matterviz 0.1.12 → 0.1.13

package/dist/composition/BubbleChart.svelte.d.ts

@@ -8,7 +8,7 @@ type BubbleSegmentData = ChartSegmentData & {
     x: number;
     y: number;
 };
-interface Props extends SVGAttributes<SVGSVGElement> {
+type $$ComponentProps = SVGAttributes<SVGSVGElement> & {
     composition: CompositionType;
     size?: number;
     padding?: number;
@@ -18,7 +18,7 @@ interface Props extends SVGAttributes<SVGSVGElement> {
     bubble_content?: Snippet<[BubbleSegmentData]>;
     interactive?: boolean;
     svg_node?: SVGSVGElement | null;
-}
-declare const BubbleChart: import("svelte").Component<Props, {}, "svg_node">;
+};
+declare const BubbleChart: import("svelte").Component<$$ComponentProps, {}, "svg_node">;
 type BubbleChart = ReturnType<typeof BubbleChart>;
 export default BubbleChart;

package/dist/composition/Composition.svelte.d.ts

@@ -1,12 +1,12 @@
 import type { ColorSchemeName, CompositionType } from '..';
 import type { SVGAttributes } from 'svelte/elements';
 type CompositionChartMode = `pie` | `bubble` | `bar`;
-interface Props extends SVGAttributes<SVGSVGElement> {
+type $$ComponentProps = SVGAttributes<SVGSVGElement> & {
     composition: string | CompositionType;
     mode?: CompositionChartMode;
     on_composition_change?: (composition: CompositionType) => void;
     color_scheme?: ColorSchemeName;
-}
-declare const Composition: import("svelte").Component<Props, {}, "">;
+};
+declare const Composition: import("svelte").Component<$$ComponentProps, {}, "">;
 type Composition = ReturnType<typeof Composition>;
 export default Composition;

package/dist/composition/PieChart.svelte

@@ -81,7 +81,7 @@ let segments = $derived.by(() => {
         const color = element_colors[element] || `#cccccc`;
         return {
             element,
-            amount: amount,
+            amount,
             fraction,
             color,
             start_angle,

package/dist/composition/PieChart.svelte.d.ts

@@ -11,7 +11,7 @@ type PieSegmentData = ChartSegmentData & {
     label_y: number;
     is_outside_slice: boolean;
 };
-interface Props extends SVGAttributes<SVGSVGElement> {
+type $$ComponentProps = SVGAttributes<SVGSVGElement> & {
     composition: CompositionType;
     size?: number;
     stroke_width?: number;
@@ -27,7 +27,7 @@ interface Props extends SVGAttributes<SVGSVGElement> {
     segment_content?: Snippet<[PieSegmentData]>;
     interactive?: boolean;
     svg_node?: SVGSVGElement | null;
-}
-declare const PieChart: import("svelte").Component<Props, {}, "svg_node">;
+};
+declare const PieChart: import("svelte").Component<$$ComponentProps, {}, "svg_node">;
 type PieChart = ReturnType<typeof PieChart>;
 export default PieChart;

