/);\n const soEkb: number[] = [];\n for (let p = 1; p < soHeaderParts.length; p++) {\n soEkb.push(parseFortranNumber(soHeaderParts[p]));\n }\n // Data: mmax lines of (index, r, beta_so_1, beta_so_2, ...)\n const nProjSo = nprojso[l - 1];\n const soProjectorData: Float64Array[] = [];\n for (let p = 0; p < nProjSo; p++) {\n soProjectorData.push(new Float64Array(mmax));\n }\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n for (let p = 0; p < nProjSo && p + 2 < parts.length; p++) {\n soProjectorData[p][i] = parseFortranNumber(parts[p + 2]);\n }\n }\n // Add SO projectors with \"so\" label suffix\n for (let p = 0; p < nProjSo; p++) {\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}-so`,\n beta: soProjectorData[p],\n });\n }\n }\n }\n }\n\n // Parse NLCC block if present\n let nlcc: Float64Array | undefined;\n if (fchrg > 0) {\n nlcc = new Float64Array(mmax);\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 3) {\n nlcc[i] = parseFortranNumber(parts[2]);\n }\n }\n }\n\n // Parse pseudo valence charge block if extension_switch == 1 or 3\n const rhoatom = new Float64Array(mmax);\n if (extensionSwitch === 1 || extensionSwitch === 3) {\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 3) {\n rhoatom[i] = parseFortranNumber(parts[2]);\n }\n }\n }\n\n // Build mesh\n const rmax = rValues[mmax - 1] || 0;\n const dr = mmax > 1 ? rmax / (mmax - 1) : 0;\n const rab = new Float64Array(mmax).fill(dr);\n\n const mesh: PseudopotentialMesh = {\n gridType: \"linear\",\n rmax,\n r: rValues,\n rab,\n };\n\n // Build D_ij matrix from ekb values\n // For single projectors per l: dij[i][i] = ekb[i]\n // For multiple projectors: dij is block-diagonal\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n let ekbIdx = 0;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) continue;\n if (nproj[l] > 0) {\n const nProjL = nproj[l];\n const ekbL = ekbValues[ekbIdx++] ?? [];\n for (let i = 0; i < nProjL; i++) {\n for (let j = 0; j < nProjL; j++) {\n const val = i === j ? (ekbL[i] ?? 1.0) : 0;\n dij.push([projIdx + i, projIdx + j, val]);\n }\n }\n projIdx += nProjL;\n }\n }\n\n // Guess element from zatom\n const element = guessElement(zatom);\n\n // Map pspxc to functional string\n const functional = pspxcToFunctional(pspxc);\n\n return {\n format: \"PSP8\",\n version: \"2.0.1\",\n header: {\n element,\n generated: title,\n date: pspd,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: extensionSwitch === 2 || extensionSwitch === 3,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: fchrg > 0,\n functional,\n zValence: zion,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: lmax,\n lMaxRho: lmax,\n lLocal: lloc,\n meshSize: mmax,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n xcCode: pspxc,\n extensionSwitch,\n },\n mesh,\n local: { vloc: localVloc },\n nonlocal: { betas, dij },\n pswfc: [],\n rhoatom,\n nlcc: nlcc,\n };\n}\n\n/**\n * Serialize a Pseudopotential to PSP8 format.\n */\nexport function toPSP8(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const lmax = pp.header.lMax;\n const mmax = pp.mesh.r.length;\n const lloc = pp.header.lLocal ?? 0;\n const nproj: number[] = new Array(lmax + 1).fill(0);\n\n // Count projectors per l channel\n for (const beta of pp.nonlocal.betas) {\n if (beta.angularMomentum <= lmax) {\n nproj[beta.angularMomentum]++;\n }\n }\n\n // Header\n const zatom = elementToZ(pp.header.element);\n lines.push(pp.header.generated ?? `${pp.header.element} ${pp.header.functional}`);\n const pspd = pp.header.date ?? \"000000\";\n lines.push(\n `${zatom.toFixed(4).padStart(12)} ${pp.header.zValence.toFixed(4).padStart(12)} ${pspd.padStart(8)}`,\n );\n lines.push(\n ` 8 ${pp.header.xcCode ?? 