matterviz 0.4.1 → 0.4.3

package/dist/symmetry/SymmetryElements.svelte

@@ -20,6 +20,7 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
 <script lang="ts">
   import type { Matrix3x3, Vec2, Vec3 } from '../math'
   import * as math from '../math'
+  import { quaternion_from_direction } from '../structure/geometry'
   import type { ShowSymmetryKinds, SymmetryElement } from './symmetry-elements'
   import {
     clip_line_to_cell,
@@ -39,7 +40,6 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
     LinearFilter,
     Matrix4,
     OctahedronGeometry,
-    Quaternion,
     RepeatWrapping,
     RGBAFormat,
     Vector3,
@@ -92,7 +92,6 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
     inversion_color?: string
   } = $props()
 
-  const UP = new Vector3(0, 1, 0)
   const UNIT_SCALE = new Vector3(1, 1, 1)
 
   // 1D stripe alpha texture for glide fills (three.js alphaMap samples the GREEN
@@ -136,14 +135,12 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
     dir_unit: Vector3,
     radius: number,
     length: number,
-  ): CylinderGeometry =>
-    new CylinderGeometry(radius, radius, length, 12).applyMatrix4(
-      new Matrix4().compose(
-        center,
-        new Quaternion().setFromUnitVectors(UP, dir_unit),
-        UNIT_SCALE,
-      ),
+  ): CylinderGeometry => {
+    const orientation = quaternion_from_direction(dir_unit.toArray() as Vec3)
+    return new CylinderGeometry(radius, radius, length, 12).applyMatrix4(
+      new Matrix4().compose(center, orientation, UNIT_SCALE),
     )
+  }
 
   // Axes (cylinders) + rotoinversion center markers (spheres), merged per color/radius.
   // Pure rotations render solid; screw axes render DASHED so the two are
@@ -152,9 +149,9 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
   const axis_groups: MaterialGroup[] = $derived.by(() => {
     const axis_elements = elements.filter(
       (elem) =>
-        (elem.kind === `rotation` || elem.kind === `screw` ||
-          elem.kind === `rotoinversion`) &&
-        show_kinds[elem.kind] && elem.axis,
+        (elem.kind === `rotation` || elem.kind === `screw` || elem.kind === `rotoinversion`) &&
+        show_kinds[elem.kind] &&
+        elem.axis,
     )
     // Drop 2-fold axes coincident with a higher-order axis (4 contains 2, 6 contains
     // 2 and 3, -4 contains 2, …) to reduce visual clutter. Computed over the VISIBLE
@@ -168,9 +165,8 @@ color/opacity instead of one mesh per element) and disposed on change/unmount. -
 
     const parts_by_group = new Map<string, BufferGeometry[]>()
     for (const elem of axis_elements) {
-      if (
-        hide_redundant_axes && elem.order < (max_order_by_line.get(line_key(elem)) ?? 0)
-      ) continue
+      if (hide_redundant_axes && elem.order < (max_order_by_line.get(line_key(elem)) ?? 0))
+        continue
       const clipped = clip_line_to_cell(elem.point, elem.axis as Vec3, lattice)
       if (!clipped) continue
       const [start, end] = clipped

package/dist/symmetry/SymmetryStats.svelte

@@ -61,9 +61,8 @@
     const crystal_sys = spg.spacegroup_to_crystal_sys(sym_data.number)
     const lattice_sys = spg.spacegroup_num_to_lattice_system(sym_data.number)
     if (!crystal_sys) return `?`
-    const suffix = lattice_sys && lattice_sys !== crystal_sys
-      ? ` (${lattice_sys} lattice)`
-      : ``
+    const suffix =
+      lattice_sys && lattice_sys !== crystal_sys ? ` (${lattice_sys} lattice)` : ``
     return `${crystal_sys}${suffix}`
   })
 