package/dist/composition/parse.d.ts

@@ -1,8 +1,8 @@
 import type { AnyStructure, CompositionType, ElementSymbol } from '..';
 export declare const atomic_number_to_symbol: Record<number, ElementSymbol>;
 export declare const symbol_to_atomic_number: Partial<Record<ElementSymbol, number>>;
-export declare const atomic_weights: Map<"K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "S" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
-export declare const element_electronegativity_map: Map<"K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "S" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
+export declare const atomic_weights: Map<"S" | "K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
+export declare const element_electronegativity_map: Map<"S" | "K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og", number>;
 export declare const elem_name_to_symbol: Record<string, ElementSymbol>;
 export declare const elem_symbol_to_name: Record<ElementSymbol, string>;
 export declare const atomic_num_to_symbols: (atomic_composition: Record<number, number>) => CompositionType;
@@ -14,5 +14,5 @@ export declare const get_total_atoms: (composition: CompositionType) => number;
 export declare const parse_composition: (input: string | CompositionType | Record<number, number> | Record<string | number, number>) => CompositionType;
 export declare const format_composition_formula: (composition: CompositionType, sort_fn: (symbols: ElementSymbol[]) => ElementSymbol[], plain_text?: boolean, delim?: string, amount_format?: string) => string;
 export declare const get_alphabetical_formula: (input: string | CompositionType | AnyStructure, plain_text?: boolean, delim?: string, amount_format?: string) => string;
-export declare const sort_by_electronegativity: (symbols: ElementSymbol[]) => ("K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "S" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og")[];
+export declare const sort_by_electronegativity: (symbols: ElementSymbol[]) => ("S" | "K" | "H" | "He" | "Li" | "Be" | "B" | "C" | "N" | "O" | "F" | "Ne" | "Na" | "Mg" | "Al" | "Si" | "P" | "Cl" | "Ar" | "Ca" | "Sc" | "Ti" | "V" | "Cr" | "Mn" | "Fe" | "Co" | "Ni" | "Cu" | "Zn" | "Ga" | "Ge" | "As" | "Se" | "Br" | "Kr" | "Rb" | "Sr" | "Y" | "Zr" | "Nb" | "Mo" | "Tc" | "Ru" | "Rh" | "Pd" | "Ag" | "Cd" | "In" | "Sn" | "Sb" | "Te" | "I" | "Xe" | "Cs" | "Ba" | "La" | "Ce" | "Pr" | "Nd" | "Pm" | "Sm" | "Eu" | "Gd" | "Tb" | "Dy" | "Ho" | "Er" | "Tm" | "Yb" | "Lu" | "Hf" | "Ta" | "W" | "Re" | "Os" | "Ir" | "Pt" | "Au" | "Hg" | "Tl" | "Pb" | "Bi" | "Po" | "At" | "Rn" | "Fr" | "Ra" | "Ac" | "Th" | "Pa" | "U" | "Np" | "Pu" | "Am" | "Cm" | "Bk" | "Cf" | "Es" | "Fm" | "Md" | "No" | "Lr" | "Rf" | "Db" | "Sg" | "Bh" | "Hs" | "Mt" | "Ds" | "Rg" | "Cn" | "Nh" | "Fl" | "Mc" | "Lv" | "Ts" | "Og")[];
 export declare const get_electro_neg_formula: (input: string | CompositionType | AnyStructure, plain_text?: boolean, delim?: string, amount_format?: string) => string;

