matterviz 0.3.0 → 0.3.2

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

@@ -1,15 +1,51 @@
 import type { HTMLAttributes } from 'svelte/elements';
 import type { FormulaSearchMode } from './index';
+type SearchExampleCategory = {
+    label: string;
+    description: string;
+    examples: string[];
+};
+export type FormulaFilterToken = {
+    raw: string;
+    element: string;
+    operator: `include` | `exclude`;
+    constraint: string | null;
+    is_wildcard: boolean;
+    is_valid: boolean;
+};
+export type FormulaFilterParseResult = {
+    value: string;
+    normalized_value: string;
+    search_mode: FormulaSearchMode;
+    tokens: FormulaFilterToken[];
+    has_wildcards: boolean;
+    is_valid: boolean;
+    error_message: string | null;
+};
+export type FormulaFilterValidation = {
+    state: `valid` | `warning` | `invalid`;
+    message: string | null;
+};
 type $$ComponentProps = {
     value: string;
     search_mode?: FormulaSearchMode;
     input_element?: HTMLInputElement | null;
     show_clear_button?: boolean;
     show_examples?: boolean;
+    show_mode_lock?: boolean;
+    show_chip_editor?: boolean;
+    normalize_exact?: boolean;
+    examples?: SearchExampleCategory[];
     disabled?: boolean;
+    mode_locked?: boolean;
+    max_history?: number;
+    history_key?: string;
+    validate?: (value: string, search_mode: FormulaSearchMode, parsed: FormulaFilterParseResult) => FormulaFilterValidation | null;
+    onparse?: (parsed: FormulaFilterParseResult) => void;
+    on_validation?: (validation: FormulaFilterValidation) => void;
     onchange?: (value: string, search_mode: FormulaSearchMode) => void;
     onclear?: () => void;
 } & HTMLAttributes<HTMLDivElement>;
-declare const FormulaFilter: import("svelte").Component<$$ComponentProps, {}, "value" | "search_mode" | "input_element">;
+declare const FormulaFilter: import("svelte").Component<$$ComponentProps, {}, "value" | "search_mode" | "input_element" | "mode_locked">;
 type FormulaFilter = ReturnType<typeof FormulaFilter>;
 export default FormulaFilter;

package/dist/composition/PieChart.svelte

@@ -1,5 +1,5 @@
-<script lang="ts">import { format_num } from '../labels';
-import { ELEMENT_COLOR_SCHEMES, pick_contrast_color } from '../colors';
+<script lang="ts">import { ELEMENT_COLOR_SCHEMES, pick_contrast_color } from '../colors';
+import { format_num } from '../labels';
 import { get_chart_font_scale } from './index';
 import { count_atoms_in_composition, fractional_composition } from './parse';
 // Constants for pie chart calculations
@@ -21,8 +21,34 @@ let segments = $derived.by(() => {
         .map(([element_key, amount]) => {
         const element = element_key;
         const fraction = fractions[element] || 0;
-        // use 359.99° to avoid 360° for single-element compositions which cause SVG arc issues
-        const angle_span = fraction === 1 ? 359.99 : fraction * 360;
+        const color = element_colors[element] || `#cccccc`;
+        // Single element: full circle with no radial stroke line, label at center
+        if (fraction === 1) {
+            const r = outer_radius;
+            const ir = inner_radius_adjusted;
+            // Two semicircular arcs to form a full circle (avoids SVG 360° arc bug)
+            const outer_arc = `M ${center} ${center - r} A ${r} ${r} 0 1 1 ${center} ${center + r} A ${r} ${r} 0 1 1 ${center} ${center - r} Z`;
+            const path = ir > 0
+                ? `${outer_arc} M ${center} ${center - ir} A ${ir} ${ir} 0 1 0 ${center} ${center + ir} A ${ir} ${ir} 0 1 0 ${center} ${center - ir} Z`
+                : outer_arc;
+            const label_text = element + (show_amounts ? String(amount) : ``) +
+                (show_percentages ? `${format_num(fraction, `.1~%`)}` : ``);
+            return {
+                element,
+                amount,
+                fraction,
+                color,
+                start_angle: -90,
+                end_angle: 270,
+                path,
+                label_x: center,
+                label_y: center,
+                is_outside_slice: false,
+                font_scale: get_chart_font_scale(2.6, label_text, r * 2),
+                text_color: pick_contrast_color({ bg_color: color }),
+            };
+        }
+        const angle_span = fraction * 360;
         const start_angle = current_angle;
         const end_angle = current_angle + angle_span;
         current_angle = end_angle;
@@ -78,7 +104,6 @@ let segments = $derived.by(() => {
             : Math.min(outer_radius - inner_radius_adjusted, // Radial space
             (angle_span * Math.PI / 180) * label_radius * 0.8);
         const font_scale = get_chart_font_scale(base_scale, label_text, available_space);
-        const color = element_colors[element] || `#cccccc`;
         return {
             element,
             amount,
@@ -102,6 +127,7 @@ let hovered_element = $state(null);
 