0} ${lmax} ${lloc} ${mmax} 0`,\n );\n const rchrg = 0;\n const fchrg = pp.header.coreCorrection ? 1.0 : 0.0;\n const qchrg = 0;\n lines.push(`${rchrg.toFixed(4).padStart(12)} ${fchrg.toFixed(4).padStart(12)} ${qchrg.toFixed(4).padStart(12)}`);\n lines.push(` ${nproj.join(\" \")}`);\n lines.push(` ${pp.header.extensionSwitch ?? 0}`);\n\n // Projector blocks\n const ekb = pp.nonlocal.dij;\n let projOffset = 1;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) continue;\n if (nproj[l] === 0) continue;\n\n // Find ekb values for this l channel using global projector indices\n const lBetas = pp.nonlocal.betas.filter((b) => b.angularMomentum === l);\n const ekbValues = lBetas.map((_, i) => {\n const globalIdx = projOffset + i;\n const entry = ekb.find(([nb, mb]) => nb === globalIdx && mb === globalIdx);\n return entry ? entry[2] : 1.0;\n });\n\n lines.push(` ${l} ${ekbValues.map((e) => formatFortranNumber(e)).join(\" \")}`);\n\n for (let i = 0; i < mmax; i++) {\n const parts = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(pp.mesh.r[i]),\n ];\n for (const beta of lBetas) {\n parts.push(formatFortranNumber(beta.beta[i] ?? 0));\n }\n lines.push(parts.join(\" \"));\n }\n\n projOffset += lBetas.length;\n }\n\n // Local potential block\n lines.push(` ${lloc}`);\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.local.vloc[i])}`,\n );\n }\n\n // NLCC block\n if (pp.nlcc) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.nlcc[i])}`,\n );\n }\n }\n\n // Pseudo valence charge block (if extension_switch == 1 or 3)\n if (pp.header.extensionSwitch === 1 || pp.header.extensionSwitch === 3) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.rhoatom[i])}`,\n );\n }\n }\n\n return lines.join(\"\\n\");\n}\n\n\n\nfunction pspxcToFunctional(pspxc: number): string {\n const map: Record<number, string> = {\n 1: \"LDA (PW)\",\n 2: \"LDA (PW92)\",\n 7: \"PW92\",\n 11: \"PBE\",\n 14: \"PBEsol\",\n 23: \"B3LYP\",\n };\n return map[pspxc] ?? `xc=${pspxc}`;\n}\n","/**\n * PSML (PSeudopotential Markup Language) pseudopotential parser and serializer.\n *\n * PSML is an XML-based format for norm-conserving pseudopotentials,\n * created by the ESL (Electronic Structure Library) initiative.\n * Units: Hartree (energy), Bohr (length) — mandatory per schema.\n *\n * Reference: https://siesta-project.github.io/psml-docs/\n * Schema: http://esl.cecam.org/PSML/ns/1.2\n */\n\nimport { XMLParser, XMLBuilder } from \"fast-xml-parser\";\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n Provenance,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n textOf,\n toArray,\n} from \"./xml-helpers\";\n\nimport { guessElement, elementToZ } from \"./elements\";\n\nconst PSML_NS = \"http://esl.cecam.org/PSML/ns/1.2\";\nconst PSML_NS_11 = \"http://esl.cecam.org/PSML/ns/1.1\";\n\nfunction localName(name: string): string {\n // Strip namespace URI if present\n const idx = name.indexOf(\":\");\n return idx >= 0 ? name.substring(idx + 1) : name;\n}\n\nconst parser = new XMLParser({\n ignoreAttributes: false,\n attributeNamePrefix: \"@_\",\n isArray: (name) => {\n const ln = localName(name);\n return (\n ln === \"provenance\" ||\n ln === \"slps\" ||\n ln === \"proj\" ||\n ln === \"pswf\" ||\n ln === \"shell\" ||\n ln === \"functional\"\n );\n },\n});\n\nconst builder = new XMLBuilder({\n ignoreAttributes: false,\n attributeNamePrefix: \"@_\",\n format: true,\n suppressBooleanAttributes: false,\n});\n\n/**\n * Parse a PSML pseudopotential file.