package/dist/coordination/CoordinationBarPlot.svelte

@@ -0,0 +1,241 @@
+<script lang="ts">import { plot_colors } from '../colors';
+import { decompress_file, handle_url_drop } from '../io';
+import { format_value } from '../labels';
+import { BarPlot } from '../plot';
+import { parse_any_structure } from '../structure/parse';
+import { SvelteMap, SvelteSet } from 'svelte/reactivity';
+import { calc_coordination_numbers, } from './calc-coordination';
+let { structures, strategy = `electroneg_ratio`, split_mode = `by_element`, mode = $bindable(`grouped`), orientation = `vertical`, x_axis = $bindable({ label: `Coordination Number`, format: `d` }), y_axis = $bindable({ label: `Count`, format: `d` }), allow_file_drop = true, on_file_drop, loading = $bindable(false), error_msg = $bindable(undefined), ...rest } = $props();
+let dragover = $state(false);
+let dropped_entries = $state([]);
+// Normalize input to consistent array of { label, structure, color }
+const structure_entries = $derived.by(() => {
+    if (!structures)
+        return [];
+    const base_entries = Array.isArray(structures)
+        ? structures
+        : (`sites` in structures
+            ? [{ label: `Structure`, structure: structures }]
+            : Object.entries(structures).map(([label, value]) => `structure` in value
+                ? { label, ...value }
+                : { label, structure: value }));
+    // Merge user-provided structures with dropped structures
+    return [...base_entries, ...dropped_entries];
+});
+// Compute coordination data for each structure
+const entries_with_data = $derived(structure_entries.map((entry) => ({
+    ...entry,
+    data: calc_coordination_numbers(entry.structure, strategy),
+})));
+// Compute appropriate ranges
+const ranges = $derived.by(() => {
+    // CN axis should always start at 0 and show at least [0,4]
+    let max_cn = 4; // minimum max value
+    for (const entry of entries_with_data) {
+        for (const [cn] of entry.data.cn_histogram)
+            max_cn = Math.max(max_cn, cn);
+    }
+    const cn_range = [-0.5, max_cn + 0.5];
+    return { count: [0, null], cn: cn_range }; // Count axis should always start at 0
+});
+// Derive integer CN ticks for axis labels
+const cn_ticks = $derived.by(() => {
+    const all_cns = new SvelteSet();
+    // Always include minimum CN values 0-4
+    for (let idx = 0; idx <= 4; idx++)
+        all_cns.add(idx);
+    // Add actual CN values from data
+    for (const entry of entries_with_data) {
+        for (const [cn] of entry.data.cn_histogram)
+            all_cns.add(cn);
+    }
+    return Array.from(all_cns).sort((cn1, cn2) => cn1 - cn2);
+});
+// Build BarPlot series based on split_mode
+const bar_series = $derived.by(() => {
+    if (split_mode === `by_element`) {
+        // One series per element across all structures
+        const element_series_map = new SvelteMap();
+        // Collect all unique CNs across all elements
+        const all_cns = new SvelteSet();
+        for (const entry of entries_with_data) {
+            for (const [element, cn_histogram] of entry.data.cn_histogram_by_element) {
+                if (!element_series_map.has(element)) {
+                    element_series_map.set(element, new SvelteMap());
+                }
+                const element_map = element_series_map.get(element);
+                for (const [cn, count] of cn_histogram) {
+                    all_cns.add(cn);
+                    element_map.set(cn, (element_map.get(cn) ?? 0) + count);
+                }
+            }
+        }
+        // Sort CNs for consistent x-axis
+        const sorted_cns = Array.from(all_cns).sort((a, b) => a - b);
+        // Convert map to array and ensure all series have same x-values
+        return Array.from(element_series_map.entries())
+            .sort((a, b) => a[0].localeCompare(b[0]))
+            .map(([element, cn_map], idx) => {
+            return {
+                x: sorted_cns,
+                y: sorted_cns.map((cn) => cn_map.get(cn) ?? 0),
+                label: element,
+                color: plot_colors[idx % plot_colors.length],
+                bar_width: 0.8,
+                visible: true,
+                metadata: { element },
+            };
+        });
+    }
+    else if (split_mode === `by_structure`) {
+        // One series per structure
+        // First collect all unique CNs
+        const all_cns = new SvelteSet();
+        for (const entry of entries_with_data) {
+            for (const [cn] of entry.data.cn_histogram) {
+                all_cns.add(cn);
+            }
+        }
+        const sorted_cns = Array.from(all_cns).sort((a, b) => a - b);
+        return entries_with_data.map((entry, idx) => {
+            return {
+                x: sorted_cns,
+                y: sorted_cns.map((cn) => entry.data.cn_histogram.get(cn) ?? 0),
+                label: entry.label,
+                color: entry.color ?? plot_colors[idx % plot_colors.length],
+                bar_width: 0.8,
+                visible: true,
+                metadata: { structure_label: entry.label },
+            };
+        });
+    }
+    else {
+        // split_mode === 'none': combine all into single series
+        const combined_histogram = new SvelteMap();
+        for (const entry of entries_with_data) {
+            for (const [cn, count] of entry.data.cn_histogram) {
+                combined_histogram.set(cn, (combined_histogram.get(cn) ?? 0) + count);
+            }
+        }
+        const x_vals = Array.from(combined_histogram.keys()).sort((a, b) => a - b);
+        const y_vals = x_vals.map((cn) => combined_histogram.get(cn));
+        return [
+            {
+                x: x_vals,
+                y: y_vals,
+                label: `All Sites`,
+                color: plot_colors[0],
+                bar_width: 0.8,
+                visible: true,
+                metadata: {},
+            },
+        ];
+    }
+});
+async function handle_file_drop(event) {
+    event.preventDefault();
+    dragover = false;
+    if (!allow_file_drop)
+        return;
+    loading = true;
+    error_msg = undefined;
+    const compute_and_add = (content, filename) => {
+        try {
+            const text_content = content instanceof ArrayBuffer
+                ? new TextDecoder().decode(content)
+                : content;
+            const parsed_structure = parse_any_structure(text_content, filename);
+            if (parsed_structure && `lattice` in parsed_structure) {
+                const label = filename || `Dropped structure`;
+                // Prepend latest dropped structure for visibility
+                dropped_entries = [
+                    { label, structure: parsed_structure },
+                    ...dropped_entries,
+                ];
+            }
+            else if (parsed_structure && !(`lattice` in parsed_structure)) {
+                error_msg = `Structure has no lattice; cannot compute coordination`;
+            }
+            else {
+                error_msg = `Failed to parse structure from ${filename}`;
+            }
+        }
+        catch (exc) {
+            error_msg = `Failed to process structure: ${exc instanceof Error ? exc.message : String(exc)}`;
+        }
+    };
+    try {
+        // Handle URL-based drops
+        const handled = await handle_url_drop(event, on_file_drop || compute_and_add)
+            .catch(() => false);
+        if (handled)
+            return;
+        // Handle file system drops
+        const file = event.dataTransfer?.files?.[0];
+        if (file) {
+            try {
+                const { content, filename } = await decompress_file(file);
+                if (content)
+                    (on_file_drop || compute_and_add)(content, filename);
+            }
+            catch (exc) {
+                error_msg = `Failed to load file ${file.name}: ${exc instanceof Error ? exc.message : String(exc)}`;
+            }
+        }
+    }
+    finally {
+        loading = false;
+    }
+}
+</script>
+
+{#snippet tooltip(info: BarTooltipProps)}
+  {@const cn = info.x}
+  {@const count = info.y}
+  {@const element = info.metadata?.element as string | undefined}
+  {@const structure_label = info.metadata?.structure_label as string | undefined}
+  {#if element}
+    {element} —
+  {/if}
+  {#if structure_label}
+    {structure_label} —
+  {/if}
+  CN: {format_value(cn, `.0f`)}
+  <br />
+  Sites: {format_value(count, `.0f`)}
+{/snippet}
+
+<BarPlot
+  {...rest}
+  series={bar_series}
+  bind:orientation
+  bind:mode
+  x_axis={{
+    label_shift: { y: 20 },
+    range: orientation === `horizontal` ? ranges.count : ranges.cn,
+    ticks: orientation === `horizontal` ? undefined : cn_ticks,
+    ...(orientation === `horizontal` ? y_axis : x_axis),
+  }}
+  y_axis={{
+    label_shift: { x: 2 },
+    range: orientation === `horizontal` ? ranges.cn : ranges.count,
+    ticks: orientation === `horizontal` ? cn_ticks : undefined,
+    ...orientation === `horizontal` ? x_axis : y_axis,
+  }}
+  display={{
+    x_zero_line: orientation === `horizontal`,
+    y_zero_line: orientation === `vertical`,
+  }}
+  {tooltip}
+  ondrop={handle_file_drop}
+  ondragover={(event) => {
+    event.preventDefault()
+    if (!allow_file_drop) return
+    dragover = true
+  }}
+  ondragleave={(event) => {
+    event.preventDefault()
+    dragover = false
+  }}
+  class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
+/>

