matterviz 0.4.0 → 0.4.1

package/dist/symmetry/WyckoffTable.svelte

@@ -2,17 +2,27 @@
   import { contrast_color } from '../colors'
   import { format_fractional } from '../labels'
   import { colors } from '../state.svelte'
+  import type { MoyoWyckoffPosition } from '@spglib/moyo-wasm'
+  import { SvelteSet } from 'svelte/reactivity'
   import type { HTMLAttributes } from 'svelte/elements'
   import type { WyckoffPos } from '.'
+  import { enrich_wyckoff_rows, wyckoff_letter } from '.'
 
   let {
     wyckoff_positions,
+    // Full Wyckoff-position database of the space group (from
+    // spacegroup_wyckoff_positions). When given, occupied rows gain an ITA coordinates
+    // column and unoccupied positions can be listed via show_unoccupied.
+    db_positions = [],
+    show_unoccupied = false,
     on_hover,
     on_click,
     active_color = `#2563eb`,
     ...rest
   }: HTMLAttributes<HTMLTableElement> & {
     wyckoff_positions: WyckoffPos[]
+    db_positions?: MoyoWyckoffPosition[]
+    show_unoccupied?: boolean
     on_hover?: (site_indices: number[] | null) => void
     on_click?: (site_indices: number[] | null) => void
     active_color?: string
@@ -20,12 +30,33 @@
 
   let selected_key = $state<string | null>(null)
 
+  // Occupied orbits enriched with ITA representative coordinates + site symmetry
+  const rows = $derived(enrich_wyckoff_rows(wyckoff_positions ?? [], db_positions))
+  // Wyckoff positions of the space group not occupied by any atom, smallest
+  // multiplicity first (matches the ascending sort of occupied rows)
+  const unoccupied_rows = $derived.by(() => {
+    if (!show_unoccupied) return []
+    const occupied_letters = new SvelteSet(rows.map((row) => wyckoff_letter(row.wyckoff)))
+    return db_positions
+      .filter((pos) => !occupied_letters.has(pos.letter))
+      .toSorted((pos_1, pos_2) =>
+        pos_1.multiplicity - pos_2.multiplicity ||
+        pos_1.letter.localeCompare(pos_2.letter)
+      )
+  })
+  const has_ita_coords = $derived(
+    rows.some((pos) => pos.coordinates) || unoccupied_rows.length > 0,
+  )
+  const has_site_symmetry = $derived(
+    rows.some((pos) => pos.site_symmetry) || unoccupied_rows.length > 0,
+  )
+
   const get_row_key = (wyckoff_pos: WyckoffPos, row_idx: number) =>
     `${wyckoff_pos.wyckoff}-${wyckoff_pos.elem}-${
       wyckoff_pos.site_indices?.join(`,`) ?? `none`
     }-${row_idx}`
   $effect(() => {
-    if (!selected_key || wyckoff_positions?.some((pos, idx) => get_row_key(pos, idx) === selected_key)) {
+    if (!selected_key || rows.some((pos, idx) => get_row_key(pos, idx) === selected_key)) {
       return
     }
     selected_key = null
@@ -33,7 +64,7 @@
   })
 </script>
 