\n */\nexport function fromPSML(text: string): Pseudopotential {\n const parsed = parser.parse(text) as XmlNode;\n\n // Find root element (may have namespace prefix)\n const root = parsed[\"psml\"] ?? parsed[`${PSML_NS}:psml`] ?? parsed;\n\n // Provenance\n const provenanceData = root[\"provenance\"];\n let provenance: Provenance | undefined;\n if (provenanceData) {\n const provArr = toArray(provenanceData);\n if (provArr.length > 0) {\n const first = provArr[0];\n provenance = {\n creator: attr(first, \"creator\"),\n date: attr(first, \"date\"),\n };\n }\n }\n\n // Pseudo-atom spec\n const spec = root[\"pseudo-atom-spec\"] ?? {};\n const element = attr(spec, \"atomic-label\") || guessElement(attrInt(spec, \"atomic-number\"));\n const zValence = attrNum(spec, \"z-pseudo\");\n const relativity = attr(spec, \"relativity\") || \"scalar\";\n const coreCorrections = attr(spec, \"core-corrections\") === \"yes\";\n\n // XC functional from libxc-info\n const xcInfo = spec[\"exchange-correlation\"]?.[\"libxc-info\"];\n let functional = \"\";\n if (xcInfo) {\n const funchs = toArray(xcInfo[\"functional\"]);\n functional = funchs.map((f: XmlNode) => attr(f, \"name\")).join(\"+\");\n }\n\n // Grid\n const gridNode = root[\"grid\"];\n let r = new Float64Array(0);\n if (gridNode) {\n const gridData = gridNode[\"grid-data\"];\n if (gridData) r = parseFloat64Array(textOf(gridData));\n }\n if (r.length === 0) throw new Error(\"Missing or empty grid in PSML file\");\n\n // Compute rab from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"custom\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Local potential\n const localNode = root[\"local-potential\"];\n let localVloc = new Float64Array(r.length);\n if (localNode) {\n const dataNode = localNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) localVloc = parseFloat64Array(textOf(dataNode));\n }\n\n // Semilocal potentials\n const slNode = root[\"semilocal-potentials\"];\n const semilocalPotentials: Pseudopotential[\"semilocal\"] = [];\n const slSet = toArray(slNode);\n if (slSet.length > 0) {\n const slpsNodes = toArray(slSet[0][\"slps\"]);\n for (const slps of slpsNodes) {\n const l = lFromLetter(attr(slps, \"l\"));\n const dataNode = slps[\"radfunc\"]?.[\"data\"];\n const vnl = dataNode ? parseFloat64Array(textOf(dataNode)) : new Float64Array(r.length);\n semilocalPotentials.push({ l, vnl });\n }\n }\n\n // Nonlocal projectors\n const nlNode = root[\"nonlocal-projectors\"];\n const betas: BetaProjector[] = [];\n const nlSet = toArray(nlNode);\n if (nlSet.length > 0) {\n const projNodes = toArray(nlSet[0][\"proj\"]);\n for (const proj of projNodes) {\n const l = lFromLetter(attr(proj, \"l\"));\n const ekb = attrNum(proj, \"ekb\");\n const dataNode = proj[\"radfunc\"]?.[\"data\"];\n const betaData = dataNode ? parseFloat64Array(textOf(dataNode)) : new Float64Array(r.length);\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${String.fromCharCode(115 + l)}`,\n beta: betaData,\n });\n }\n }\n\n // Build D_ij from ekb values (diagonal)\n const dij: Array<[number, number, number]> = [];\n const nlSetForEkb = toArray(nlNode);\n if (nlSetForEkb.length > 0) {\n const projNodes = toArray(nlSetForEkb[0][\"proj\"]);\n let idx = 1;\n for (const proj of projNodes) {\n const ekb = attrNum(proj, \"ekb\");\n dij.push([idx, idx, ekb]);\n idx++;\n }\n }\n\n // Pseudo wavefunctions\n const pswfcNodes = toArray(root[\"pseudo-wave-functions\"]);\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcNodes.length > 0) {\n const pswfNodes = toArray(pswfcNodes[0][\"pswf\"]);\n for (const pswf of pswfNodes) {\n const l = lFromLetter(attr(pswf, \"l\"));\n const n = attrInt(pswf, \"n\");\n const dataNode = pswf[\"radfunc\"]?.