matterviz 0.4.0 → 0.4.2

package/dist/fermi-surface/compute.js

@@ -2,7 +2,9 @@
 import * as math from '../math';
 import { EPS } from '../math';
 import { CLOSED_CONTOUR_TOLERANCE, IRREDUCIBLE_BZ_MIN_VERTICES, IRREDUCIBLE_BZ_TOLERANCE, SPANNING_THRESHOLD, } from './constants';
-import { marching_cubes } from './marching-cubes';
+import { marching_cubes } from '../marching-cubes';
+// clamp01 guards float jitter at the cell boundary
+import { clamp01 } from '../utils';
 const safe_mod = (val, dim) => ((val % dim) + dim) % dim;
 // Precompute Catmull-Rom coefficients for a given t value
 // Returns [c0, c1, c2, c3] where result = c0*p0 + c1*p1 + c2*p2 + c3*p3
@@ -29,7 +31,7 @@ function tricubic_interpolate(grid, fx, fy, fz, px, py, pz) {
     const [cz0, cz1, cz2, cz3] = catmull_rom_coeffs(fz - iz);
     // Wrapped stencil indices (modulo hoisted out of the inner loop); a zero period
     // (single-point axis) has no neighbours, so collapse the stencil onto index 0
-    const stencil = (idx, period) => [idx - 1, idx, idx + 1, idx + 2].map((v) => period > 0 ? ((v % period) + period) % period : 0);
+    const stencil = (idx, period) => [idx - 1, idx, idx + 1, idx + 2].map((stencil_idx) => period > 0 ? ((stencil_idx % period) + period) % period : 0);
     const [wx, wy, wz] = [stencil(ix, px), stencil(iy, py), stencil(iz, pz)];
     // Interpolate along z, then y, then x (fully inlined)
     let result = 0;
@@ -60,8 +62,8 @@ function upsample_grid(grid, factor, periodic = false) {
     // period (count of unique points) doubles as the resampling span numerator
     const endpoint = periodic ? 0 : 1;
     const dims = [grid.length, grid[0]?.length || 0, grid[0]?.[0]?.length || 0];
-    const [px, py, pz] = dims.map((n) => n - endpoint);
-    const [new_nx, new_ny, new_nz] = [px, py, pz].map((p) => Math.round(p * factor) + endpoint);
+    const [px, py, pz] = dims.map((dim) => dim - endpoint);
+    const [new_nx, new_ny, new_nz] = [px, py, pz].map((period) => Math.round(period * factor) + endpoint);
     // Map new index → source coordinate; a single-point axis (span 0) pins its lone
     // output to source 0 to avoid 0/0 = NaN
     const src_coords = (new_n, period) => {
@@ -142,7 +144,8 @@ export function extract_fermi_surface(band_data, options = {}) {
             if (compute_velocities && band_data.velocities) {
                 isosurface.properties = compute_fermi_velocities(isosurface, band_data.velocities[spin_idx][band_idx], band_data.k_lattice, band_data.k_grid, periodic);
                 isosurface.avg_velocity =
-                    isosurface.properties.reduce((s, v) => s + v, 0) / isosurface.properties.length;
+                    isosurface.properties.reduce((sum, velocity) => sum + velocity, 0) /
+                        isosurface.properties.length;
             }
             // Compute dimensionality if requested
             if (compute_dimensionality) {
@@ -203,7 +206,7 @@ export function compute_surface_area(surface) {
         const cy = e1z * e2x - e1x * e2z;
         const cz = e1x * e2y - e1y * e2x;
         // Area is half the magnitude of cross product
-        total_area += Math.sqrt(cx * cx + cy * cy + cz * cz) * 0.5;
+        total_area += Math.hypot(cx, cy, cz) * 0.5;
     }
     return total_area;
 }
@@ -217,8 +220,6 @@ function compute_fermi_velocities(surface, velocity_grid, k_lattice, k_grid, per
     const k_inv = math.matrix_inverse_3x3(math.transpose_3x3_matrix(k_lattice));
     // Grid point i sits at frac i/(n−1) (endpoint-inclusive BXSF) or i/n (periodic)
     const [sx, sy, sz] = periodic ? [nx, ny, nz] : [nx - 1, ny - 1, nz - 1];
-    // Clamp guards float jitter at the cell boundary
-    const clamp01 = (val) => Math.min(Math.max(val, 0), 1);
     for (const vertex of surface.vertices) {
         const frac = math.mat3x3_vec3_multiply(k_inv, vertex); // centered, in [-0.5, 0.5]
         const gx = clamp01(frac[0] + 0.5) * sx;
@@ -348,19 +349,19 @@ function compute_edge_intersection(surface, vertex_distances, v0_idx, v1_idx) {
     // Edge must cross the plane (opposite signs)
     if (d0 * d1 >= 0)
         return null;
-    const t = d0 / (d0 - d1);
+    const frac = d0 / (d0 - d1);
     const v0 = surface.vertices[v0_idx];
     const v1 = surface.vertices[v1_idx];
     const point = [
-        v0[0] + t * (v1[0] - v0[0]),
-        v0[1] + t * (v1[1] - v0[1]),
-        v0[2] + t * (v1[2] - v0[2]),
+        v0[0] + frac * (v1[0] - v0[0]),
+        v0[1] + frac * (v1[1] - v0[1]),
+        v0[2] + frac * (v1[2] - v0[2]),
     ];
     let property;
     if (surface.properties) {
         property =
             surface.properties[v0_idx] +
-                t * (surface.properties[v1_idx] - surface.properties[v0_idx]);
+                frac * (surface.properties[v1_idx] - surface.properties[v0_idx]);
     }
     return { point, property };
 }

