matterviz 0.3.1 → 0.3.3

package/dist/symmetry/index.js

@@ -1,5 +1,6 @@
 import { ATOMIC_NUMBER_TO_SYMBOL, SYMBOL_TO_ATOMIC_NUMBER } from '../composition/parse';
 import { DEFAULTS } from '../settings';
+import { merge_split_partial_sites } from '../structure/partial-occupancy';
 import init, { analyze_cell } from '@spglib/moyo-wasm';
 import moyo_wasm_url from '@spglib/moyo-wasm/moyo_wasm_bg.wasm?url';
 export * from './cell-transform';
@@ -21,6 +22,7 @@ export const default_sym_settings = {
     algo: DEFAULTS.symmetry.algo,
 };
 let initialized = false;
+const OCCUPANCY_EPS = 1e-8;
 export async function ensure_moyo_wasm_ready(wasm_url) {
     if (initialized)
         return;
@@ -29,34 +31,89 @@ export async function ensure_moyo_wasm_ready(wasm_url) {
     await init({ module_or_path: url });
     initialized = true;
 }
-export function to_cell_json(structure) {
+function get_site_atomic_number(site, site_idx) {
+    const occupancy_by_element = new Map();
+    for (const { element, occu } of site.species) {
+        if (occu <= OCCUPANCY_EPS)
+            continue;
+        occupancy_by_element.set(element, (occupancy_by_element.get(element) ?? 0) + occu);
+    }
+    let selected_element = site.species[0]?.element;
+    let best_occupancy = -Infinity;
+    occupancy_by_element.forEach((occupancy, element) => {
+        if (occupancy > best_occupancy ||
+            (occupancy === best_occupancy && element.localeCompare(selected_element ?? ``) < 0)) {
+            selected_element = element;
+            best_occupancy = occupancy;
+        }
+    });
+    if (selected_element === undefined) {
+        throw new Error(`Unknown element at site ${site_idx}: ${selected_element}`);
+    }
+    const atomic_number = SYMBOL_TO_ATOMIC_NUMBER[selected_element];
+    if (atomic_number === undefined) {
+        throw new Error(`Unknown element at site ${site_idx}: ${selected_element}`);
+    }
+    return atomic_number;
+}
+function build_moyo_input_cell(structure) {
+    const merged_render_sites = merge_split_partial_sites(structure.sites);
+    return {
+        positions: merged_render_sites.map(({ site }) => site.abc),
+        numbers: merged_render_sites.map(({ site, site_idx }) => get_site_atomic_number(site, site_idx)),
+        orig_site_indices_by_input_idx: merged_render_sites.map(({ source_site_indices }) => source_site_indices),
+    };
+}
+function build_moyo_cell(structure, positions, numbers) {
     // nalgebra Matrix3 deserializes as a flat list in COLUMN-MAJOR of the internal basis B
     // Internal B = transpose(row-basis RB). column-major(B) == row-major(RB).
     // So supply row-major of the pymatgen lattice.matrix (RB).
