matterviz 0.3.6 → 0.4.0

package/dist/isosurface/parse.js

@@ -0,0 +1,552 @@
+// Parsers for volumetric data file formats (VASP CHGCAR, Gaussian .cube)
+import { COMPRESSION_EXTENSIONS_REGEX, VASP_VOLUMETRIC_REGEX } from '../constants';
+import { ELEM_SYMBOLS } from '../labels';
+import * as math from '../math';
+import { wrap_to_unit_cell } from '../structure/pbc';
+// Bohr radius in Angstroms (for Gaussian .cube unit conversion)
+const BOHR_TO_ANGSTROM = 0.529177249;
+// === Fast number parsing utilities ===
+// Parse whitespace-separated numbers directly from a string, starting at `pos`.
+// Writes into a pre-allocated Float64Array and returns { count, end_pos }.
+// Stops at `max_count` numbers, end of string, or when encountering a line
+// starting with a letter (e.g. "augmentation" in CHGCAR).
+function parse_float_block(text, pos, max_count, data, data_offset = 0) {
+    let idx = data_offset;
+    const target = data_offset + max_count;
+    const len = text.length;
+    while (idx < target && pos < len) {
+        // Skip whitespace
+        let char_code = text.charCodeAt(pos);
+        while (pos < len && char_code <= 32) {
+            // After a newline, check if the next non-space char is a letter (section break)
+            if (char_code === 10 || char_code === 13) {
+                let peek = pos + 1;
+                // Skip \r\n combo
+                if (char_code === 13 && peek < len && text.charCodeAt(peek) === 10)
+                    peek++;
+                // Skip leading spaces on the new line
+                while (peek < len && text.charCodeAt(peek) === 32)
+                    peek++;
+                if (peek < len) {
+                    const next_char = text.charCodeAt(peek);
+                    // Letter a-z or A-Z signals a non-numeric line (e.g. "augmentation")
+                    if ((next_char >= 65 && next_char <= 90) || (next_char >= 97 && next_char <= 122)) {
+                        return { count: idx - data_offset, end_pos: pos };
+                    }
+                }
+            }
+            char_code = text.charCodeAt(++pos);
+        }
+        if (pos >= len)
+            break;
+        // Find end of token
+        const start = pos;
+        while (pos < len && text.charCodeAt(pos) > 32)
+            pos++;
+        // Parse number (handles scientific notation)
+        const num = Number(text.slice(start, pos));
+        if (!Number.isNaN(num)) {
+            data[idx++] = num;
+        }
+    }
+    return { count: idx - data_offset, end_pos: pos };
+}
+// Find the character offset for line N in a string (0-indexed).
+// Much faster than splitting the entire string into lines.
+function find_line_offset(text, target_line) {
+    let line = 0;
+    let pos = 0;
+    while (line < target_line && pos < text.length) {
+        if (text.charCodeAt(pos) === 10)
+            line++;
+        pos++;
+    }
+    return pos;
+}
+// Read a single line from text at the given offset, returning the line and next offset
+function read_line(text, pos) {
+    let end = pos;
+    while (end < text.length && text.charCodeAt(end) !== 10 && text.charCodeAt(end) !== 13)
+        end++;
+    const line = text.slice(pos, end);
+    let next = end;
+    if (next < text.length && text.charCodeAt(next) === 13)
+        next++; // skip \r
+    if (next < text.length && text.charCodeAt(next) === 10)
+        next++; // skip \n
+    return { line, next };
+}
+// Read N lines starting from pos, returning array of trimmed lines and final offset
+function read_lines(text, pos, count) {
+    const result = [];
+    for (let idx = 0; idx < count; idx++) {
+        const { line, next } = read_line(text, pos);
+        result.push(line.trim());
+        pos = next;
+    }
+    return { lines: result, next: pos };
+}
+function build_grid({ data, nx, ny, nz, divisor = 1, data_order = `z_fastest`, }) {
+    const grid = Array(nx);
+    let [min_val, max_val, sum] = [Infinity, -Infinity, 0];
+    const total = nx * ny * nz;
+    const data_len = Math.min(data.length, total);
+    if (data_len === 0) {
+        // Empty data: return zeroed grid with neutral data_range
+        for (let ix = 0; ix < nx; ix++) {
+            const plane = Array(ny);
+            for (let iy = 0; iy < ny; iy++)
+                plane[iy] = Array(nz).fill(0);
+            grid[ix] = plane;
+        }
+        return { grid, data_range: { min: 0, max: 0, abs_max: 0, mean: 0 } };
+    }
+    if (data_order === `z_fastest`) {
+        // .cube convention: z varies fastest, then y, then x.