package/dist/fermi-surface/export.js

@@ -1,16 +1,5 @@
+import { download } from '../io/fetch';
 import { to_error } from '../utils';
-// Helper to trigger file download
-function download_file(content, filename, mime_type) {
-    const blob = new Blob([content], { type: mime_type });
-    const url = URL.createObjectURL(blob);
-    const link = document.createElement(`a`);
-    link.href = url;
-    link.download = filename;
-    document.body.append(link);
-    link.click();
-    document.body.removeChild(link);
-    URL.revokeObjectURL(url);
-}
 // Export scene to STL format (good for 3D printing)
 export async function export_to_stl(scene, filename) {
     const { STLExporter } = await import(`three/addons/exporters/STLExporter.js`);
@@ -18,14 +7,14 @@ export async function export_to_stl(scene, filename) {
     const result = exporter.parse(scene, { binary: true });
     // Binary STL returns DataView, convert to ArrayBuffer for Blob
     const buffer = result instanceof DataView ? result.buffer : result;
-    download_file(buffer, `${filename}.stl`, `application/octet-stream`);
+    download(buffer, `${filename}.stl`, `application/octet-stream`);
 }
 // Export scene to OBJ format (widely compatible)
 export async function export_to_obj(scene, filename) {
     const { OBJExporter } = await import(`three/addons/exporters/OBJExporter.js`);
     const exporter = new OBJExporter();
     const result = exporter.parse(scene);
-    download_file(result, `${filename}.obj`, `text/plain`);
+    download(result, `${filename}.obj`, `text/plain`);
 }
 // Export scene to GLTF format (modern web/AR standard)
 export async function export_to_gltf(scene, filename) {
@@ -34,7 +23,7 @@ export async function export_to_gltf(scene, filename) {
     return new Promise((resolve, reject) => {
         exporter.parse(scene, (gltf) => {
             const output = JSON.stringify(gltf, null, 2);
-            download_file(output, `${filename}.gltf`, `application/json`);
+            download(output, `${filename}.gltf`, `application/json`);
             resolve();
         }, (error) => reject(to_error(error)), { binary: false });
     });

package/dist/fermi-surface/index.d.ts

@@ -6,7 +6,6 @@ export { default as FermiSurfaceTooltip } from './FermiSurfaceTooltip.svelte';
 export * from './compute';
 export * from './constants';
 export * from './export';
-export * from './marching-cubes';
 export * from './parse';
 export * from './symmetry';
 export * from './types';

package/dist/fermi-surface/index.js

@@ -7,7 +7,6 @@ export { default as FermiSurfaceTooltip } from './FermiSurfaceTooltip.svelte';
 export * from './compute';
 export * from './constants';
 export * from './export';
-export * from './marching-cubes';
 export * from './parse';
 export * from './symmetry';
 export * from './types';