 <svg
   viewBox="0 0 {size} {size}"
+  style:max-width="{size}px"
   {...rest}
   class="pie-chart {rest.class ?? ``}"
   bind:this={svg_node}
@@ -111,7 +137,11 @@ let hovered_element = $state(null);
       d={segment.path}
       fill={segment.color}
       stroke="white"
-      stroke-width={hovered_element === segment.element ? stroke_width + 1 : stroke_width}
+      stroke-width={segments.length === 1
+      ? 0
+      : hovered_element === segment.element
+      ? stroke_width + 1
+      : stroke_width}
       class="pie-segment"
       class:interactive
       class:hovered={hovered_element === segment.element}
@@ -154,14 +184,12 @@ let hovered_element = $state(null);
           <span class="element-symbol" style:font-size="{14 * segment.font_scale}px">{
             segment.element
           }</span>
-          {#if show_amounts}
-            <sub class="amount" style:font-size="{10 * segment.font_scale}px">
-              {segment.amount}
-            </sub>{/if}
-          {#if show_percentages}
-            <sub class="percentage" style:font-size="{11 * segment.font_scale}px">
-              {format_num(segment.fraction, `.1~%`)}
-            </sub>
+          {#if show_amounts || show_percentages}
+            <sub class="amount" style:font-size="{8 * segment.font_scale}px">{
+              show_amounts ? segment.amount : ``
+            }{show_amounts && show_percentages ? `=` : ``}{
+              show_percentages ? format_num(segment.fraction, `.1~%`) : ``
+            }</sub>
           {/if}
         </div>
       </foreignObject>
@@ -215,9 +243,6 @@ let hovered_element = $state(null);
   }
   .amount {
     margin-left: 1px;
-    transform: translateY(9pt);
-  }
-  .percentage {
-    transform: translateY(4px);
+    transform: translateY(5pt);
   }
 </style>

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

@@ -1,6 +1,6 @@
+import type { ColorSchemeName } from '../colors';
 import type { CompositionType } from './';
 import type { ElementSymbol } from '../element';
-import type { ColorSchemeName } from '../colors';
 import type { Snippet } from 'svelte';
 import type { SVGAttributes } from 'svelte/elements';
 import { type ChartSegmentData } from './index';

package/dist/constants.d.ts

@@ -21,6 +21,7 @@ export declare const STRUCTURE_EXTENSIONS_REGEX: RegExp;
 export declare const TRAJ_FALLBACK_EXTENSIONS: readonly string[];
 export declare const TRAJ_FALLBACK_EXTENSIONS_REGEX: RegExp;
 export declare const VASP_FILES_REGEX: RegExp;
+export declare const VASP_VOLUMETRIC_REGEX: RegExp;
 export declare const XDATCAR_REGEX: RegExp;
 export declare const CONFIG_DIRS_REGEX: RegExp;
 export declare const MD_SIM_EXCLUDE_REGEX: RegExp;