[\"data\"];\n const chi = dataNode ? parseFloat64Array(textOf(dataNode)) : new Float64Array(r.length);\n pswfc.push({\n l,\n occupation: 0,\n label: `${n}${String.fromCharCode(115 + l)}`,\n n,\n chi,\n });\n }\n }\n\n // Valence charge (store as rhoatom)\n const vcNode = root[\"valence-charge\"];\n let rhoatom = new Float64Array(r.length);\n if (vcNode) {\n const dataNode = vcNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) rhoatom = parseFloat64Array(textOf(dataNode));\n }\n\n // Core charge (NLCC)\n const ccNode = root[\"pseudocore-charge\"];\n let nlcc: Float64Array | undefined;\n if (ccNode) {\n const dataNode = ccNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) nlcc = parseFloat64Array(textOf(dataNode));\n }\n\n return {\n format: \"PSML\",\n version: \"2.0.1\",\n provenance,\n header: {\n element,\n pseudoType: \"NC\",\n relativistic: relativity as PseudopotentialHeader[\"relativistic\"],\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: coreCorrections,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: semilocalPotentials.length > 0\n ? Math.max(...semilocalPotentials.map((s) => s.l))\n : betas.length > 0\n ? Math.max(...betas.map((b) => b.angularMomentum))\n : 0,\n lMaxRho: 0,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: pswfc.length,\n numberOfProj: betas.length,\n },\n mesh,\n local: { vloc: localVloc },\n semilocal: semilocalPotentials.length > 0 ? semilocalPotentials : undefined,\n nonlocal: { betas, dij },\n pswfc,\n rhoatom,\n nlcc,\n };\n}\n\n/**\n * Serialize a Pseudopotential to PSML format.\n */\nexport function toPSML(pp: Pseudopotential): string {\n const r = pp.mesh.r;\n const npts = r.length;\n\n let xml = `<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\\n`;\n xml += `<psml version=\"1.2\" energy_unit=\"hartree\" length_unit=\"bohr\" uuid=\"matsci-parse\">\\n`;\n\n // Provenance\n if (pp.provenance) {\n const provCreator = pp.provenance.creator ?? \"matsci-parse\";\n const provDate = pp.provenance.date ?? new Date().toISOString().split(\"T\")[0];\n xml += ` <provenance creator=\"${provCreator}\" date=\"${provDate}\">\\n`;\n xml += ` <annotation type=\"generated-by\" value=\"matsci-parse pseudopotential library\" />\\n`;\n xml += ` </provenance>\\n`;\n }\n\n // Pseudo-atom spec\n xml += ` <pseudo-atom-spec atomic-label=\"${pp.header.element}\" atomic-number=\"${elementToZ(pp.header.element)}\" z-pseudo=\"${pp.header.zValence}\" relativity=\"${pp.header.relativistic}\" core-corrections=\"${pp.header.coreCorrection ? \"yes\" : \"no\"}\">\\n`;\n if (pp.header.functional) {\n xml += ` <exchange-correlation>\\n`;\n xml += ` <libxc-info number-of-functionals=\"0\">\\n`;\n xml += ` <functional name=\"${pp.header.functional}\" />\\n`;\n xml += ` </libxc-info>\\n`;\n xml += ` </exchange-correlation>\\n`;\n }\n xml += ` </pseudo-atom-spec>\\n`;\n\n // Grid\n xml += ` <grid npts=\"${npts}\">\\n`;\n xml += ` <grid-data>\\n`;\n xml += ` ${Array.from(r).map((v) => formatFortranNumber(v).trim()).join(\" \")}\\n`;\n xml += ` </grid-data>\\n`;\n xml += ` </grid>\\n`;\n\n // Local potential\n xml += ` <local-potential>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">\\n`;\n xml += ` ${formatDataArray(pp.local.vloc)}\\n`;\n xml += ` </data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </local-potential>\\n`;\n\n // Semilocal potentials\n if (pp.semilocal && pp.semilocal.length > 0) {\n xml += ` <semilocal-potentials set=\"scalar_relativistic\">\\n`;\n for (const sl of pp.semilocal) {\n xml += ` <slps l=\"${lToLetter(sl.l)}\" n=\"${sl.l + 1}\" rc=\"0\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(sl.vnl)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </slps>\\n`;\n }\n xml += ` </semilocal-potentials>\\n`;\n }\n\n // Nonlocal projectors\n if (pp.nonlocal.betas.length > 0) {\n xml += ` <nonlocal-projectors set=\"scalar_relativistic\">\\n`;\n let idx = 1;\n for (const beta of pp.nonlocal.betas) {\n const ekbEntry = pp.nonlocal.dij.find(([nb]) => nb === idx);\n const ekb = ekbEntry ? ekbEntry[2] : 1.0;\n xml += ` <proj l=\"${lToLetter(beta.angularMomentum)}\" seq=\"${idx}\" ekb=\"${formatFortranNumber(ekb).trim()}\" type=\"kb\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(beta.beta)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </proj>\\n`;\n idx++;\n }\n xml += ` </nonlocal-projectors>\\n`;\n }\n\n // Pseudo wavefunctions\n if (pp.pswfc.length > 0) {\n xml += ` <pseudo-wave-functions set=\"pseudo\">\\n`;\n for (const wfc of pp.pswfc) {\n xml += ` <pswf l=\"${lToLetter(wfc.l)}\" n=\"${wfc.n ?? wfc.l + 1}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(wfc.chi)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pswf>\\n`;\n }\n xml += ` </pseudo-wave-functions>\\n`;\n }\n\n // Valence charge\n if (pp.rhoatom.length > 0) {\n xml += ` <valence-charge total-charge=\"${pp.header.zValence}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(pp.rhoatom)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </valence-charge>\\n`;\n }\n\n // Core charge (NLCC)\n if (pp.nlcc && pp.nlcc.length > 0) {\n xml += ` <pseudocore-charge>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${pp.nlcc.length}\">${formatDataArray(pp.nlcc)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pseudocore-charge>\\n`;\n }\n\n xml += `</psml>\\n`;\n return xml;\n}\n\nfunction lFromLetter(letter: string): number {\n const map: Record<string, number> = { s: 0, p: 1, d: 2, f: 3, g: 4 };\n return map[letter.toLowerCase()] ?? 0;\n}\n\nfunction lToLetter(l: number): string {\n return String.fromCharCode(115 + l); // 115 = 's'\n}\n\n\n","/**\n * GTH/HGH (Goedecker-Teter-Hutter / Hartwigsen-Goedecker-Hutter) parser.\n *\n * GTH/HGH pseudopotentials are analytical, defined by Gaussian functions\n * rather than tabulated on a radial grid. At parse time, we evaluate the\n * analytical expressions on a logarithmic grid for the IR.\n *\n * Units: Hartree (energy), Bohr (length).\n *\n * Reference:\n * - GTH: Goedecker, Teter, Hutter, PRB 54, 1703 (1996)\n * - HGH: Hartwigsen, Goedecker, Teter, Hutter, PRB 58, 3641 (1998)\n */\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n GthData,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\ninterface GthParsedEntry {\n element: string;\n potentialName: string;\n aliases: string[];\n nElec: number[];\n rLoc: number;\n nexpPpl: number;\n cexpPpl: number[];\n nprj: number;\n channels: Array<{\n r: number;\n nprjPpnl: number;\n hprj: number[][];\n }>;\n hasKprj: boolean;\n kprj?: number[][][];\n}\n\n/**\n * Parse a monolithic GTH_POTENTIALS file into individual element entries.