+        const ny_nz = ny * nz;
+        for (let ix = 0; ix < nx; ix++) {
+            const plane = Array(ny);
+            for (let iy = 0; iy < ny; iy++) {
+                const row = Array(nz).fill(0);
+                const base = ix * ny_nz + iy * nz;
+                const row_end = Math.min(base + nz, data_len);
+                for (let flat_idx = base; flat_idx < row_end; flat_idx++) {
+                    const val = data[flat_idx] / divisor;
+                    row[flat_idx - base] = val;
+                    if (val < min_val)
+                        min_val = val;
+                    if (val > max_val)
+                        max_val = val;
+                    sum += val;
+                }
+                plane[iy] = row;
+            }
+            grid[ix] = plane;
+        }
+    }
+    else {
+        // VASP CHGCAR/ELFCAR/LOCPOT convention: x varies fastest, then y, then z.
+        for (let ix = 0; ix < nx; ix++) {
+            const plane = Array(ny);
+            for (let iy = 0; iy < ny; iy++)
+                plane[iy] = Array(nz).fill(0);
+            grid[ix] = plane;
+        }
+        let [flat_idx, data_exhausted] = [0, false];
+        for (let iz = 0; iz < nz; iz++) {
+            for (let iy = 0; iy < ny; iy++) {
+                for (let ix = 0; ix < nx; ix++) {
+                    if (flat_idx >= data_len) {
+                        data_exhausted = true;
+                        break;
+                    }
+                    const val = data[flat_idx] / divisor;
+                    grid[ix][iy][iz] = val;
+                    if (val < min_val)
+                        min_val = val;
+                    if (val > max_val)
+                        max_val = val;
+                    sum += val;
+                    flat_idx++;
+                }
+                if (data_exhausted)
+                    break;
+            }
+            if (data_exhausted)
+                break;
+        }
+    }
+    const abs_max = Math.max(Math.abs(min_val), Math.abs(max_val));
+    const data_range = { min: min_val, max: max_val, abs_max, mean: sum / data_len };
+    return { grid, data_range };
+}
+// === CHGCAR Parser ===
+// Parse VASP CHGCAR/AECCAR/ELFCAR/LOCPOT/PARCHG file format.
+// CHGCAR/PARCHG consists of a POSCAR header followed by volumetric data on a 3D grid.
+// Spin-polarized files contain two data blocks (total charge + magnetization).