package/dist/coordination/CoordinationBarPlot.svelte.d.ts

@@ -0,0 +1,29 @@
+import type { AnyStructure, AxisConfig } from '..';
+import { BarPlot } from '../plot';
+import type { BondingStrategy } from '../structure/bonding';
+import type { ComponentProps } from 'svelte';
+import { type CoordinationData } from './calc-coordination';
+import type { SplitMode } from './index';
+interface StructureEntry {
+    label: string;
+    structure: AnyStructure;
+    color?: string;
+    data?: CoordinationData;
+}
+type $$ComponentProps = ComponentProps<typeof BarPlot> & {
+    structures: AnyStructure | Record<string, AnyStructure | {
+        structure: AnyStructure;
+        color?: string;
+    }> | StructureEntry[];
+    strategy?: BondingStrategy;
+    split_mode?: SplitMode;
+    x_axis?: AxisConfig;
+    y_axis?: AxisConfig;
+    allow_file_drop?: boolean;
+    on_file_drop?: (content: string | ArrayBuffer, filename: string) => void;
+    loading?: boolean;
+    error_msg?: string;
+};
+declare const CoordinationBarPlot: import("svelte").Component<$$ComponentProps, {}, "loading" | "mode" | "y_axis" | "x_axis" | "error_msg">;
+type CoordinationBarPlot = ReturnType<typeof CoordinationBarPlot>;
+export default CoordinationBarPlot;