\n */\nexport function parseGTHFile(text: string): GthParsedEntry[] {\n const entries: GthParsedEntry[] = [];\n const lines = text.split(\"\\n\");\n let i = 0;\n\n while (i < lines.length) {\n const line = lines[i].trim();\n\n // Skip comment lines and blank lines\n if (line.startsWith(\"#\") || line === \"\") {\n i++;\n continue;\n }\n\n // This should be an element header line\n const headerParts = line.split(/\\s+/);\n if (headerParts.length < 2) {\n i++;\n continue;\n }\n\n const element = headerParts[0];\n const potentialName = headerParts[1] ?? \"\";\n const aliases = headerParts.slice(2);\n i++;\n\n // Skip comment lines between entries\n while (i < lines.length && (lines[i].trim().startsWith(\"#\") || lines[i].trim() === \"\")) {\n i++;\n }\n\n if (i >= lines.length) break;\n\n // Valence electron configuration\n const nElec = lines[i++].trim().split(/\\s+/).map(Number);\n\n // Local part\n const localParts = lines[i++].trim().split(/\\s+/);\n const rLoc = parseFortranNumber(localParts[0]);\n const nexpPpl = parseInt(localParts[1]);\n const cexpPpl: number[] = [];\n for (let k = 0; k < nexpPpl; k++) {\n cexpPpl.push(parseFortranNumber(localParts[2 + k]));\n }\n\n // Number of non-local projector channels\n const nprj = parseInt(lines[i++].trim());\n\n // Non-local projector channels\n const channels: GthParsedEntry[\"channels\"] = [];\n let hasKprj = false;\n const kprjArrays: number[][][] = [];\n\n for (let l = 0; l < nprj && i < lines.length; l++) {\n const channelParts = lines[i++].trim().split(/\\s+/);\n const r = parseFortranNumber(channelParts[0]);\n const nprjPpnl = parseInt(channelParts[1]);\n\n // Read h-matrix upper triangle.\n // CP2K format puts values on the same line after r and nprjPpnl;\n // the hand-crafted format puts them on separate lines.\n const hprj: number[][] = [];\n let inlineIdx = 2;\n for (let ii = 0; ii < nprjPpnl; ii++) {\n hprj.push([]);\n for (let jj = ii; jj < nprjPpnl; jj++) {\n if (inlineIdx < channelParts.length) {\n hprj[ii].push(parseFortranNumber(channelParts[inlineIdx++]));\n } else if (i < lines.length) {\n hprj[ii].push(parseFortranNumber(lines[i++].trim().split(/\\s+/)[0]));\n } else {\n hprj[ii].push(0);\n }\n }\n }\n\n channels.push({ r, nprjPpnl, hprj });\n\n // Check for k-matrix (SOC) — follows h-matrix if present\n // In GTH_SOC_POTENTIALS, the k-matrix has the same structure\n // For now, we don't parse it from the standard GTH_POTENTIALS\n }\n\n entries.push({\n element,\n potentialName,\n aliases,\n nElec,\n rLoc,\n nexpPpl,\n cexpPpl,\n nprj,\n channels,\n hasKprj,\n kprj: hasKprj ? kprjArrays : undefined,\n });\n }\n\n return entries;\n}\n\n/**\n * Evaluate the GTH local potential on a radial grid.\n *\n * V_local(r) = -Zval/r * erf(r / (sqrt(2) * r_loc))\n * + exp(-r²/(2r_loc²)) * (c0 + c1*(r/r_loc)² + c2*(r/r_loc)⁴ + c3*(r/r_loc)⁶)\n */\nfunction evalGthLocal(r: Float64Array, zVal: number, rLoc: number, cexpPpl: number[]): Float64Array {\n const vloc = new Float64Array(r.length);\n const c = [0, 0, 0, 0];\n for (let k = 0; k < cexpPpl.length && k < 4; k++) {\n c[k] = cexpPpl[k];\n }\n\n for (let i = 0; i < r.length; i++) {\n const ri = r[i];\n if (ri < 1e-15) {\n // At r=0, use L'Hopital: V_local(0) = -2*Zval/(sqrt(2*pi)*rLoc) + c[0]\n vloc[i] = -2 * zVal / (Math.sqrt(2 * Math.PI) * rLoc) + c[0];\n continue;\n }\n\n const t = ri / rLoc;\n const t2 = t * t;\n const erfArg = ri / (Math.sqrt(2) * rLoc);\n const erfVal = erf(erfArg);\n const gauss = Math.exp(-t2 / 2);\n\n const coulomb = (-zVal / ri) * erfVal;\n const gaussian = gauss * (c[0] + c[1] * t2 + c[2] * t2 * t2 + c[3] * t2 * t2 * t2);\n\n vloc[i] = coulomb + gaussian;\n }\n\n return vloc;\n}\n\n/**\n * Evaluate a GTH projector on a radial grid.