+export function parse_chgcar(content) {
+    // Strip leading whitespace
+    let pos = 0;
+    while (pos < content.length && content.charCodeAt(pos) <= 32)
+        pos++;
+    // Parse header line by line (only the first ~20 lines, not the whole file)
+    // Line 0: comment
+    let cur = read_line(content, pos);
+    pos = cur.next;
+    // Line 1: scale factor
+    cur = read_line(content, pos);
+    const scale_factor = parseFloat(cur.line);
+    if (isNaN(scale_factor)) {
+        console.error(`Invalid scaling factor in CHGCAR`);
+        return null;
+    }
+    pos = cur.next;
+    // Lines 2-4: lattice vectors
+    const parse_vector = (line) => math.scale(line.trim().split(/\s+/).slice(0, 3).map(Number), scale_factor);
+    const lat_lines = read_lines(content, pos, 3);
+    const lattice = [
+        parse_vector(lat_lines.lines[0]),
+        parse_vector(lat_lines.lines[1]),
+        parse_vector(lat_lines.lines[2]),
+    ];
+    pos = lat_lines.next;
+    // Lines 5+: element symbols and atom counts
+    let element_symbols = [];
+    let atom_counts = [];
+    cur = read_line(content, pos);
+    if (pos >= content.length) {
+        console.error(`CHGCAR: file ends before element/count lines`);
+        return null;
+    }
+    // Detect VASP 5+ format (has element symbols before counts)
+    const first_token = cur.line.trim().split(/\s+/)[0];
+    const has_element_symbols = isNaN(parseInt(first_token, 10));
+    if (has_element_symbols) {
+        element_symbols = cur.line.trim().split(/\s+/);
+        pos = cur.next;
+        cur = read_line(content, pos);
+        if (pos >= content.length) {
+            console.error(`CHGCAR: file ends before atom counts line`);
+            return null;
+        }
+        atom_counts = cur.line.trim().split(/\s+/).map(Number);
+    }
+    else {
+        atom_counts = cur.line.trim().split(/\s+/).map(Number);
+        const fallback_elements = [`H`, `He`, `Li`, `Be`, `B`, `C`, `N`, `O`, `F`, `Ne`];
+        element_symbols = atom_counts.map((_count, idx) => fallback_elements[idx % fallback_elements.length]);
+    }
+    pos = cur.next;
+    if (pos >= content.length) {
+        console.error(`CHGCAR: file ends before coordinate mode line`);
+        return null;
+    }
+    // Check for selective dynamics line
+    cur = read_line(content, pos);
+    if (cur.line.trim().toUpperCase().startsWith(`S`)) {
+        pos = cur.next; // skip selective dynamics line
+        cur = read_line(content, pos);
+    }
+    if (pos >= content.length) {
+        console.error(`CHGCAR: file ends before coordinate mode line`);
+        return null;
+    }
+    // Coordinate mode line
+    const is_direct = cur.line.trim().toUpperCase().startsWith(`D`);
+    pos = cur.next;
+    // Parse atomic positions
+    let cart_to_frac;
+    let frac_to_cart;
+    try {
+        ;
+        ({ cart_to_frac, frac_to_cart } = math.create_lattice_converters(lattice));
+    }
+    catch {
+        console.error(`CHGCAR: lattice matrix is singular; cannot convert coordinates`);
+        return null;
+    }
+    const sites = [];
+    let atom_idx = 0;
+    for (let elem_idx = 0; elem_idx < element_symbols.length; elem_idx++) {
+        const symbol = element_symbols[elem_idx].split(/[_/]/)[0];
+        const element = (ELEM_SYMBOLS.includes(symbol) ? symbol : `H`);
+        const count = atom_counts[elem_idx];
+        for (let count_idx = 0; count_idx < count; count_idx++) {
+            if (pos >= content.length) {
+                console.error(`CHGCAR: file ends before all atom coordinates are read`);
+                return null;
+            }
+            cur = read_line(content, pos);
+            const coords = cur.line.trim().split(/\s+/).slice(0, 3).map(Number);
+            pos = cur.next;
+            let abc;
+            let xyz;
+            if (is_direct) {
+                abc = wrap_to_unit_cell(coords);
+                xyz = frac_to_cart(abc);
+            }
+            else {
+                xyz = math.scale(coords, scale_factor);
+                const raw = cart_to_frac(xyz);
+                abc = wrap_to_unit_cell(raw);
+            }
+            sites.push({
+                species: [{ element, occu: 1, oxidation_state: 0 }],
+                abc,
+                xyz,
+                label: `${element}${atom_idx + count_idx + 1}`,
+                properties: {},
+            });
+        }
+        atom_idx += count;
+    }
+    // Build the structure (volumetric files are always periodic)
+    const lattice_params = math.calc_lattice_params(lattice);
+    const structure = {
+        sites,
+        lattice: { matrix: lattice, pbc: [true, true, true], ...lattice_params },
+    };
+    // Parse volumetric data blocks
+    const volumes = [];
+    const volume_labels = [`charge density`, `magnetization density`];
+    for (let vol_idx = 0; vol_idx < 2; vol_idx++) {
+        // Skip blank lines
+        while (pos < content.length) {
+            cur = read_line(content, pos);
+            if (cur.line.trim() !== ``)
+                break;
+            pos = cur.next;
+        }
+        if (pos >= content.length)
+            break;
+        // Parse grid dimensions: NGX NGY NGZ
+        cur = read_line(content, pos);
+        const grid_tokens = cur.line.trim().split(/\s+/).map(Number);
+        if (grid_tokens.length < 3 || grid_tokens.some(isNaN))
+            break;
+        const [ngx, ngy, ngz] = grid_tokens;
+        pos = cur.next;
+        // Fast-parse volumetric data directly from the string
+        const total_points = ngx * ngy * ngz;
+        const data = new Float64Array(total_points);
+        const { count: parsed_count, end_pos } = parse_float_block(content, pos, total_points, data);
+        pos = end_pos;
+        if (parsed_count < total_points) {
+            console.warn(`CHGCAR volume ${vol_idx}: expected ${total_points} values, got ${parsed_count}`);
+            if (parsed_count === 0)
+                break;
+        }
+        // CHGCAR stores rho * V_cell, so normalize by dividing by cell volume.