     const [v_a, v_b, v_c] = structure.lattice.matrix;
-    const basis = [...v_a, ...v_b, ...v_c];
-    const positions = structure.sites.map((site) => site.abc);
-    const numbers = structure.sites.map((site, idx) => {
-        const sym = site.species?.[0]?.element;
-        const num = sym !== null ? SYMBOL_TO_ATOMIC_NUMBER[sym] : undefined;
-        if (typeof num !== `number`) {
-            throw new Error(`Unknown element at site ${idx}: ${String(sym)}`);
+    return {
+        lattice: { basis: [...v_a, ...v_b, ...v_c] },
+        positions,
+        numbers,
+    };
+}
+export function to_cell_json(structure) {
+    const { positions, numbers } = build_moyo_input_cell(structure);
+    return JSON.stringify(build_moyo_cell(structure, positions, numbers));
+}
+const fractional_sq_dist = (pos_1, pos_2) => (pos_1[0] - pos_2[0] - Math.round(pos_1[0] - pos_2[0])) ** 2 +
+    (pos_1[1] - pos_2[1] - Math.round(pos_1[1] - pos_2[1])) ** 2 +
+    (pos_1[2] - pos_2[2] - Math.round(pos_1[2] - pos_2[2])) ** 2;
+export function map_std_to_orig_site_indices(std_positions, std_numbers, input_positions, input_numbers, orig_site_indices_by_input_idx) {
+    return std_positions.map((std_pos, std_idx) => {
+        const std_number = std_numbers[std_idx];
+        let nearest_input_idx = -1;
+        let nearest_sq_dist = Infinity;
+        for (let input_idx = 0; input_idx < input_positions.length; input_idx += 1) {
+            if (input_numbers[input_idx] !== std_number)
+                continue;
+            const sq_dist = fractional_sq_dist(std_pos, input_positions[input_idx]);
+            if (sq_dist < nearest_sq_dist) {
+                nearest_sq_dist = sq_dist;
+                nearest_input_idx = input_idx;
+            }
         }
-        return num;
+        if (nearest_input_idx === -1)
+            return [];
+        return orig_site_indices_by_input_idx[nearest_input_idx] ?? [];
     });
-    const cell = { lattice: { basis }, positions, numbers };
-    return JSON.stringify(cell);
 }
 export async function analyze_structure_symmetry(struct_or_mol, settings) {
     await ensure_moyo_wasm_ready();
     if (!(`lattice` in struct_or_mol)) {
         throw new Error(`Symmetry analysis requires a periodic structure with a lattice`);
     }
-    const cell_json = to_cell_json(struct_or_mol);
+    const moyo_input_cell = build_moyo_input_cell(struct_or_mol);
+    const cell_json = JSON.stringify(build_moyo_cell(struct_or_mol, moyo_input_cell.positions, moyo_input_cell.numbers));
     const { symprec, algo } = { ...default_sym_settings, ...settings };
     // Map "Moyo" to "Standard" for moyo-wasm
     const moyo_algo = algo === `Moyo` ? `Standard` : algo;
-    return analyze_cell(cell_json, symprec, moyo_algo);
+    const sym_data = analyze_cell(cell_json, symprec, moyo_algo);
+    const orig_site_indices_by_std_idx = map_std_to_orig_site_indices(sym_data.std_cell.positions, sym_data.std_cell.numbers, moyo_input_cell.positions, moyo_input_cell.numbers, moyo_input_cell.orig_site_indices_by_input_idx);
+    return { ...sym_data, orig_site_indices_by_std_idx };
 }
 // Helper function to score coordinate simplicity for Wyckoff table
 export function simplicity_score(vec) {
@@ -64,7 +121,9 @@ export function simplicity_score(vec) {