\n *\n * |r_{l,i}> = N * r^(l+2i-1) * exp(-r²/(2r_l²))\n */\nfunction evalGthProjector(\n r: Float64Array,\n l: number,\n i: number,\n rL: number,\n): Float64Array {\n const beta = new Float64Array(r.length);\n const exponent = l + 2 * (i + 1) - 1;\n\n // Normalization constant\n const norm = Math.sqrt(2) * Math.pow(2 / (rL * rL), exponent + 0.5) /\n Math.sqrt(gamma(exponent + 0.5));\n\n for (let k = 0; k < r.length; k++) {\n const ri = r[k];\n if (ri < 1e-15) {\n beta[k] = exponent === 0 ? norm : 0;\n } else {\n beta[k] = norm * Math.pow(ri, exponent) * Math.exp(-ri * ri / (2 * rL * rL));\n }\n }\n\n return beta;\n}\n\n/**\n * Parse a single GTH/HGH entry and convert to Pseudopotential IR.\n */\nexport function fromGTH(text: string): Pseudopotential {\n const entries = parseGTHFile(text);\n if (entries.length === 0) {\n throw new Error(\"No GTH entries found in file\");\n }\n return fromGthEntry(entries[0]);\n}\n\n/**\n * Parse a single GTH entry into a Pseudopotential.\n */\nexport function fromGthEntry(entry: GthParsedEntry): Pseudopotential {\n const zVal = entry.nElec.reduce((a, b) => a + b, 0);\n const lMax = entry.channels.length > 0 ? entry.channels.length - 1 : 0;\n\n // Build a logarithmic radial grid\n const npts = 500;\n const rmax = 20.0; // Bohr, sufficient for most pseudopotentials\n const r = new Float64Array(npts);\n const rab = new Float64Array(npts);\n const dx = Math.log(rmax) / (npts - 1);\n for (let i = 0; i < npts; i++) {\n r[i] = Math.exp(dx * i);\n rab[i] = r[i] * dx;\n }\n if (npts > 1) {\n r[0] = r[1] * 0.01; // Avoid r=0 for erf evaluation\n rab[0] = r[0] * dx;\n }\n\n // Evaluate local potential\n const localVloc = evalGthLocal(r, zVal, entry.rLoc, entry.cexpPpl);\n\n // Evaluate projectors\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n\n for (let l = 0; l < entry.channels.length; l++) {\n const ch = entry.channels[l];\n for (let p = 0; p < ch.nprjPpnl; p++) {\n const betaData = evalGthProjector(r, l, p, ch.r);\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${String.fromCharCode(115 + l)}${p + 1}`,\n beta: betaData,\n });\n\n // D_ij from h-matrix (diagonal for single projectors)\n const hij = ch.hprj[p]?.[p] ?? 1.0;\n dij.push([projIdx, projIdx, hij]);\n projIdx++;\n }\n }\n\n // GTH analytical data\n const gthData: GthData = {\n nElec: entry.nElec,\n rLoc: entry.rLoc,\n cexpPpl: entry.cexpPpl,\n rPs: entry.channels.map((ch) => ch.r),\n hprj: entry.channels.map((ch) => ch.hprj),\n kprj: entry.kprj,\n };\n\n return {\n format: \"GTH\",\n version: \"2.0.1\",\n header: {\n element: entry.element,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: entry.hasKprj,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: false,\n functional: entry.potentialName,\n zValence: zVal,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: npts,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n },\n mesh: {\n gridType: \"logarithmic\",\n rmax: rmax,\n r,\n rab,\n },\n local: { vloc: localVloc },\n nonlocal: { betas, dij },\n pswfc: [],\n rhoatom: new Float64Array(npts),\n gth: gthData,\n };\n}\n\n/**\n * Serialize a Pseudopotential to GTH format (single element entry).\n */\nexport function toGTH(pp: Pseudopotential): string {\n if (!pp.gth) {\n throw new Error(\"Pseudopotential does not have GTH analytical parameters\");\n }\n\n const lines: string[] = [];\n const gth = pp.gth;\n\n lines.push(`# ${pp.header.element} ${pp.header.functional}`);\n lines.push(`# Element symbol Name of the potential Alias names`);\n lines.push(`# n_elec(s) n_elec(p) n_elec(d) ...