+        // Use Math.abs to guard against negative determinant (left-handed lattice).
+        const cell_volume = Math.abs(lattice_params.volume);
+        const divisor = cell_volume > 1e-30 ? cell_volume : 1;
+        const { grid, data_range } = build_grid({
+            data: data.subarray(0, parsed_count),
+            nx: ngx,
+            ny: ngy,
+            nz: ngz,
+            divisor,
+            data_order: `x_fastest`,
+        });
+        volumes.push({
+            grid,
+            grid_dims: [ngx, ngy, ngz],
+            lattice,
+            origin: [0, 0, 0],
+            data_range,
+            data_order: `x_fastest`,
+            periodic: true, // VASP grids span [0,1) with N points, wrapping at boundaries
+            label: volume_labels[vol_idx],
+        });
+        // Skip augmentation occupancies and any remaining non-numeric lines
+        while (pos < content.length) {
+            cur = read_line(content, pos);
+            const trimmed = cur.line.trim();
+            if (trimmed === `` || /^\d+\s+\d+\s+\d+$/.test(trimmed))
+                break;
+            pos = cur.next;
+        }
+    }
+    if (volumes.length === 0) {
+        console.error(`No volumetric data found in CHGCAR`);
+        return null;
+    }
+    return { structure, volumes };
+}
+// === Gaussian .cube Parser ===
+// Parse Gaussian .cube file format.
+// Contains atomic structure and volumetric data in a single file.
+// Units: if grid dimensions are positive, coordinates are in Bohr; if negative, in Angstrom.
+export function parse_cube(content, options = {}) {
+    // Quick line count check: need at least 7 lines (2 title + 1 header + 3 voxel + 1 atom)
+    let line_count = 0;
+    for (let idx = 0; idx < content.length && line_count < 7; idx++) {
+        if (content.charCodeAt(idx) === 10)
+            line_count++;
+    }
+    if (line_count < 6) {
+        console.error(`.cube file too short`);
+        return null;
+    }
+    // Parse header (first 6 lines + atom lines)
+    let pos = 0;
+    const header = read_lines(content, pos, 6);
+    pos = header.next;
+    // Line 2: n_atoms, origin_x, origin_y, origin_z
+    // (negative n_atoms indicates orbital data with extra header line)
+    const line2 = header.lines[2].split(/\s+/).map(Number);
+    if (line2.length < 4 || line2.some(isNaN)) {
+        console.error(`.cube header line 3 malformed: expected 4 numbers`);
+        return null;
+    }
+    const n_atoms = Math.abs(line2[0]);
+    const has_orbital_header = line2[0] < 0;
+    const raw_origin = [line2[1], line2[2], line2[3]];
+    // Lines 3-5: grid dimensions and voxel vectors
+    // Positive N means coordinates in Bohr, negative N means Angstrom
+    const voxel_lines = [
+        header.lines[3].split(/\s+/).map(Number),
+        header.lines[4].split(/\s+/).map(Number),
+        header.lines[5].split(/\s+/).map(Number),
+    ];
+    if (voxel_lines.some((line) => line.length < 4 || line.some(isNaN))) {
+        console.error(`.cube voxel lines malformed: expected 4 numbers per line`);
+        return null;
+    }
+    const n_grid = [
+        Math.abs(voxel_lines[0][0]),
+        Math.abs(voxel_lines[1][0]),
+        Math.abs(voxel_lines[2][0]),
+    ];
+    // Per Gaussian .cube convention, the sign of the first axis N determines units
+    const is_bohr = voxel_lines[0][0] > 0;
+    const unit_scale = is_bohr ? BOHR_TO_ANGSTROM : 1.0;
+    // Voxel vectors (convert to Angstrom if needed)
+    const [voxel_a, voxel_b, voxel_c] = voxel_lines.map((line) => math.scale(line.slice(1, 4), unit_scale));
+    // Lattice vectors = grid_dim * voxel_vector
+    const lattice = [
+        math.scale(voxel_a, n_grid[0]),
+        math.scale(voxel_b, n_grid[1]),
+        math.scale(voxel_c, n_grid[2]),
+    ];
+    const origin = math.scale(raw_origin, unit_scale);
+    // Periodicity: use explicit override if provided, else heuristic based on origin.