     const near_zero = (v) => Math.min(v, 1 - v);
     const near_half = (v) => Math.abs(v - 0.5);
     const [ax, ay, az] = vec?.map(to_unit) ?? [];
-    return (near_zero(ax) + near_zero(ay) + near_zero(az) +
+    return (near_zero(ax) +
+        near_zero(ay) +
+        near_zero(az) +
         0.5 * (near_half(ax) + near_half(ay) + near_half(az)));
 }
 // Generate Wyckoff table rows from symmetry data
@@ -72,7 +131,7 @@ export function wyckoff_positions_from_moyo(sym_data) {
     if (!sym_data)
         return [];
     const { positions, numbers } = sym_data.std_cell;
-    const { wyckoffs, orig_indices } = sym_data;
+    const { wyckoffs, orig_indices, orig_site_indices_by_std_idx } = sym_data;
     // Group sites by letter-element combination and track all indices
     const groups = new Map();
     // Process all atoms in the standardized cell
@@ -80,7 +139,7 @@ export function wyckoff_positions_from_moyo(sym_data) {
     for (let idx = 0; idx < numbers.length; idx++) {
         // Use wyckoff letter if available, otherwise mark as non-symmetric
         const full = idx < wyckoffs.length ? wyckoffs[idx] : null;
-        const letter = (full?.match(/[a-z]+$/)?.[0] ?? full ?? ``).toString();
+        const letter = full?.match(/[a-z]+$/)?.[0] ?? full ?? ``;
         const atomic_num = numbers[idx];
         const elem = ATOMIC_NUMBER_TO_SYMBOL[atomic_num] ?? `?`;
         const position = positions[idx];
@@ -97,11 +156,18 @@ export function wyckoff_positions_from_moyo(sym_data) {
             return score < best.score ? { pos, score } : best;
         }, { pos: positions[0], score: simplicity_score(positions[0]) }).pos;
         // Map standardized cell indices back to original structure indices
-        const orig_site_indices = orig_indices
-            ? indices.map((i) => orig_indices[i]).filter((idx) => idx !== undefined)
-            : indices;
+        const orig_site_indices = orig_site_indices_by_std_idx
+            ? indices.flatMap((std_idx) => orig_site_indices_by_std_idx[std_idx] ?? [])
+            : orig_indices
+                ? indices.map((std_idx) => orig_indices[std_idx]).filter((idx) => idx !== undefined)
+                : indices;
         const wyckoff = letter ? `${indices.length}${letter}` : `1`;
-        return { wyckoff, elem, abc: best_pos, site_indices: orig_site_indices };
+        return {
+            wyckoff,
+            elem,
+            abc: best_pos,
+            site_indices: [...new Set(orig_site_indices)].sort((idx_a, idx_b) => idx_a - idx_b),
+        };
     });
     rows.sort((w1, w2) => {
         const [w1_mult, w2_mult] = [parseInt(w1.wyckoff), parseInt(w2.wyckoff)];
@@ -141,7 +207,7 @@ export function map_wyckoff_to_all_atoms(wyckoff_positions, displayed_structure,
     const periodic_distance = (pos1, pos2) => Math.sqrt(pos1.reduce((sum, coord, idx) => {
         // Wrap delta into [-0.5, 0.5) using safe modulo
         const delta = coord - pos2[idx];
-        const wrapped = (((delta + 0.5) % 1) + 1) % 1 - 0.5;
+        const wrapped = ((((delta + 0.5) % 1) + 1) % 1) - 0.5;
         const d = Math.abs(wrapped);
         return sum + d * d;
     }, 0));

package/dist/symmetry/spacegroups.js