package/dist/fermi-surface/parse.d.ts

@@ -1,2 +1,2 @@
 import type { BandGridData, FermiSurfaceData } from './types';
-export declare function parse_fermi_file(content: string, filename?: string): BandGridData | FermiSurfaceData | null;
+export declare function parse_fermi_file(content: string, filename?: string): BandGridData | FermiSurfaceData;

package/dist/fermi-surface/parse.js

@@ -1,10 +1,13 @@
+import * as math from '../math';
+import { is_plain_object, normalize_scientific_notation, parse_leading_num, to_error, } from '../utils';
 import * as constants from './constants';
-import { compute_vertex_normals } from './marching-cubes';
+import { compute_vertex_normals } from '../marching-cubes';
 const parse_number_tokens = (line) => line.split(/\s+/).filter(Boolean);
-// Parse whitespace-separated floats from a line (optimized with unary +)
-const parse_floats = (line) => parse_number_tokens(line).map(Number);
+// Parse whitespace-separated floats from a line. Normalizes Fortran D-exponents
+// (`0.1234D+01`) which Fortran codes emit in BXSF/FRMSF and Number() rejects
+const parse_floats = (line) => parse_number_tokens(normalize_scientific_notation(line)).map(Number);
 // Parse whitespace-separated integers from a line
-const parse_ints = (line) => parse_number_tokens(line).map((part) => parseInt(part, 10));
+const parse_ints = (line) => parse_number_tokens(line).map((part) => Math.trunc(Number(part)));
 // Parse BXSF (Band-XSF) format used by XCrySDen, Quantum ESPRESSO, etc.
 // Format specification: http://www.xcrysden.org/doc/XSF.html
 function parse_bxsf(content) {
@@ -38,7 +41,7 @@ function parse_bxsf(content) {
         throw new Error(`Expected BANDGRID_3D header, got: ${bandgrid_line}`);
     }
     // Parse number of bands
-    const n_bands = parseInt(next_line(), 10);
+    const n_bands = Math.trunc(Number(next_line()));
     if (isNaN(n_bands) || n_bands <= 0) {
         throw new Error(`Invalid number of bands in BXSF file`);
     }
@@ -112,9 +115,9 @@ function parse_bxsf(content) {
         const lower = line.toLowerCase();
         if (lower.includes(`fermi`) && lower.includes(`energy`)) {
             // Match patterns like "Fermi Energy = 5.123" or "fermi_energy: -0.5"
-            const match = /(?:=|:)\s*([-+]?\d*\.?\d+(?:[eE][-+]?\d+)?)/i.exec(line);
+            const match = /(?:=|:)\s*(?<value>[-+]?\d*\.?\d+(?:[eE][-+]?\d+)?)/i.exec(line);
             if (match) {
-                fermi_energy = parseFloat(match[1]);
+                fermi_energy = Number(match[1]);
                 break;
             }
         }
@@ -147,12 +150,12 @@ function parse_frmsf(content) {
     // 0 = Monkhorst-Pack grid (shifted)
     // 1 = Gamma-centered grid
     // 2 = Gamma + half grid shift
-    const lshift = parseInt(lines[line_idx++], 10);
+    const lshift = Math.trunc(Number(lines[line_idx++]));
     if (isNaN(lshift) || lshift < 0 || lshift > 2) {
         throw new Error(`FRMSF: Invalid lshift value (expected 0, 1, or 2)`);
     }
     // Line 3: number of bands
-    const n_bands = parseInt(lines[line_idx++], 10);
+    const n_bands = Math.trunc(Number(lines[line_idx++]));
     if (isNaN(n_bands) || n_bands <= 0) {
         throw new Error(`FRMSF: Invalid number of bands`);
     }
@@ -181,17 +184,14 @@ function parse_frmsf(content) {
         energies[spin_idx] = [];
         for (let band_idx = 0; band_idx < n_bands; band_idx++) {
             const energy_values = [];
-            // Read energy values (first value per line only, ignore auxiliary columns)
+            // Read energy values (first value per line only, ignore auxiliary columns;
+            // normalize Fortran D-exponents like parse_floats does)
             while (energy_values.length < total_points && line_idx < lines.length) {
-                const line = lines[line_idx];
-                const first_token = line?.split(/\s+/)[0];
-                if (first_token && !isNaN(parseFloat(first_token))) {