+    // Molecular .cube files have a non-zero origin (bounding box offset); periodic
+    // systems (QE, CP2K) have origin at (0,0,0). Pass { periodic: true/false } to
+    // override when the heuristic is wrong (e.g. molecule centered at origin).
+    const is_periodic = options.periodic ?? Math.hypot(...origin) < 1e-6;
+    // Parse atomic positions
+    const sites = [];
+    let cube_cart_to_frac;
+    try {
+        cube_cart_to_frac = math.create_cart_to_frac(lattice);
+    }
+    catch {
+        // Non-periodic system (molecule), use identity
+        cube_cart_to_frac = (v) => [v[0], v[1], v[2]];
+    }
+    for (let atom_idx = 0; atom_idx < n_atoms; atom_idx++) {
+        const cur = read_line(content, pos);
+        const atom_line = cur.line.trim().split(/\s+/).map(Number);
+        pos = cur.next;
+        // Validate: need atomic_number, charge, x, y, z (5 tokens, indices 2-4 finite)
+        if (atom_line.length < 5 ||
+            !isFinite(atom_line[2]) ||
+            !isFinite(atom_line[3]) ||
+            !isFinite(atom_line[4])) {
+            console.warn(`.cube atom ${atom_idx}: malformed line "${cur.line.trim()}", skipping`);
+            continue;
+        }
+        // atom_line[1] is the charge (often 0)
+        const raw_xyz = math.scale([atom_line[2], atom_line[3], atom_line[4]], unit_scale);
+        // Convert Cartesian to fractional, accounting for origin offset.
+        // Store lattice-frame xyz (shifted) so abc and xyz stay consistent.
+        const xyz = math.subtract(raw_xyz, origin);
+        const abc = cube_cart_to_frac(xyz);
+        const element = atomic_number_to_symbol(atom_line[0]);
+        sites.push({
+            species: [{ element, occu: 1, oxidation_state: 0 }],
+            abc,
+            xyz,
+            label: `${element}${atom_idx + 1}`,
+            properties: {},
+        });
+    }
+    // Build structure
+    const lattice_params = math.calc_lattice_params(lattice);
+    const structure = {
+        sites,
+        lattice: {
+            matrix: lattice,
+            pbc: [is_periodic, is_periodic, is_periodic],
+            ...lattice_params,
+        },
+    };
+    // Skip orbital header line if present
+    if (has_orbital_header && pos < content.length) {
+        const cur = read_line(content, pos);
+        pos = cur.next;
+    }
+    // Fast-parse volumetric data directly from the string
+    const total_points = n_grid[0] * n_grid[1] * n_grid[2];
+    const data = new Float64Array(total_points);
+    const { count: parsed_count } = parse_float_block(content, pos, total_points, data);
+    if (parsed_count < total_points) {
+        console.warn(`.cube: expected ${total_points} data values, got ${parsed_count}`);
+        if (parsed_count === 0) {
+            console.error(`No volumetric data found in .cube file`);
+            return null;
+        }
+    }
+    const { grid, data_range } = build_grid({
+        data: data.subarray(0, parsed_count),
+        nx: n_grid[0],
+        ny: n_grid[1],
+        nz: n_grid[2],
+        data_order: `z_fastest`,
+    });
+    const volumes = [
+        {
+            grid,
+            grid_dims: n_grid,
+            lattice,
+            origin,
+            data_range,
+            data_order: `z_fastest`,
+            periodic: is_periodic, // periodic systems wrap; molecular .cube files include both endpoints
+            label: `volumetric data`,
+        },
+    ];
+    return { structure, volumes };
+}
+// Convert atomic number to element symbol using ELEM_SYMBOLS (1-indexed: H=1, He=2, ...)