@@ -61,16 +61,16 @@ export function normalize_spacegroup(spacegroup) {
 }
 export const SPACEGROUP_SYMBOL_TO_NUM = {
     // Triclinic
-    'P1': 1,
+    P1: 1,
     'P-1': 2,
     // Monoclinic
-    'P2': 3,
-    'P2_1': 4,
-    'C2': 5,
-    'Pm': 6,
-    'Pc': 7,
-    'Cm': 8,
-    'Cc': 9,
+    P2: 3,
+    P2_1: 4,
+    C2: 5,
+    Pm: 6,
+    Pc: 7,
+    Cm: 8,
+    Cc: 9,
     'P2/m': 10,
     'P2_1/m': 11,
     'C2/m': 12,
@@ -78,72 +78,72 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'P2_1/c': 14,
     'C2/c': 15,
     // Orthorhombic
-    'P222': 16,
-    'P222_1': 17,
-    'P2_12_12': 18,
-    'P2_12_12_1': 19,
-    'C222_1': 20,
-    'C222': 21,
-    'F222': 22,
-    'I222': 23,
-    'I2_12_12_1': 24,
-    'Pmm2': 25,
-    'Pmc2_1': 26,
-    'Pcc2': 27,
-    'Pma2': 28,
-    'Pca2_1': 29,
-    'Pnc2': 30,
-    'Pmn2_1': 31,
-    'Pba2': 32,
-    'Pna2_1': 33,
-    'Pnn2': 34,
-    'Cmm2': 35,
-    'Cmc2_1': 36,
-    'Ccc2': 37,
-    'Amm2': 38,
-    'Aem2': 39,
-    'Ama2': 40,
-    'Aea2': 41,
-    'Fmm2': 42,
-    'Fdd2': 43,
-    'Imm2': 44,
-    'Iba2': 45,
-    'Ima2': 46,
-    'Pmmm': 47,
-    'Pnnn': 48,
-    'Pccm': 49,
-    'Pban': 50,
-    'Pmma': 51,
-    'Pnna': 52,
-    'Pmna': 53,
-    'Pcca': 54,
-    'Pbam': 55,
-    'Pccn': 56,
-    'Pbcm': 57,
-    'Pnnm': 58,
-    'Pmmn': 59,
-    'Pbcn': 60,
-    'Pbca': 61,
-    'Pnma': 62,
-    'Cmcm': 63,
-    'Cmce': 64,
-    'Cmmm': 65,
-    'Cccm': 66,
-    'Cmme': 67,
-    'Ccce': 68,
-    'Fmmm': 69,
-    'Fddd': 70,
-    'Immm': 71,
-    'Ibam': 72,
-    'Ibca': 73,
-    'Imma': 74,
+    P222: 16,
+    P222_1: 17,
+    P2_12_12: 18,
+    P2_12_12_1: 19,
+    C222_1: 20,
+    C222: 21,
+    F222: 22,
+    I222: 23,
+    I2_12_12_1: 24,
+    Pmm2: 25,
+    Pmc2_1: 26,
+    Pcc2: 27,
+    Pma2: 28,
+    Pca2_1: 29,
+    Pnc2: 30,
+    Pmn2_1: 31,
+    Pba2: 32,
+    Pna2_1: 33,
+    Pnn2: 34,
+    Cmm2: 35,
+    Cmc2_1: 36,
+    Ccc2: 37,
+    Amm2: 38,
+    Aem2: 39,
+    Ama2: 40,
+    Aea2: 41,
+    Fmm2: 42,
+    Fdd2: 43,
+    Imm2: 44,
+    Iba2: 45,
+    Ima2: 46,
+    Pmmm: 47,
+    Pnnn: 48,
+    Pccm: 49,
+    Pban: 50,
+    Pmma: 51,
+    Pnna: 52,
+    Pmna: 53,
+    Pcca: 54,
+    Pbam: 55,
+    Pccn: 56,
+    Pbcm: 57,
+    Pnnm: 58,
+    Pmmn: 59,
+    Pbcn: 60,
+    Pbca: 61,
+    Pnma: 62,
+    Cmcm: 63,
+    Cmce: 64,
+    Cmmm: 65,
+    Cccm: 66,
+    Cmme: 67,
+    Ccce: 68,
+    Fmmm: 69,
+    Fddd: 70,
+    Immm: 71,
+    Ibam: 72,
+    Ibca: 73,
+    Imma: 74,
     // Tetragonal
-    'P4': 75,
-    'P4_1': 76,
-    'P4_2': 77,
-    'P4_3': 78,
-    'I4': 79,
-    'I4_1': 80,
+    P4: 75,
+    P4_1: 76,
+    P4_2: 77,
+    P4_3: 78,
+    I4: 79,
+    I4_1: 80,
     'P-4': 81,
     'I-4': 82,
     'P4/m': 83,
@@ -152,28 +152,28 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'P4_2/n': 86,
     'I4/m': 87,
     'I4_1/a': 88,
-    'P422': 89,
-    'P42_12': 90,
-    'P4_122': 91,
-    'P4_12_12': 92,
-    'P4_222': 93,
-    'P4_22_12': 94,
-    'P4_322': 95,
-    'P4_32_12': 96,
-    'I422': 97,
-    'I4_122': 98,
-    'P4mm': 99,
-    'P4bm': 100,
-    'P4_2cm': 101,
-    'P4_2nm': 102,
-    'P4cc': 103,
-    'P4nc': 104,
-    'P4_2mc': 105,
-    'P4_2bc': 106,
-    'I4mm': 107,
-    'I4cm': 108,
-    'I4_1md': 109,
-    'I4_1cd': 110,