package/dist/coordination/calc-coordination.d.ts

@@ -0,0 +1,15 @@
+import type { AnyStructure } from '..';
+import type { BondingStrategy } from '../structure/bonding';
+export interface CoordinationSite {
+    site_idx: number;
+    element: string;
+    coordination_number: number;
+    neighbor_elements: string[];
+}
+export interface CoordinationData {
+    sites: CoordinationSite[];
+    cn_by_element: Map<string, number[]>;
+    cn_histogram: Map<number, number>;
+    cn_histogram_by_element: Map<string, Map<number, number>>;
+}
+export declare function calc_coordination_numbers(structure: AnyStructure, strategy?: BondingStrategy): CoordinationData;

package/dist/coordination/calc-coordination.js

@@ -0,0 +1,66 @@
+import { BONDING_STRATEGIES } from '../structure/bonding';
+// Calculate coordination numbers for all sites in a structure using the specified bonding strategy
+export function calc_coordination_numbers(structure, strategy = `electroneg_ratio`) {
+    // Get bonds using the specified strategy
+    const bonds = BONDING_STRATEGIES[strategy](structure);
+    // Count neighbors for each site
+    const neighbor_counts = new Map();
+    const sites = structure.sites;
+    for (const bond of bonds) {
+        const { site_idx_1, site_idx_2 } = bond;
+        if (!neighbor_counts.has(site_idx_1)) {
+            neighbor_counts.set(site_idx_1, new Set());
+        }
+        if (!neighbor_counts.has(site_idx_2)) {
+            neighbor_counts.set(site_idx_2, new Set());
+        }
+        const neighbors_1 = neighbor_counts.get(site_idx_1);
+        const neighbors_2 = neighbor_counts.get(site_idx_2);
+        if (neighbors_1)
+            neighbors_1.add(site_idx_2);
+        if (neighbors_2)
+            neighbors_2.add(site_idx_1);
+    }
+    // Build coordination site data
+    const coordination_sites = [];
+    const cn_by_element = new Map();
+    const cn_histogram = new Map();
+    const cn_histogram_by_element = new Map();
+    for (let site_idx = 0; site_idx < sites.length; site_idx++) {
+        const site = sites[site_idx];
+        const element = site.species[0]?.element ?? `Unknown`;
+        const neighbors_set = neighbor_counts.get(site_idx) ?? new Set();
+        const coordination_number = neighbors_set.size;
+        // Get neighbor elements
+        const neighbor_elements = Array.from(neighbors_set).map((neighbor_idx) => sites[neighbor_idx].species[0]?.element ?? `Unknown`);
+        coordination_sites.push({
+            site_idx,
+            element,
+            coordination_number,
+            neighbor_elements,
+        });
+        // Update cn_by_element
+        if (!cn_by_element.has(element)) {
+            cn_by_element.set(element, []);
+        }
+        const element_array = cn_by_element.get(element);
+        if (element_array)
+            element_array.push(coordination_number);
+        // Update overall cn_histogram
+        cn_histogram.set(coordination_number, (cn_histogram.get(coordination_number) ?? 0) + 1);
+        // Update cn_histogram_by_element
+        if (!cn_histogram_by_element.has(element)) {
+            cn_histogram_by_element.set(element, new Map());
+        }
+        const element_histogram = cn_histogram_by_element.get(element);
+        if (element_histogram) {
+            element_histogram.set(coordination_number, (element_histogram.get(coordination_number) ?? 0) + 1);
+        }
+    }
+    return {
+        sites: coordination_sites,
+        cn_by_element,
+        cn_histogram,
+        cn_histogram_by_element,
+    };
+}

package/dist/coordination/index.d.ts

@@ -0,0 +1,8 @@
+export * from './calc-coordination';
+export { default as CoordinationBarPlot } from './CoordinationBarPlot.svelte';
+export declare const SPLIT_MODES: {
+    readonly by_element: "By Element";
+    readonly by_structure: "By Structure";
+    readonly none: "Combined";
+};
+export type SplitMode = keyof typeof SPLIT_MODES;

package/dist/coordination/index.js

@@ -0,0 +1,7 @@
+export * from './calc-coordination';
+export { default as CoordinationBarPlot } from './CoordinationBarPlot.svelte';
+export const SPLIT_MODES = {
+    by_element: `By Element`,
+    by_structure: `By Structure`,
+    none: `Combined`,
+};