@@ -89,33 +88,17 @@
   })
 
   const titles = {
-    symprec:
-      `Symmetry precision control in spglib/moyo. Lower values (e.g. 1e-4, the default) are more strict, higher values (e.g. 1e-1) are more tolerant of numerical errors in atomic positions.`,
-    algo:
-      `Symmetry detection algorithm: Moyo uses moyo's newer recommended settings, Spglib is useful if you need compatible results to an existing set of spglib-detected symmetries.`,
-    space_group:
-      `International Tables Space group number (1-230) - unique identifier for each space group. Higher numbers indicate more symmetries in the crystal.`,
-    crystal_system:
-      `Crystal system classification based on the unit cell symmetry. Seven systems: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, and cubic. For trigonal space groups, the lattice system (rhombohedral for R-centered groups, hexagonal otherwise) is shown in parentheses when it differs from the crystal system.`,
-    hermann_mauguin:
-      `Hermann-Mauguin symbol describes symmetry operations. Format: Lattice type + Point group symmetry. Example: P4/mmm = Primitive + 4-fold rotation + mirror planes`,
-    hall_number:
-      `Hall number: alternative numbering system for space groups. Useful for crystallographic software compatibility.`,
-    pearson_symbol:
-      `Pearson symbol. Format: Crystal system + Number of atoms per unit cell. Example: tP2 = tetragonal primitive with 2 atoms`,
-    symmetry_operations:
-      `Total symmetry operations that map the crystal structure onto itself. Includes rotations, translations, and combinations.`,
-    distinct_orbits:
-      `Number of unique Wyckoff positions (symmetry-equivalent atomic sites) in the crystal structure.`,
-    wyckoff_sequence:
-      `Wyckoff sequence: letters of all occupied Wyckoff positions in descending alphabetical order, with superscript counts for letters occupied by multiple orbits. A standard structure-type fingerprint (complements the Pearson symbol).`,
-    free_params:
-      `Internal degrees of freedom: number of free fractional-coordinate parameters (x, y, z in the ITA representative coordinates) summed over occupied Wyckoff orbits. 0 means all atomic positions are fully fixed by symmetry.`,
-    settings:
-      `All settings of this space group in the International Tables (origin choices, unique axes, cell choices, hexagonal vs rhombohedral axes). The setting detected for this structure is highlighted.`,
-    translations: `Number of translations in the crystal structure.`,
-    rotations: `Number of rotations in the crystal structure.`,
-    roto_translations: `Number of roto-translations in the crystal structure.`,
+    symprec: `Symmetry precision control in spglib/moyo. Lower values (e.g. 1e-4, the default) are more strict, higher values (e.g. 1e-1) are more tolerant of numerical errors in atomic positions.`,
+    algo: `Symmetry detection algorithm: Moyo uses moyo's newer recommended settings, Spglib is useful if you need compatible results to an existing set of spglib-detected symmetries.`,
+    space_group: `International Tables Space group number (1-230) - unique identifier for each space group. Higher numbers indicate more symmetries in the crystal.`,
+    crystal_system: `Crystal system classification based on the unit cell symmetry. Seven systems: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, and cubic. For trigonal space groups, the lattice system (rhombohedral for R-centered groups, hexagonal otherwise) is shown in parentheses when it differs from the crystal system.`,
+    hermann_mauguin: `Hermann-Mauguin symbol describes symmetry operations. Format: Lattice type + Point group symmetry. Example: P4/mmm = Primitive + 4-fold rotation + mirror planes`,
+    hall_number: `Hall number: alternative numbering system for space groups. Useful for crystallographic software compatibility.`,
+    pearson_symbol: `Pearson symbol. Format: Crystal system + Number of atoms per unit cell. Example: tP2 = tetragonal primitive with 2 atoms`,
+    distinct_orbits: `Number of unique Wyckoff positions (symmetry-equivalent atomic sites) in the crystal structure.`,
+    wyckoff_sequence: `Wyckoff sequence: letters of all occupied Wyckoff positions in descending alphabetical order, with superscript counts for letters occupied by multiple orbits. A standard structure-type fingerprint (complements the Pearson symbol).`,
+    free_params: `Internal degrees of freedom: number of free fractional-coordinate parameters (x, y, z in the ITA representative coordinates) summed over occupied Wyckoff orbits. 0 means all atomic positions are fully fixed by symmetry.`,
+    settings: `All settings of this space group in the International Tables (origin choices, unique axes, cell choices, hexagonal vs rhombohedral axes). The setting detected for this structure is highlighted.`,
   }
   const tooltips: Record<string, string> = $derived(show_tooltips ? titles : {})
 
@@ -128,7 +111,7 @@
   const symprec_step = $derived(get_step_from_order_of_magnitude(settings.symprec))
 </script>
 