-                    energy_values.push(parseFloat(first_token));
-                    line_idx++;
-                }
-                else {
+                const energy = parse_leading_num(normalize_scientific_notation(lines[line_idx] ?? ``));
+                if (isNaN(energy))
                     break;
-                }
+                energy_values.push(energy);
+                line_idx++;
             }
             if (energy_values.length < total_points) {
                 throw new Error(`FRMSF spin ${spin_idx} band ${band_idx}: expected ${total_points} values, got ${energy_values.length}`);
@@ -224,14 +224,9 @@ function parse_frmsf(content) {
 }
 // Validate that an object has the required Isosurface shape
 function is_valid_isosurface(obj) {
-    if (!obj || typeof obj !== `object`)
+    if (!is_plain_object(obj))
         return false;
-    const isosurface_obj = obj;
-    const vertices = isosurface_obj.vertices;
-    const faces = isosurface_obj.faces;
-    const normals = isosurface_obj.normals;
-    const band_index = isosurface_obj.band_index;
-    const spin = isosurface_obj.spin;
+    const { vertices, faces, normals, band_index, spin } = obj;
     if (!Array.isArray(vertices) || vertices.length === 0)
         return false;
     if (!Array.isArray(faces))
@@ -246,27 +241,35 @@ function is_valid_isosurface(obj) {
 }
 // Validate FermiSurfaceData shape
 function is_valid_fermi_surface_data(obj) {
-    if (!obj || typeof obj !== `object`)
+    if (!is_plain_object(obj))
         return false;
-    const data = obj;
     // Check required fields
-    if (!Array.isArray(data.isosurfaces))
+    if (!Array.isArray(obj.isosurfaces))
         return false;
-    if (!Array.isArray(data.k_lattice) || data.k_lattice.length !== 3)
+    if (!math.is_square_matrix(obj.k_lattice, 3))
         return false;
-    if (typeof data.fermi_energy !== `number`)
+    if (typeof obj.fermi_energy !== `number`)
         return false;
-    if (data.reciprocal_cell !== `wigner_seitz` && data.reciprocal_cell !== `parallelepiped`) {
+    if (obj.reciprocal_cell !== `wigner_seitz` && obj.reciprocal_cell !== `parallelepiped`) {
         return false;
     }
-    if (!data.metadata || typeof data.metadata !== `object`)
+    if (!obj.metadata || typeof obj.metadata !== `object`)
         return false;
     // Validate each isosurface
-    for (const iso of data.isosurfaces) {
-        if (!is_valid_isosurface(iso))
-            return false;
-    }
-    return true;
+    return obj.isosurfaces.every(is_valid_isosurface);
+}
+// Validate BandGridData shape: non-empty energies grid, 3 k-grid dims, 3x3 k-lattice
+function is_valid_band_grid_data(obj) {
+    if (!is_plain_object(obj))
+        return false;
+    const { energies, k_grid, k_lattice } = obj;
+    if (!Array.isArray(energies) || energies.length === 0)
+        return false;
+    if (!Array.isArray(k_grid) ||
+        k_grid.length !== 3 ||
+        !k_grid.every((dim) => Number.isInteger(dim) && dim > 0))
+        return false;
+    return math.is_square_matrix(k_lattice, 3);
 }
 // Parse Matterviz/IFermi JSON format for Fermi surface data
 // Throws on invalid input; returns parsed data on success
@@ -287,22 +290,21 @@ function parse_fermi_json(content) {
     }
     // Check if it's BandGridData (raw grid data)
     if (data.energies && data.k_grid && data.k_lattice) {
-        // Minimal validation of required fields
-        if (!Array.isArray(data.energies) ||
-            !Array.isArray(data.k_grid) ||
-            data.k_grid.length !== 3 ||
-            !Array.isArray(data.k_lattice) ||
-            data.k_lattice.length !== 3)
-            throw new Error(`Invalid BandGridData JSON: malformed required fields`);
+        if (!is_valid_band_grid_data(data)) {
+            throw new Error(`Invalid BandGridData JSON: expected non-empty 'energies' grid, 3 'k_grid' dims, and 3x3 'k_lattice'`);
+        }
         return data;
     }