package/dist/element/BohrAtom.svelte.d.ts

@@ -1,5 +1,5 @@
 import type { SVGAttributes } from 'svelte/elements';
-interface Props extends SVGAttributes<SVGSVGElement> {
+type $$ComponentProps = SVGAttributes<SVGSVGElement> & {
     symbol?: string;
     name?: string;
     shells: number[];
@@ -14,7 +14,7 @@ interface Props extends SVGAttributes<SVGSVGElement> {
     highlight_shell?: number | null;
     number_electrons?: boolean | `hierarchical` | `sequential` | ((idx: number) => string);
     electron_label_props?: Record<string, string | number>;
-}
-declare const BohrAtom: import("svelte").Component<Props, {}, "">;
+};
+declare const BohrAtom: import("svelte").Component<$$ComponentProps, {}, "">;
 type BohrAtom = ReturnType<typeof BohrAtom>;
 export default BohrAtom;

package/dist/element/ElementHeading.svelte.d.ts

@@ -1,8 +1,8 @@
 import type { ChemicalElement } from '..';
 import type { HTMLAttributes } from 'svelte/elements';
-interface Props extends HTMLAttributes<HTMLHeadingElement> {
+type $$ComponentProps = HTMLAttributes<HTMLHeadingElement> & {
     element: ChemicalElement;
-}
-declare const ElementHeading: import("svelte").Component<Props, {}, "">;
+};
+declare const ElementHeading: import("svelte").Component<$$ComponentProps, {}, "">;
 type ElementHeading = ReturnType<typeof ElementHeading>;
 export default ElementHeading;

package/dist/element/ElementPhoto.svelte.d.ts

@@ -1,9 +1,9 @@
 import type { ChemicalElement } from '..';
 import type { HTMLAttributes } from 'svelte/elements';
-interface Props extends HTMLAttributes<HTMLImageElement | HTMLDivElement> {
+type $$ComponentProps = HTMLAttributes<HTMLImageElement | HTMLDivElement> & {
     element: ChemicalElement;
     missing_msg?: string;
-}
-declare const ElementPhoto: import("svelte").Component<Props, {}, "">;
+};
+declare const ElementPhoto: import("svelte").Component<$$ComponentProps, {}, "">;
 type ElementPhoto = ReturnType<typeof ElementPhoto>;
 export default ElementPhoto;

package/dist/element/ElementStats.svelte.d.ts

@@ -1,8 +1,8 @@
 import type { ChemicalElement } from '..';
 import type { HTMLAttributes } from 'svelte/elements';
-interface Props extends HTMLAttributes<HTMLDivElement> {
+type $$ComponentProps = HTMLAttributes<HTMLDivElement> & {
     element: ChemicalElement | null;
-}
-declare const ElementStats: import("svelte").Component<Props, {}, "">;
+};
+declare const ElementStats: import("svelte").Component<$$ComponentProps, {}, "">;
 type ElementStats = ReturnType<typeof ElementStats>;
 export default ElementStats;

package/dist/element/ElementTile.svelte

@@ -99,7 +99,7 @@ const layout_config = $derived.by(() => {
   style:color={text_color}
   {@attach text_color ? null : contrast_color()}
   {...(href ? { role: `link`, tabindex: 0 } : {})}
-  onclick={(event) => onclick?.({ element, event })}
+  onclick={(event: MouseEvent) => onclick?.({ element, event })}
   {...rest}
 >
   {#if should_show_number}

package/dist/element/ElementTile.svelte.d.ts

@@ -1,13 +1,13 @@
 import type { ChemicalElement } from '..';
 import type { HTMLAttributes } from 'svelte/elements';
 type SplitLayout = `diagonal` | `horizontal` | `vertical` | `triangular` | `quadrant`;
-interface Props extends Omit<HTMLAttributes<HTMLElement>, `onclick`> {
+type $$ComponentProps = Omit<HTMLAttributes<HTMLElement>, `onclick`> & {
     element: ChemicalElement;
     bg_color?: string;
     show_symbol?: boolean;
     show_number?: boolean;
     show_name?: boolean;
-    value?: number | number[] | string | string[] | false | undefined;
+    value?: number | number[] | string | string[] | false;
     symbol_style?: string;
     active?: boolean;
     href?: string;
@@ -23,7 +23,7 @@ interface Props extends Omit<HTMLAttributes<HTMLElement>, `onclick`> {
         element: ChemicalElement;
         event: MouseEvent;
     }) => void;
-}
-declare const ElementTile: import("svelte").Component<Props, {}, "node" | "text_color">;
+};
+declare const ElementTile: import("svelte").Component<$$ComponentProps, {}, "node" | "text_color">;
 type ElementTile = ReturnType<typeof ElementTile>;
 export default ElementTile;