-<div {...rest} class="symmetry-stats {rest.class ?? ``}">
+<div {...rest} class={[`symmetry-stats`, rest.class]}>
   {#if sym_data}
     {@render header?.({ sym_data, settings })}
   {/if}
@@ -168,10 +151,10 @@
       <select
         value={settings.algo}
         onchange={(evt) =>
-        settings = {
-          ...settings,
-          algo: evt.currentTarget.value as `Moyo` | `Spglib`,
-        }}
+          (settings = {
+            ...settings,
+            algo: evt.currentTarget.value as `Moyo` | `Spglib`,
+          })}
       >
         {#each Object.keys(SETTINGS_CONFIG.symmetry.algo.enum ?? {}) as value (value)}
           <option {value}>{value}</option>
@@ -182,48 +165,50 @@
 
   {@render children?.({ sym_data, settings })}
   {#if sym_data}
+    {@const stat_tiles = [
+      {
+        label: `Space Group`,
+        title: `${tooltips?.space_group} at ${settings.symprec} (using ${settings.algo} algo). ${tooltips?.hermann_mauguin}`,
+        value: `${sym_data.number} (${display_hm_symbol})`,
+      },
+      {
+        label: `Crystal System`,
+        title: tooltips?.crystal_system,
+        value: crystal_system_label,
+      },
+      {
+        label: `Hall Number`,
+        title: tooltips?.hall_number,
+        value: `${sym_data.hall_number}${
+          current_setting ? ` (${current_setting.hall_symbol})` : ``
+        }`,
+      },
+      { label: `Pearson`, title: tooltips?.pearson_symbol, value: sym_data.pearson_symbol },
+      { label: `Wyckoff Positions`, title: tooltips?.distinct_orbits, value: wyckoff_count },
+      wyckoff_seq && {
+        label: `Wyckoff Sequence`,
+        title: tooltips?.wyckoff_sequence,
+        value: wyckoff_seq,
+      },
+      free_params !== null && {
+        label: `Free Parameters`,
+        title: tooltips?.free_params,
+        value: free_params,
+      },
+    ].filter((tile) => typeof tile === `object`)}
     <div class="stats-grid">
-      <div
-        title="{tooltips?.space_group} at {settings.symprec} (using {settings.algo} algo). {tooltips?.hermann_mauguin}"
-        {@attach tooltip()}
-      >
-        Space Group <strong>{sym_data.number} ({display_hm_symbol})</strong>
-      </div>
-      <div title={tooltips?.crystal_system} {@attach tooltip()}>
-        Crystal System <strong>{crystal_system_label}</strong>
-      </div>
-      <div title={tooltips?.hall_number} {@attach tooltip()}>
-        Hall Number <strong>
-          {sym_data.hall_number}{
-            current_setting ? ` (${current_setting.hall_symbol})` : ``
-          }
-        </strong>
-      </div>
-      <div title={tooltips?.pearson_symbol} {@attach tooltip()}>
-        Pearson <strong>{sym_data.pearson_symbol}</strong>
-      </div>
-      <div title={tooltips?.distinct_orbits} {@attach tooltip()}>
-        Wyckoff Positions <strong>{wyckoff_count}</strong>
-      </div>
-      {#if wyckoff_seq}
-        <div title={tooltips?.wyckoff_sequence} {@attach tooltip()}>
-          Wyckoff Sequence <strong>{wyckoff_seq}</strong>
-        </div>
-      {/if}
-      {#if free_params !== null}
-        <div title={tooltips?.free_params} {@attach tooltip()}>
-          Free Parameters <strong>{free_params}</strong>
+      {#each stat_tiles as tile (tile.label)}
+        <div title={tile.title} {@attach tooltip()}>
+          {tile.label} <strong>{tile.value}</strong>
         </div>
-      {/if}
+      {/each}
       <div
         class="sym-ops-summary"
         title="{sym_ops_counts.translations} translations + {sym_ops_counts.rotations} rotations + {sym_ops_counts.roto_translations} roto-translations"
         {@attach tooltip()}
       >
         Total sym ops: <strong>{sym_data.operations.length}</strong>
-        ({sym_ops_counts.translations}T + {sym_ops_counts.rotations}R + {
-          sym_ops_counts.roto_translations
-        }RT)
+        ({sym_ops_counts.translations}T + {sym_ops_counts.rotations}R + {sym_ops_counts.roto_translations}RT)
       </div>
     </div>
     {#if settings_entries.length > 1}
@@ -287,8 +272,7 @@
   }
   .stats-grid {
     display: var(--sym-stats-display, grid);
-    grid-template-columns:
-      var(--sym-stats-grid-columns, repeat(auto-fit, minmax(275px, 1fr)));
+    grid-template-columns: var(--sym-stats-grid-columns, repeat(auto-fit, minmax(275px, 1fr)));
     gap: var(--sym-stats-grid-gap, 1ex 1em);
     margin-block: var(--sym-stats-grid-margin-block, 1ex);
     align-items: var(--sym-stats-grid-align, start);