+    P422: 89,
+    P42_12: 90,
+    P4_122: 91,
+    P4_12_12: 92,
+    P4_222: 93,
+    P4_22_12: 94,
+    P4_322: 95,
+    P4_32_12: 96,
+    I422: 97,
+    I4_122: 98,
+    P4mm: 99,
+    P4bm: 100,
+    P4_2cm: 101,
+    P4_2nm: 102,
+    P4cc: 103,
+    P4nc: 104,
+    P4_2mc: 105,
+    P4_2bc: 106,
+    I4mm: 107,
+    I4cm: 108,
+    I4_1md: 109,
+    I4_1cd: 110,
     'P-42m': 111,
     'P-42c': 112,
     'P-42_1m': 113,
@@ -206,26 +206,26 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'I4/mcm': 140,
     'I4_1/amd': 141,
     'I4_1/acd': 142,
-    'P3': 143,
-    'P3_1': 144,
-    'P3_2': 145,
-    'R3': 146,
+    P3: 143,
+    P3_1: 144,
+    P3_2: 145,
+    R3: 146,
     'P-3': 147,
     'R-3': 148,
     // Trigonal
-    'P312': 149,
-    'P321': 150,
-    'P3_112': 151,
-    'P3_121': 152,
-    'P3_212': 153,
-    'P3_221': 154,
-    'R32': 155,
-    'P3m1': 156,
-    'P31m': 157,
-    'P3c1': 158,
-    'P31c': 159,
-    'R3m': 160,
-    'R3c': 161,
+    P312: 149,
+    P321: 150,
+    P3_112: 151,
+    P3_121: 152,
+    P3_212: 153,
+    P3_221: 154,
+    R32: 155,
+    P3m1: 156,
+    P31m: 157,
+    P3c1: 158,
+    P31c: 159,
+    R3m: 160,
+    R3c: 161,
     'P-31m': 162,
     'P-31c': 163,
     'P-3m1': 164,
@@ -233,25 +233,25 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'R-3m': 166,
     'R-3c': 167,
     // Hexagonal
-    'P6': 168,
-    'P6_1': 169,
-    'P6_5': 170,
-    'P6_2': 171,
-    'P6_4': 172,
-    'P6_3': 173,
+    P6: 168,
+    P6_1: 169,
+    P6_5: 170,
+    P6_2: 171,
+    P6_4: 172,
+    P6_3: 173,
     'P-6': 174,
     'P6/m': 175,
     'P6_3/m': 176,
-    'P622': 177,
-    'P6_122': 178,
-    'P6_522': 179,
-    'P6_222': 180,
-    'P6_422': 181,
-    'P6_322': 182,
-    'P6mm': 183,
-    'P6cc': 184,
-    'P6_3cm': 185,
-    'P6_3mc': 186,
+    P622: 177,
+    P6_122: 178,
+    P6_522: 179,
+    P6_222: 180,
+    P6_422: 181,
+    P6_322: 182,
+    P6mm: 183,
+    P6cc: 184,
+    P6_3cm: 185,
+    P6_3mc: 186,
     'P-6m2': 187,
     'P-6c2': 188,
     'P-62m': 189,
@@ -261,11 +261,11 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'P6_3/mcm': 193,
     'P6_3/mmc': 194,
     // Cubic
-    'P23': 195,
-    'F23': 196,
-    'I23': 197,
-    'P2_13': 198,
-    'I2_13': 199,
+    P23: 195,
+    F23: 196,
+    I23: 197,
+    P2_13: 198,
+    I2_13: 199,
     'Pm-3': 200,
     'Pn-3': 201,
     'Fm-3': 202,
@@ -273,14 +273,14 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'Im-3': 204,
     'Pa-3': 205,
     'Ia-3': 206,
-    'P432': 207,
-    'P4_232': 208,
-    'F432': 209,
-    'F4_132': 210,
-    'I432': 211,
-    'P4_332': 212,
-    'P4_132': 213,
-    'I4_132': 214,
+    P432: 207,
+    P4_232: 208,
+    F432: 209,
+    F4_132: 210,
+    I432: 211,
+    P4_332: 212,
+    P4_132: 213,
+    I4_132: 214,
     'P-43m': 215,
     'F-43m': 216,
     'I-43m': 217,
@@ -298,13 +298,13 @@ export const SPACEGROUP_SYMBOL_TO_NUM = {
     'Im-3m': 229,
     'Ia-3d': 230,
     // Special cases
-    'P121': 3,
-    'P12_11': 4,
-    'C121': 5,
-    'P1m1': 6,
-    'P1c1': 7,
-    'C1m1': 8,
-    'C1c1': 9,
+    P121: 3,
+    P12_11: 4,
+    C121: 5,
+    P1m1: 6,
+    P1c1: 7,
+    C1m1: 8,
+    C1c1: 9,
     'P12/m1': 10,
     'P12_1/m1': 11,
     'C12/m1': 12,