package/dist/element/Nucleus.svelte.d.ts

@@ -1,5 +1,5 @@
 import type { SVGAttributes } from 'svelte/elements';
-interface Props extends SVGAttributes<SVGSVGElement> {
+type $$ComponentProps = SVGAttributes<SVGSVGElement> & {
     protons: number;
     neutrons: number;
     radius?: number;
@@ -11,7 +11,7 @@ interface Props extends SVGAttributes<SVGSVGElement> {
     neutron_label?: string;
     text_color?: string;
     symbol?: string;
-}
-declare const Nucleus: import("svelte").Component<Props, {}, "radius">;
+};
+declare const Nucleus: import("svelte").Component<$$ComponentProps, {}, "radius">;
 type Nucleus = ReturnType<typeof Nucleus>;
 export default Nucleus;

package/dist/icons.d.ts

@@ -117,6 +117,10 @@ export declare const icon_data: {
         readonly viewBox: "0 0 24 24";
         readonly path: "M19.75 2A2.25 2.25 0 0 1 22 4.25v5.462a3.25 3.25 0 0 1-.952 2.298l-.026.026a6.476 6.476 0 0 0-1.43-.692l.396-.395a1.75 1.75 0 0 0 .512-1.237V4.25a.75.75 0 0 0-.75-.75h-5.465c-.465 0-.91.185-1.239.513l-8.512 8.523a1.75 1.75 0 0 0 .015 2.462l4.461 4.454a1.755 1.755 0 0 0 2.33.13c.165.487.386.947.654 1.375a3.256 3.256 0 0 1-4.043-.443L3.489 16.06a3.25 3.25 0 0 1-.003-4.596l8.5-8.51A3.25 3.25 0 0 1 14.284 2h5.465zM17 5.502a1.5 1.5 0 1 1 0 3a1.5 1.5 0 0 1 0-3zM23 17.5a5.5 5.5 0 1 0-11 0a5.5 5.5 0 0 0 11 0zm-6.125 3.005a.625.625 0 1 1 1.25 0a.625.625 0 0 1-1.25 0zm-1.228-4.548c-.011-1.137.805-1.954 1.853-1.954c1.031 0 1.853.846 1.853 1.95c0 .566-.185.913-.663 1.447l-.265.29l-.101.116c-.248.292-.324.462-.324.695a.5.5 0 1 1-1 0c0-.576.187-.926.671-1.468l.265-.29l.1-.113c.242-.286.317-.453.317-.677c0-.558-.38-.95-.853-.95c-.494 0-.859.366-.853.945a.5.5 0 1 1-1 .01z";
     };
+    readonly Search: {
+        readonly viewBox: "0 0 24 24";
+        readonly path: "M10 4a6 6 0 1 0 0 12a6 6 0 0 0 0-12m-8 6a8 8 0 1 1 14.32 4.906l5.387 5.387a1 1 0 0 1-1.414 1.414l-5.387-5.387A8 8 0 0 1 2 10";
+    };
     readonly Paper: {
         readonly viewBox: "0 0 24 24";
         readonly path: "M16.5 19q1.05 0 1.775-.725T19 16.5t-.725-1.775T16.5 14t-1.775.725T14 16.5t.725 1.775T16.5 19m5.8 3.3q-.275.275-.7.275t-.7-.275l-2-2q-.525.35-1.137.525T16.5 21q-1.875 0-3.187-1.312T12 16.5t1.313-3.187T16.5 12t3.188 1.313T21 16.5q0 .65-.175 1.263T20.3 18.9l2 2q.275.275.275.7t-.275.7M5 22q-.825 0-1.412-.587T3 20V4q0-.825.588-1.412T5 2h7.175q.4 0 .763.15t.637.425l4.85 4.85q.275.275.425.638t.15.762v.45q0 .45-.363.725t-.812.15q-.325-.075-.65-.113T16.5 10q-2.95 0-4.75 2t-1.8 4.525q0 1.1.388 2.175t1.212 2.025q.35.375.162.825t-.637.45zm7-18v4q0 .425.288.713T13 9h4zl5 5z";