-{#if wyckoff_positions && wyckoff_positions.length > 0}
+{#if rows.length > 0 || unoccupied_rows.length > 0}
   <table {...rest} class="wyckoff-table {rest.class ?? ``}">
     <thead>
       <tr>
@@ -41,6 +72,18 @@
           [`Wyckoff`, `Wyckoff position: Multiplicity + Letter`],
           [`Element`, `Chemical element symbol`],
           [`Fractional Coords`, `Fractional coordinates within the unit cell`],
+          ...(has_ita_coords
+          ? [[
+            `ITA Coords`,
+            `Representative coordinates from the International Tables: x/y/z mark free parameters, fractions mark symmetry-fixed coordinates`,
+          ]]
+          : []),
+          ...(has_site_symmetry
+          ? [[
+            `Site Symm.`,
+            `Site symmetry: point group of operations leaving the site invariant`,
+          ]]
+          : []),
         ] as
           [col, title]
           (col)
@@ -50,11 +93,7 @@
       </tr>
     </thead>
     <tbody>
-      {#each wyckoff_positions as
-        wyckoff_pos,
-        row_idx
-        (get_row_key(wyckoff_pos, row_idx))
-      }
+      {#each rows as wyckoff_pos, row_idx (get_row_key(wyckoff_pos, row_idx))}
         {@const { wyckoff, elem, abc, site_indices } = wyckoff_pos}
         {@const row_key = get_row_key(wyckoff_pos, row_idx)}
         {@const is_selected = selected_key === row_key}
@@ -89,6 +128,25 @@
             </span>
           </td>
           <td>({abc?.map(format_fractional).join(` , `) ?? `N/A`})</td>
+          {#if has_ita_coords}
+            <td>{wyckoff_pos.coordinates ? `(${wyckoff_pos.coordinates})` : ``}</td>
+          {/if}
+          {#if has_site_symmetry}
+            <td>{wyckoff_pos.site_symmetry ?? ``}</td>
+          {/if}
+        </tr>
+      {/each}
+      {#each unoccupied_rows as db_pos (db_pos.letter)}
+        <tr class="unoccupied" title="Wyckoff position not occupied in this structure">
+          <td>{db_pos.multiplicity}{db_pos.letter}</td>
+          <td>&mdash;</td>
+          <td>&mdash;</td>
+          {#if has_ita_coords}
+            <td>({db_pos.coordinates})</td>
+          {/if}
+          {#if has_site_symmetry}
+            <td>{db_pos.site_symmetry}</td>
+          {/if}
         </tr>
       {/each}
     </tbody>
@@ -117,4 +175,7 @@
   .wyckoff-row.selected:hover {
     background-color: color-mix(in srgb, var(--active-color) 35%, transparent);
   }
+  .unoccupied {
+    opacity: 0.5;
+  }
 </style>

package/dist/symmetry/WyckoffTable.svelte.d.ts

@@ -1,7 +1,10 @@
+import type { MoyoWyckoffPosition } from '@spglib/moyo-wasm';
 import type { HTMLAttributes } from 'svelte/elements';
 import type { WyckoffPos } from '.';
 type $$ComponentProps = HTMLAttributes<HTMLTableElement> & {
     wyckoff_positions: WyckoffPos[];
+    db_positions?: MoyoWyckoffPosition[];
+    show_unoccupied?: boolean;
     on_hover?: (site_indices: number[] | null) => void;
     on_click?: (site_indices: number[] | null) => void;
     active_color?: string;

package/dist/symmetry/cell-transform.js

@@ -1,6 +1,7 @@
 import { ATOMIC_NUMBER_TO_SYMBOL } from '../composition/parse';
 import * as math from '../math';
 import { wrap_to_unit_cell } from '../structure/pbc';
+import { make_site } from '../structure/site';
 const transferable_properties = (properties) => {
     if (properties === undefined)
         return undefined;
@@ -13,17 +14,10 @@ const transferable_properties = (properties) => {
 // the full Crystal with lattice parameters and element symbols.
 export function moyo_cell_to_structure(cell, // The MoyoCell from symmetry analysis (std_cell or prim_std_cell)
 original_structure) {
-    // Convert flat 9-element basis to 3x3 matrix
-    // moyo-wasm uses the same row-major serialization for both input and output
-    // (see to_cell_json comment: column-major(B) == row-major(RB))
-    // So the flat array is row-major: [a1, a2, a3, b1, b2, b3, c1, c2, c3]
-    // where each row is a lattice vector in the pymatgen convention
-    const basis = cell.lattice.basis;
-    const lattice_matrix = [
-        [basis[0], basis[1], basis[2]], // First lattice vector (a)
-        [basis[3], basis[4], basis[5]], // Second lattice vector (b)
-        [basis[6], basis[7], basis[8]], // Third lattice vector (c)
-    ];
+    // Convert flat 9-element basis to 3x3 matrix. moyo-wasm uses the same row-major
+    // serialization for both input and output (see to_cell_json: column-major(B) ==
+    // row-major(RB)), so the flat array is row-major with each row a lattice vector.
+    const lattice_matrix = math.vec9_to_mat3x3([...cell.lattice.basis]);
     // Calculate lattice parameters from matrix
     const lattice_params = math.calc_lattice_params(lattice_matrix);
     const frac_to_cart = math.create_frac_to_cart(lattice_matrix);
@@ -40,8 +34,7 @@ original_structure) {
         // Oxidation state is set to 0 (unknown) because moyo-wasm only provides atomic numbers.
         // transformed cell may have different/reordered sites, making it non-trivial to
         // map oxidation states from original structure.
-        const species = [{ element, occu: 1, oxidation_state: 0 }];
-        return { species, abc: wrapped_abc, xyz, label: element, properties: {} };
+        return make_site(element, wrapped_abc, xyz, element);
     });
     const lattice = {
         matrix: lattice_matrix,
@@ -86,6 +79,6 @@ sym_data) {
     if (cell_type === `primitive`) {
         return get_primitive_cell(structure, sym_data);
     }
-    // Fallback to original (should never reach here with proper typing)
+    // Unknown cell_type at runtime (e.g. from stale persisted settings): leave unchanged
     return structure;
 }