package/dist/constants.js

@@ -75,6 +75,7 @@ export const STRUCTURE_EXTENSIONS = Object.freeze([
     `.mcif`,
     `.poscar`,
     `.vasp`,
+    `.cube`,
     `.lmp`,
     `.data`,
     `.dump`,
@@ -95,6 +96,7 @@ export const TRAJ_FALLBACK_EXTENSIONS = Object.freeze([
 export const TRAJ_FALLBACK_EXTENSIONS_REGEX = new RegExp(`\\.(${TRAJ_FALLBACK_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`, `i`);
 // Special regex patterns
 export const VASP_FILES_REGEX = /(?:^|[\\/_.-])(poscar|contcar|potcar|incar|kpoints|outcar)(?:[\\/_.-]|$)/i;
+export const VASP_VOLUMETRIC_REGEX = /(?:^|[\\/_.-])(chgcar|aeccar[012]?|elfcar|locpot|parchg)(?:[\\/_.-]|$)/i;
 export const XDATCAR_REGEX = /xdatcar/i;
 export const CONFIG_DIRS_REGEX = /(?:^|[\\/])(\.vscode|\.idea|\.nyc_output|\.cache|\.tmp|\.temp|node_modules|dist|build|coverage)(?:[\\/]|$)/i;
 export const MD_SIM_EXCLUDE_REGEX = /md_simulation\.(out|txt|yml|py|csv|html|css|md|js|ts)$/i;

package/dist/convex-hull/ConvexHull.svelte

@@ -1,11 +1,12 @@
 <script lang="ts">import { extract_formula_elements } from '../composition/parse';
+import { DEFAULTS } from '../settings';
 import { SvelteSet } from 'svelte/reactivity';
 import ConvexHull2D from './ConvexHull2D.svelte';
 import ConvexHull3D from './ConvexHull3D.svelte';
 import ConvexHull4D from './ConvexHull4D.svelte';
 let { entries = [], 
 // bindable props not part of rest because Svelte 5 doesn't support spreading bindable props.
-fullscreen = $bindable(false), wrapper = $bindable(), show_stable = $bindable(true), show_unstable = $bindable(true), show_hull_faces = $bindable(true), hull_face_opacity = $bindable(0.3), color_mode = $bindable(`energy`), color_scale = $bindable(`interpolateViridis`), info_pane_open = $bindable(false), legend_pane_open = $bindable(false), max_hull_dist_show_phases = $bindable(0.1), max_hull_dist_show_labels = $bindable(0.1), show_stable_labels = $bindable(true), show_unstable_labels = $bindable(false), energy_source_mode = $bindable(`precomputed`), phase_stats = $bindable(null), display = $bindable({ x_grid: false, y_grid: false }), stable_entries = $bindable([]), unstable_entries = $bindable([]), highlighted_entries = $bindable([]), selected_entry = $bindable(null), temperature = $bindable(), gas_pressures = $bindable({}), ...rest } = $props();
+fullscreen = $bindable(false), wrapper = $bindable(), show_stable = $bindable(true), show_unstable = $bindable(true), show_hull_faces = $bindable(true), hull_face_opacity: hull_face_opacity_prop = $bindable(undefined), color_mode = $bindable(`energy`), color_scale = $bindable(`interpolateViridis`), info_pane_open = $bindable(false), legend_pane_open = $bindable(false), max_hull_dist_show_phases = $bindable(0.1), max_hull_dist_show_labels = $bindable(0.1), show_stable_labels = $bindable(true), show_unstable_labels = $bindable(false), energy_source_mode = $bindable(`precomputed`), phase_stats = $bindable(null), display = $bindable({ x_grid: false, y_grid: false }), stable_entries = $bindable([]), unstable_entries = $bindable([]), highlighted_entries = $bindable([]), selected_entry = $bindable(null), temperature = $bindable(), gas_pressures = $bindable({}), ...rest } = $props();
 // Lightweight element extraction - count unique elements, stripping oxidation states
 // (e.g. "V4+" -> "V") to avoid counting the same element multiple times
 function extract_unique_elements(entries) {
@@ -23,6 +24,18 @@ function extract_unique_elements(entries) {
 // Detect dimensionality by counting unique elements (lightweight operation)
 const elements = $derived(extract_unique_elements(entries));
 const element_count = $derived(elements.length);
+// Resolve hull face opacity: use caller's value if provided,
+// otherwise pick the right default for the dimensionality (ternary=30%, quaternary=3%).
+// Use writable derived so child bind updates can sync back to parent.
+const default_opacity = $derived(element_count === 4
+    ? DEFAULTS.convex_hull.quaternary.hull_face_opacity
+    : DEFAULTS.convex_hull.ternary.hull_face_opacity);
+let hull_face_opacity = $derived(hull_face_opacity_prop ?? default_opacity);
+$effect(() => {
+    if (hull_face_opacity_prop === hull_face_opacity)
+        return;
+    hull_face_opacity_prop = hull_face_opacity;
+});
 // Map element count to corresponding component
 // Note: Type assertion needed because TypeScript can't infer that all components
 // accept a compatible superset of props (BaseConvexHullProps + dimension-specific)