+function atomic_number_to_symbol(atomic_number) {
+    // ELEM_SYMBOLS is 0-indexed (H at index 0), atomic numbers are 1-indexed
+    const idx = atomic_number - 1;
+    return idx >= 0 && idx < ELEM_SYMBOLS.length ? ELEM_SYMBOLS[idx] : `H`;
+}
+// Auto-detect and parse volumetric file format based on filename and content
+export function parse_volumetric_file(content, filename) {
+    // Strip compression suffixes so "CHGCAR.gz" and "molecule.cube.bz2" match correctly
+    const lower_name = (filename ?? ``).toLowerCase().replace(COMPRESSION_EXTENSIONS_REGEX, ``);
+    // Extension-based detection
+    if (lower_name.endsWith(`.cube`))
+        return parse_cube(content);
+    // VASP volumetric file detection by filename
+    if (VASP_VOLUMETRIC_REGEX.test(lower_name))
+        return parse_chgcar(content);
+    // Content-based detection (only parse first few lines, not the whole file)
+    // Find enough lines for detection without splitting the entire string
+    const detection_end = find_line_offset(content, 10);
+    const detection_text = content.slice(0, detection_end);
+    const lines = detection_text.split(/\r?\n/);
+    // .cube detection: line 3 has 4 numbers (n_atoms + origin), line 4 has 4 numbers (grid dim + voxel)
+    if (lines.length > 4) {
+        const line2_tokens = lines[2].trim().split(/\s+/);
+        const line3_tokens = lines[3].trim().split(/\s+/);
+        if (line2_tokens.length === 4 &&
+            line3_tokens.length === 4 &&
+            line2_tokens.every((tok) => !isNaN(Number(tok))) &&
+            line3_tokens.every((tok) => !isNaN(Number(tok)))) {
+            return parse_cube(content);
+        }
+    }
+    // CHGCAR detection: requires POSCAR-like header (scale factor on line 2) AND
+    // a grid dimensions line (3 integers) somewhere after the header. This distinguishes
+    // CHGCAR from plain POSCAR/CONTCAR files which share the same header format.
+    if (lines.length > 2 && !isNaN(parseFloat(lines[1].trim()))) {
+        // Scan for grid dimensions line (3 integers) starting from ~line 7
+        let scan_pos = find_line_offset(content, 7);
+        // Only scan a limited window, not the entire file
+        // Scan enough to cover large atom blocks (~100 chars/atom × ~200 atoms max)
+        const scan_end = Math.min(content.length, scan_pos + 25000);
+        while (scan_pos < scan_end) {
+            const { line, next } = read_line(content, scan_pos);
+            if (/^\s*\d+\s+\d+\s+\d+\s*$/.test(line)) {
+                return parse_chgcar(content);
+            }
+            scan_pos = next;
+        }
+    }
+    return null;
+}

package/dist/isosurface/slice.d.ts

@@ -0,0 +1,11 @@
+import type { Vec3 } from '../math';
+import type { VolumetricData } from './types';
+export interface SliceResult {
+    data: Float64Array;
+    width: number;
+    height: number;
+    min: number;
+    max: number;
+}
+export declare function trilinear_interpolate(grid: number[][][], fx: number, fy: number, fz: number, periodic: boolean): number;
+export declare function sample_hkl_slice(volume: VolumetricData, miller_indices: Vec3, distance: number, n_points?: number): SliceResult | null;