`);\n lines.push(`# r_loc nexp_ppl cexp_ppl(1) ... cexp_ppl(nexp_ppl)`);\n lines.push(`# nprj`);\n lines.push(`${pp.header.element} ${pp.header.functional}`);\n\n // Valence electron configuration\n let nElec: number[];\n if (gth.nElec && gth.nElec.length > 0) {\n nElec = [...gth.nElec];\n } else {\n // Estimate from betas\n nElec = new Array(pp.header.lMax + 1).fill(0);\n for (const beta of pp.nonlocal.betas) {\n nElec[beta.angularMomentum] = Math.max(nElec[beta.angularMomentum], 1);\n }\n if (nElec[0] === 0) nElec[0] = Math.round(pp.header.zValence);\n }\n lines.push(nElec.join(\" \"));\n\n // Local part\n lines.push(`${formatFortranNumber(gth.rLoc)} ${gth.cexpPpl.length} ${gth.cexpPpl.map((c) => formatFortranNumber(c)).join(\" \")}`);\n\n // Non-local part\n lines.push(`${gth.rPs.length}`);\n for (let l = 0; l < gth.hprj.length; l++) {\n const h = gth.hprj[l];\n const nprj = h.length;\n lines.push(`${formatFortranNumber(gth.rPs[l])} ${nprj}`);\n // h-matrix upper triangle\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n const val = h[i]?.[j] ?? 0;\n lines.push(formatFortranNumber(val));\n }\n }\n }\n\n return lines.join(\"\\n\");\n}\n\n// Simple error function approximation (Abramowitz & Stegun)\nfunction erf(x: number): number {\n const a1 = 0.254829592;\n const a2 = -0.284496736;\n const a3 = 1.421413741;\n const a4 = -1.453152027;\n const a5 = 1.061405429;\n const p = 0.3275911;\n\n const sign = x >= 0 ? 1 : -1;\n const absX = Math.abs(x);\n const t = 1.0 / (1.0 + p * absX);\n const y = 1.0 - (((((a5 * t + a4) * t) + a3) * t + a2) * t + a1) * t * Math.exp(-absX * absX);\n\n return sign * y;\n}\n\n// Gamma function approximation (Stirling + Lanczos for small arguments)\nfunction gamma(z: number): number {\n if (z < 0.5) {\n return Math.PI / (Math.sin(Math.PI * z) * gamma(1 - z));\n }\n z -= 1;\n const g = 7;\n const c = [\n 0.99999999999980993,\n 676.5203681218851,\n -1259.1392167224028,\n 771.32342877765313,\n -176.61502916214059,\n 12.507343278686905,\n -0.13857109526572012,\n 9.9843695780195716e-6,\n 1.5056327351493116e-7,\n ];\n let x = c[0];\n for (let i = 1; i < g + 2; i++) {\n x += c[i] / (z + i);\n }\n const t = z + g + 0.5;\n return Math.sqrt(2 * Math.PI) * Math.pow(t, z + 0.5) * Math.exp(-t) * x;\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\n/** Serializes a Structure to a JSON-serializable object. */\nexport function toJSON(structure: Structure) {\n return {\n lattice: Array.from(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/** Deserializes a Structure from a JSON object. */\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","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/** Supported energy unit identifiers. */\nexport type EnergyUnits = \"eV\" | \"Hartree\" | \"Rydberg\" | \"kJ/mol\" | \"kcal/mol\";\n\nconst EnergyConversions: Record<EnergyUnits, number> = {\n eV: 1,\n Hartree: 27.2114,\n Rydberg: 13.6057,\n \"kJ/mol\": 0.0103643,\n \"kcal/mol\": 0.0433641,\n};\n\nconst EnergyAliases: Record<string, EnergyUnits> = {\n Ha: \"Hartree\",\n Ry: \"Rydberg\",\n ev: \"eV\",\n electronvolt: \"eV\",\n};\n\n/** Unit system for energy conversions with eV as base. */\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\n/** Supported angle unit identifiers. */\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\n/** Unit system for angle conversions with radian as base. */\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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