package/dist/convex-hull/ConvexHull.svelte.d.ts

@@ -8,6 +8,6 @@ type ConvexHullProps = BaseConvexHullProps & Hull3DProps & {
     gas_config?: GasThermodynamicsConfig;
     gas_pressures?: Partial<Record<GasSpecies, number>>;
 };
-declare const ConvexHull: Component<ConvexHullProps, {}, "temperature" | "display" | "fullscreen" | "show_hull_faces" | "hull_face_opacity" | "color_mode" | "color_scale" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "info_pane_open" | "legend_pane_open" | "wrapper" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
+declare const ConvexHull: Component<ConvexHullProps, {}, "temperature" | "display" | "color_scale" | "fullscreen" | "show_hull_faces" | "hull_face_opacity" | "color_mode" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "info_pane_open" | "legend_pane_open" | "wrapper" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
 type ConvexHull = ReturnType<typeof ConvexHull>;
 export default ConvexHull;

package/dist/convex-hull/ConvexHull2D.svelte

@@ -5,6 +5,7 @@ import { symbol_map } from '../labels';
 import { set_fullscreen_bg, setup_fullscreen_effect } from '../layout';
 import { ScatterPlot } from '../plot';
 import { DEFAULTS } from '../settings';
+import { SvelteMap } from 'svelte/reactivity';
 import ConvexHullControls from './ConvexHullControls.svelte';
 import ConvexHullInfoPane from './ConvexHullInfoPane.svelte';
 import ConvexHullTooltip from './ConvexHullTooltip.svelte';
@@ -14,7 +15,7 @@ import { CONVEX_HULL_STYLE, default_controls, default_hull_config } from './inde
 import StructurePopup from './StructurePopup.svelte';
 import TemperatureSlider from './TemperatureSlider.svelte';
 import * as thermo from './thermodynamics';
-import { is_unary_entry } from './types';
+import { HULL_STABILITY_TOL, is_unary_entry } from './types';
 // Binary convex hull rendered as energy vs composition (x in [0, 1])
 let { entries = [], controls = {}, config = {}, on_point_click, on_point_hover, fullscreen = $bindable(DEFAULTS.convex_hull.binary.fullscreen), enable_info_pane = true, wrapper = $bindable(), label_threshold = 50, show_stable = $bindable(DEFAULTS.convex_hull.binary.show_stable), show_unstable = $bindable(DEFAULTS.convex_hull.binary.show_unstable), color_mode = $bindable(DEFAULTS.convex_hull.binary.color_mode), color_scale = $bindable(DEFAULTS.convex_hull.binary.color_scale), info_pane_open = $bindable(DEFAULTS.convex_hull.binary.info_pane_open), legend_pane_open = $bindable(DEFAULTS.convex_hull.binary.legend_pane_open), max_hull_dist_show_phases = $bindable(DEFAULTS.convex_hull.binary.max_hull_dist_show_phases), max_hull_dist_show_labels = $bindable(DEFAULTS.convex_hull.binary.max_hull_dist_show_labels), show_stable_labels = $bindable(DEFAULTS.convex_hull.binary.show_stable_labels), show_unstable_labels = $bindable(DEFAULTS.convex_hull.binary.show_unstable_labels), on_file_drop, enable_click_selection = true, enable_structure_preview = true, energy_source_mode = $bindable(`precomputed`), phase_stats = $bindable(null), display = $bindable({ x_grid: false, y_grid: false }), stable_entries = $bindable([]), unstable_entries = $bindable([]), highlighted_entries = $bindable([]), highlight_style = {}, x_axis = {}, y_axis = {}, selected_entry = $bindable(null), temperature = $bindable(), interpolate_temperature = true, max_interpolation_gap = 500, gas_config, gas_pressures = $bindable({}), children, tooltip: custom_tooltip, ...rest } = $props();
 const merged_controls = $derived({ ...default_controls, ...controls });
@@ -106,36 +107,6 @@ function compute_binary_coordinates(raw_entries, elems) {