package/dist/symmetry/index.d.ts

@@ -1,8 +1,12 @@
 import type { Vec3 } from '../math';
 import type { AnyStructure, Crystal } from '../structure';
-import type { MoyoDataset } from '@spglib/moyo-wasm';
+import type { MoyoCell, MoyoDataset } from '@spglib/moyo-wasm';
 export * from './cell-transform';
 export * from './spacegroups';
+export * from './symmetry-elements';
+export * from './wyckoff-db';
+export { default as SymmetryElementControls } from './SymmetryElementControls.svelte';
+export { default as SymmetryElements } from './SymmetryElements.svelte';
 export { default as SymmetryStats } from './SymmetryStats.svelte';
 export { default as WyckoffTable } from './WyckoffTable.svelte';
 export declare const BRAVAIS_LATTICES: {
@@ -28,16 +32,22 @@ export type WyckoffPos = {
     elem: string;
     abc: Vec3;
     site_indices?: number[];
+    site_symmetry?: string;
+    coordinates?: string;
 };
 export type SymmetryDataset = MoyoDataset & {
-    orig_indices?: number[];
     orig_site_indices_by_std_idx?: number[][];
+    input_cell?: Pick<MoyoCell, `positions` | `numbers`>;
+    orig_site_indices_by_input_idx?: number[][];
 };
 export declare function ensure_moyo_wasm_ready(wasm_url?: string): Promise<void>;
 export declare function to_cell_json(structure: Crystal): string;
-export declare const map_std_to_orig_site_indices: (std_positions: Vec3[], std_numbers: number[], input_positions: Vec3[], input_numbers: number[], orig_site_indices_by_input_idx: number[][]) => number[][];
+export declare const map_std_to_orig_site_indices: (std_positions: Vec3[], std_numbers: number[], input_positions: Vec3[], input_numbers: number[], orig_site_indices_by_input_idx: number[][], transform?: {
+    std_linear: readonly number[];
+    std_origin_shift: readonly number[];
+}, tol?: number) => number[][];
 export declare function analyze_structure_symmetry(struct_or_mol: AnyStructure, settings: Partial<SymmetrySettings>): Promise<SymmetryDataset>;
 export declare function simplicity_score(vec: number[]): number;
 export declare function wyckoff_positions_from_moyo(sym_data: SymmetryDataset | null): WyckoffPos[];
-export declare function apply_symmetry_operations(position: Vec3, operations: MoyoDataset[`operations`], _tolerance?: number): Vec3[];
+export declare function apply_symmetry_operations(position: Vec3, operations: MoyoDataset[`operations`]): Vec3[];
 export declare function map_wyckoff_to_all_atoms(wyckoff_positions: WyckoffPos[], displayed_structure: Crystal, orig_structure: Crystal, sym_data: MoyoDataset | null, tolerance?: number): WyckoffPos[];