package/dist/symmetry/WyckoffTable.svelte

@@ -39,9 +39,9 @@
     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)
+      .toSorted(
+        (pos_1, pos_2) =>
+          pos_1.multiplicity - pos_2.multiplicity || pos_1.letter.localeCompare(pos_2.letter),
       )
   })
   const has_ita_coords = $derived(
@@ -65,29 +65,10 @@
 </script>
 
 {#if rows.length > 0 || unoccupied_rows.length > 0}
-  <table {...rest} class="wyckoff-table {rest.class ?? ``}">
+  <table {...rest} class={[`wyckoff-table`, rest.class]}>
     <thead>
       <tr>
-        {#each [
-          [`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)
-        }
+        {#each [[`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)}
           <th {title}>{col}</th>
         {/each}
       </tr>
@@ -121,13 +102,13 @@
           <td>
             <span
               style:background-color={colors.element[elem]}
-              style="display: inline-block; padding: 0 6pt; border-radius: 3pt; line-height: 1.4"
+              style="display: inline-block; padding: 0 4pt; border-radius: 3pt; line-height: 1.25"
               {@attach contrast_color()}
             >
               {elem}
             </span>
           </td>
-          <td>({abc?.map(format_fractional).join(` , `) ?? `N/A`})</td>
+          <td>({abc?.map(format_fractional).join(`, `) ?? `N/A`})</td>
           {#if has_ita_coords}
             <td>{wyckoff_pos.coordinates ? `(${wyckoff_pos.coordinates})` : ``}</td>
           {/if}
@@ -155,10 +136,11 @@
 
 <style>
   .wyckoff-table {
-    margin-top: 1em;
+    margin-top: 0.5em;
+    border-collapse: collapse;
   }
   .wyckoff-table :is(th, td) {
-    padding: 2px 6px;
+    padding: 1px 3px;
     text-align: center;
     vertical-align: middle;
   }

package/dist/symmetry/cell-transform.js

@@ -1,3 +1,4 @@
+// Cell transformation utilities for converting between original, conventional, and primitive cells
 import { ATOMIC_NUMBER_TO_SYMBOL } from '../composition/parse';
 import * as math from '../math';
 import { wrap_to_unit_cell } from '../structure/pbc';
@@ -18,10 +19,8 @@ original_structure) {
     // 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);
-    // Build sites from positions and atomic numbers
     const sites = cell.positions.map((abc, idx) => {
         const atomic_number = cell.numbers[idx];
         const element = ATOMIC_NUMBER_TO_SYMBOL[atomic_number];
@@ -30,11 +29,10 @@ original_structure) {
         }
         // Wrap fractional coordinates to [0, 1) range (moyo-wasm may return outside)
         const wrapped_abc = wrap_to_unit_cell(abc);
-        const xyz = frac_to_cart(wrapped_abc);
         // 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.
-        return make_site(element, wrapped_abc, xyz, element);
+        return make_site(element, wrapped_abc, frac_to_cart(wrapped_abc), element);
     });
     const lattice = {
         matrix: lattice_matrix,
@@ -54,14 +52,12 @@ original_structure) {
 // The conventional cell is the standard crystallographic setting for the space group.
 export function get_conventional_cell(original_structure, // The original input structure
 sym_data) {
-    // The conventional cell as a Crystal
     return moyo_cell_to_structure(sym_data.std_cell, original_structure);
 }
 // Get the primitive cell from symmetry analysis data.
 // The primitive cell is the smallest unit cell with one lattice point.
 export function get_primitive_cell(original_structure, // The original input structure
 sym_data) {
-    // The primitive cell as a Crystal
     return moyo_cell_to_structure(sym_data.prim_std_cell, original_structure);
 }
 // Transform a structure based on the selected cell type.
@@ -69,16 +65,12 @@ sym_data) {
 export function transform_cell(structure, // The original structure
 cell_type, // The desired cell type ('original', 'conventional', or 'primitive')
 sym_data) {
-    //transformed structure (or original if no transformation needed)
-    if (cell_type === `original` || !sym_data) {
+    if (!sym_data)
         return structure;
-    }
-    if (cell_type === `conventional`) {
+    if (cell_type === `conventional`)
         return get_conventional_cell(structure, sym_data);
-    }
-    if (cell_type === `primitive`) {
+    if (cell_type === `primitive`)
         return get_primitive_cell(structure, sym_data);
-    }
-    // Unknown cell_type at runtime (e.g. from stale persisted settings): leave unchanged
+    // 'original' or unknown runtime cell_type (e.g. stale persisted settings): unchanged
     return structure;
 }