     // Try to extract from nested structure (e.g. IFermi output)
     if (data.fermi_surface) {
+        if (!is_valid_fermi_surface_data(data.fermi_surface)) {
+            throw new Error(`Invalid nested 'fermi_surface' JSON: expected isosurfaces array, 3x3 k_lattice, numeric fermi_energy, reciprocal_cell, and metadata`);
+        }
         return data.fermi_surface;
     }
     if (data.band_structure?.energies || data.bands?.energies) {
         const bs = data.band_structure ?? data.bands;
-        return {
+        const grid_data = {
             energies: bs.energies,
             k_grid: bs.k_grid ?? bs.kgrid,
             k_lattice: bs.k_lattice ?? bs.reciprocal_lattice,
@@ -312,6 +314,10 @@ function parse_fermi_json(content) {
             // oxlint-disable-next-line @typescript-eslint/prefer-nullish-coalescing -- numeric fallback chain (0 falls through)
             n_spins: (bs.n_spins ?? bs.nspins) || bs.energies.length || 1,
         };
+        if (!is_valid_band_grid_data(grid_data)) {
+            throw new Error(`Invalid band_structure JSON: expected non-empty 'energies' grid, 3 'k_grid' dims, and 3x3 'k_lattice'`);
+        }
+        return grid_data;
     }
     // Check for pymatgen BandStructure format (k-path, not k-grid)
     // These files cannot be used for Fermi surface visualization directly
@@ -339,7 +345,7 @@ function parse_ifermi_surface(data) {
     const band_indices = new Set();
     let has_spin = false;
     for (const [band_key, iso_list] of Object.entries(isosurfaces_obj)) {
-        const band_index = parseInt(band_key, 10);
+        const band_index = Math.trunc(Number(band_key));
         // spin is determined by sign: positive = up, negative = down
         const spin = band_index < 0 ? `down` : `up`;
         const abs_band_idx = Math.abs(band_index);
@@ -365,13 +371,13 @@ function parse_ifermi_surface(data) {
             let dimensionality;
             if (ifermi_iso.dimensionality) {
                 const dim = ifermi_iso.dimensionality.toLowerCase();
-                if (dim.includes(`1d`) || dim === `1d`)
+                if (dim.includes(`1d`))
                     dimensionality = `1D`;
-                else if (dim.includes(`quasi`) || dim === `quasi-2d`)
+                else if (dim.includes(`quasi`))
                     dimensionality = `quasi-2D`;
-                else if (dim.includes(`2d`) || dim === `2d`)
+                else if (dim.includes(`2d`))
                     dimensionality = `2D`;
-                else if (dim.includes(`3d`) || dim === `3d`)
+                else if (dim.includes(`3d`))
                     dimensionality = `3D`;
             }
             // Compute area for this isosurface using fan triangulation for N-gons
@@ -387,14 +393,8 @@ function parse_ifermi_surface(data) {
                 for (let fan_idx = 1; fan_idx < face.length - 1; fan_idx++) {
                     const v1 = vertices[face[fan_idx]];
                     const v2 = vertices[face[fan_idx + 1]];
-                    const e1 = [v1[0] - v0[0], v1[1] - v0[1], v1[2] - v0[2]];
-                    const e2 = [v2[0] - v0[0], v2[1] - v0[1], v2[2] - v0[2]];
-                    const cross = [
-                        e1[1] * e2[2] - e1[2] * e2[1],
-                        e1[2] * e2[0] - e1[0] * e2[2],
-                        e1[0] * e2[1] - e1[1] * e2[0],
-                    ];
-                    area += 0.5 * Math.hypot(cross[0], cross[1], cross[2]);
+                    const cross = math.cross_3d(math.subtract(v1, v0), math.subtract(v2, v0));
+                    area += 0.5 * Math.hypot(...cross);
                 }
             }
             isosurfaces.push({
@@ -427,68 +427,55 @@ function parse_ifermi_surface(data) {
         },
     };
 }
-// Auto-detect file format and parse accordingly
+// Auto-detect file format and parse; throws an Error aggregating per-format failure reasons when nothing parses
 export function parse_fermi_file(content, filename) {