package/dist/icons.js

@@ -118,6 +118,10 @@ export const icon_data = {
         viewBox: `0 0 24 24`,
         path: `M19.75 2A2.25 2.25 0 0 1 22 4.25v5.462a3.25 3.25 0 0 1-.952 2.298l-.026.026a6.476 6.476 0 0 0-1.43-.692l.396-.395a1.75 1.75 0 0 0 .512-1.237V4.25a.75.75 0 0 0-.75-.75h-5.465c-.465 0-.91.185-1.239.513l-8.512 8.523a1.75 1.75 0 0 0 .015 2.462l4.461 4.454a1.755 1.755 0 0 0 2.33.13c.165.487.386.947.654 1.375a3.256 3.256 0 0 1-4.043-.443L3.489 16.06a3.25 3.25 0 0 1-.003-4.596l8.5-8.51A3.25 3.25 0 0 1 14.284 2h5.465zM17 5.502a1.5 1.5 0 1 1 0 3a1.5 1.5 0 0 1 0-3zM23 17.5a5.5 5.5 0 1 0-11 0a5.5 5.5 0 0 0 11 0zm-6.125 3.005a.625.625 0 1 1 1.25 0a.625.625 0 0 1-1.25 0zm-1.228-4.548c-.011-1.137.805-1.954 1.853-1.954c1.031 0 1.853.846 1.853 1.95c0 .566-.185.913-.663 1.447l-.265.29l-.101.116c-.248.292-.324.462-.324.695a.5.5 0 1 1-1 0c0-.576.187-.926.671-1.468l.265-.29l.1-.113c.242-.286.317-.453.317-.677c0-.558-.38-.95-.853-.95c-.494 0-.859.366-.853.945a.5.5 0 1 1-1 .01z`,
     },
+    Search: {
+        viewBox: `0 0 24 24`,
+        path: `M10 4a6 6 0 1 0 0 12a6 6 0 0 0 0-12m-8 6a8 8 0 1 1 14.32 4.906l5.387 5.387a1 1 0 0 1-1.414 1.414l-5.387-5.387A8 8 0 0 1 2 10`,
+    },
     Paper: {
         viewBox: `0 0 24 24`,
         path: `M16.5 19q1.05 0 1.775-.725T19 16.5t-.725-1.775T16.5 14t-1.775.725T14 16.5t.725 1.775T16.5 19m5.8 3.3q-.275.275-.7.275t-.7-.275l-2-2q-.525.35-1.137.525T16.5 21q-1.875 0-3.187-1.312T12 16.5t1.313-3.187T16.5 12t3.188 1.313T21 16.5q0 .65-.175 1.263T20.3 18.9l2 2q.275.275.275.7t-.275.7M5 22q-.825 0-1.412-.587T3 20V4q0-.825.588-1.412T5 2h7.175q.4 0 .763.15t.637.425l4.85 4.85q.275.275.425.638t.15.762v.45q0 .45-.363.725t-.812.15q-.325-.075-.65-.113T16.5 10q-2.95 0-4.75 2t-1.8 4.525q0 1.1.388 2.175t1.212 2.025q.35.375.162.825t-.637.45zm7-18v4q0 .425.288.713T13 9h4zl5 5z`,

package/dist/index.d.ts

@@ -1,7 +1,10 @@
 import type { elem_symbols, element_categories } from './labels';
+export * from './bands';
+export * from './brillouin';
 export * from './colors';
 export * from './composition';
 export { default as ContextMenu } from './ContextMenu.svelte';
+export * from './coordination';
 export { default as DraggablePane } from './DraggablePane.svelte';
 export * from './element';
 export { default as FilePicker } from './FilePicker.svelte';
@@ -10,18 +13,19 @@ export { icon_data, type IconName } from './icons';
 export { default as InfoCard } from './InfoCard.svelte';
 export * from './io';
 export * from './labels';
-export * from './material';
 export * from './math';
 export { default as Nav } from './Nav.svelte';
 export * from './periodic-table';
 export * from './phase-diagram';
 export * from './plot';
+export * from './rdf';
 export * from './settings';
 export { default as SettingsSection } from './SettingsSection.svelte';
 export { default as Spinner } from './Spinner.svelte';
 export * from './structure';
 export * from './theme';
 export { default as Trajectory } from './trajectory/Trajectory.svelte';
+export * from './utils';
 export * from './xrd';
 export type ElementCategory = (typeof element_categories)[number];
 export type ElementSymbol = (typeof elem_symbols)[number];