package/dist/symmetry/index.d.ts

@@ -48,6 +48,7 @@ export declare const map_std_to_orig_site_indices: (std_positions: Vec3[], std_n
 }, 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 const wyckoff_multiplicity: (label: string) => number;
 export declare function wyckoff_positions_from_moyo(sym_data: SymmetryDataset | null): WyckoffPos[];
 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[];

package/dist/symmetry/index.js

@@ -89,10 +89,9 @@ function get_site_atomic_number(site, site_idx) {
             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];
+    const atomic_number = selected_element
+        ? SYMBOL_TO_ATOMIC_NUMBER[selected_element]
+        : undefined;
     if (atomic_number === undefined) {
         throw new Error(`Unknown element at site ${site_idx}: ${selected_element}`);
     }
@@ -233,17 +232,20 @@ function wyckoff_rows_from_input_orbits(sym_data) {
         };
     });
 }
-// Generate Wyckoff table rows from symmetry data by grouping moyo's input-cell sites into
-// crystallographic orbits. moyo's per-site arrays (wyckoffs, orbits, site_symmetry_symbols)
-// always index the input cell and analyze_structure_symmetry always attaches input_cell, so
-// the orbit grouping is the single source of truth for any input cell setting.
+// Numeric multiplicity prefix of a Wyckoff label like `4a` (NaN when absent)
+export const wyckoff_multiplicity = (label) => Number(/^\d+/.exec(label)?.[0] ?? NaN);
+// Generate Wyckoff table rows from symmetry data via wyckoff_rows_from_input_orbits
+// (analyze_structure_symmetry always attaches the input_cell that grouping needs).
 // Rows sort by ascending multiplicity, then Wyckoff label.
 export function wyckoff_positions_from_moyo(sym_data) {
     if (!sym_data)
         return [];
     const orbit_rows = wyckoff_rows_from_input_orbits(sym_data);
     return (orbit_rows ?? []).sort((w1, w2) => {
-        const [w1_mult, w2_mult] = [parseInt(w1.wyckoff, 10), parseInt(w2.wyckoff, 10)];
+        const [w1_mult, w2_mult] = [
+            wyckoff_multiplicity(w1.wyckoff),
+            wyckoff_multiplicity(w2.wyckoff),
+        ];
         if (w1_mult !== w2_mult)
             return w1_mult - w2_mult;
         return w1.wyckoff.localeCompare(w2.wyckoff);
@@ -312,7 +314,8 @@ class WrappedPositionIndex {
     n_cells;
     constructor(positions, tolerance) {
         this.tolerance = tolerance;
-        this.n_cells = Math.min(64, Math.max(1, Math.floor(1 / Math.max(tolerance, 1e-9))));
+        const inv_tolerance = Math.floor(1 / Math.max(tolerance, 1e-9));
+        this.n_cells = Math.min(64, Math.max(1, inv_tolerance));
         this.coords = positions;
         positions.forEach((pos, idx) => {
             const key = this.cell_key(pos, 0, 0, 0);

package/dist/symmetry/spacegroups.js

@@ -66,8 +66,9 @@ export function normalize_spacegroup(spacegroup) {
     const from_symbol = SPACEGROUP_SYMBOL_TO_NUM[spacegroup];
     if (from_symbol !== undefined)
         return from_symbol;
-    const parsed = parseInt(spacegroup, 10);
-    return isNaN(parsed) ? null : normalize_spacegroup(parsed);
+    // Accept trailing setting qualifiers like `146:R` by parsing the leading integer
+    const int_match = /^\s*(?<num>\d+)/.exec(spacegroup);
+    return int_match ? normalize_spacegroup(Number(int_match[1])) : null;
 }
 export const SPACEGROUP_SYMBOL_TO_NUM = {
     // Triclinic