     const lower_name = filename?.toLowerCase() ?? ``;
-    // Detect by filename extension
-    if (lower_name.endsWith(`.bxsf`) || lower_name.endsWith(`.bxsf.gz`)) {
+    const errors = [];
+    const attempt = (format, parse) => {
         try {
-            return parse_bxsf(content);
+            return parse();
         }
         catch (error) {
-            console.error(`BXSF parse error:`, error);
+            errors.push(`${format}: ${to_error(error).message}`);
+            console.error(`${format} parse error:`, error);
             return null;
         }
+    };
+    const fail = () => {
+        const detail = errors.length ? `: ${errors.join(`; `)}` : `: unrecognized format`;
+        throw new Error(`Failed to parse Fermi surface file${filename ? ` '${filename}'` : ``}${detail}`);
+    };
+    // Detect by filename extension (authoritative: parse failure throws immediately)
+    if (lower_name.endsWith(`.bxsf`) || lower_name.endsWith(`.bxsf.gz`)) {
+        return attempt(`BXSF`, () => parse_bxsf(content)) ?? fail();
     }
     if (lower_name.endsWith(`.frmsf`) || lower_name.endsWith(`.frmsf.gz`)) {
-        try {
-            return parse_frmsf(content);
-        }
-        catch (error) {
-            console.error(`FRMSF parse error:`, error);
-            return null;
-        }
+        return attempt(`FRMSF`, () => parse_frmsf(content)) ?? fail();
     }
     if (lower_name.endsWith(`.json`) || lower_name.endsWith(`.json.gz`)) {
-        try {
-            return parse_fermi_json(content);
-        }
-        catch (error) {
-            console.error(`JSON parse error:`, error);
-            return null;
-        }
+        return attempt(`JSON`, () => parse_fermi_json(content)) ?? fail();
     }
     // Try auto-detection based on content
     const trimmed = content.trim();
     // BXSF format detection
     if (trimmed.includes(`BEGIN_BLOCK_BANDGRID_3D`) || trimmed.includes(`BEGIN_BANDGRID_3D`)) {
-        try {
-            return parse_bxsf(content);
-        }
-        catch (error) {
-            console.error(`BXSF auto-detect parse error:`, error);
-        }
+        const result = attempt(`BXSF`, () => parse_bxsf(content));
+        if (result)
+            return result;
     }
     // JSON format detection
     if (trimmed.startsWith(`{`) || trimmed.startsWith(`[`)) {
-        try {
-            return parse_fermi_json(content);
-        }
-        catch (error) {
-            console.error(`JSON auto-detect parse error:`, error);
-        }
+        const result = attempt(`JSON`, () => parse_fermi_json(content));
+        if (result)
+            return result;
     }
     // FRMSF format detection (starts with grid dimensions)
     const first_line = trimmed.split(/\r?\n/)[0];
     const first_tokens = first_line.split(/\s+/).filter(Boolean);
     if (first_tokens.length === 3 && first_tokens.every((token) => /^\d+$/.test(token))) {
-        try {
-            return parse_frmsf(content);
-        }
-        catch (error) {
-            console.error(`FRMSF auto-detect parse error:`, error);
-        }
+        const result = attempt(`FRMSF`, () => parse_frmsf(content));
+        if (result)
+            return result;
     }
-    console.warn(`Could not detect Fermi surface file format for: ${filename}`);
-    return null;
+    return fail();
 }

package/dist/fermi-surface/types.d.ts

@@ -1,4 +1,4 @@
-import type { Matrix3x3, Point2D, Vec3 } from '../math';
+import type { Matrix3x3, Point2D, Vec2, Vec3 } from '../math';
 import type { TooltipConfig, TooltipProp } from '../tooltip';
 export type SpinChannel = `up` | `down` | null;
 export type RepresentationMode = `solid` | `wireframe` | `transparent`;
@@ -62,7 +62,7 @@ export interface FermiSliceData {
 }
 export interface Isoline {
     points: Vec3[];
-    points_2d: [number, number][];
+    points_2d: Vec2[];
     properties?: number[];
     band_index: number;
     spin: SpinChannel;