     }
     return coords;
 }
-function compute_lower_hull(points) {
-    // Andrew's monotone chain for lower hull
-    const sorted = [...points].sort((p1, p2) => (p1.x - p2.x) || (p1.y - p2.y));
-    const lower = [];
-    const cross = (o, a, b) => (a.x - o.x) * (b.y - o.y) - (a.y - o.y) * (b.x - o.x);
-    for (const p of sorted) {
-        while (lower.length >= 2 &&
-            cross(lower[lower.length - 2], lower[lower.length - 1], p) <= 0)
-            lower.pop();
-        lower.push(p);
-    }
-    return lower;
-}
-function interpolate_on_hull(hull, x) {
-    if (hull.length < 2)
-        return null;
-    if (x <= hull[0].x)
-        return hull[0].y;
-    if (x >= hull[hull.length - 1].x)
-        return hull[hull.length - 1].y;
-    for (let i = 0; i < hull.length - 1; i++) {
-        const p1 = hull[i];
-        const p2 = hull[i + 1];
-        if (x >= p1.x && x <= p2.x) {
-            const t = (x - p1.x) / Math.max(1e-12, p2.x - p1.x);
-            return p1.y * (1 - t) + p2.y * t;
-        }
-    }
-    return null;
-}
 const coords_entries = $derived.by(() => {
     if (elements.length !== 2)
         return [];
@@ -152,28 +123,26 @@ const { all_enriched_entries, hull_points } = $derived.by(() => {
     if (coords_entries.length === 0) {
         return { all_enriched_entries: [], hull_points: [] };
     }
-    // Build lower hull: group by x, use lowest energy per x
-    // eslint-disable-next-line svelte/prefer-svelte-reactivity -- local var in derived
-    const by_x = new Map();
+    // Build lower hull input: one minimum-energy point per composition x.
+    const min_y_by_x = new SvelteMap();
     for (const entry of coords_entries) {
-        const group = by_x.get(entry.x);
-        if (group)
-            group.push(entry);
-        else
-            by_x.set(entry.x, [entry]);
+        const current_min_y = min_y_by_x.get(entry.x);
+        if (current_min_y === undefined || entry.y < current_min_y) {
+            min_y_by_x.set(entry.x, entry.y);
+        }
     }
-    const hull_input = [...by_x].map(([x_coord, entries]) => ({
+    const hull_input = [...min_y_by_x].map(([x_coord, min_y]) => ({
         x: x_coord,
-        y: Math.min(...entries.map((e) => e.y)),
+        y: min_y,
     }));
-    const hull_points = compute_lower_hull(hull_input);
+    const hull_points = thermo.compute_lower_hull_2d(hull_input);
     const all_enriched_entries = coords_entries.map((entry) => {
-        const y_hull = interpolate_on_hull(hull_points, entry.x);
+        const y_hull = thermo.interpolate_hull_2d(hull_points, entry.x);
         const e_above_hull = y_hull == null ? 0 : Math.max(0, entry.y - y_hull);
         return {
             ...entry,
             e_above_hull,
-            is_stable: e_above_hull <= 1e-9,
+            is_stable: e_above_hull <= HULL_STABILITY_TOL,
             visible: true,
         };
     });
@@ -647,7 +616,7 @@ let style = $derived(`--hull-stable-color:${merged_config.colors?.stable || `#00
     color: var(--text-color, currentColor);
     transition: background-color 0.2s, opacity 0.2s;
     display: flex;
-    font-size: clamp(0.85em, 2cqmin, 2.5em);
+    font-size: clamp(0.85em, 2cqmin, 1.3em);
   }
   :global(.convex-hull-2d .control-btn:hover) {
     background-color: color-mix(in srgb, currentColor 8%, transparent);

package/dist/convex-hull/ConvexHull2D.svelte.d.ts

@@ -6,6 +6,6 @@ type $$ComponentProps = BaseConvexHullProps<ConvexHullEntry> & {
     x_axis?: AxisConfig;
     y_axis?: AxisConfig;
 };
-declare const ConvexHull2D: import("svelte").Component<$$ComponentProps, {}, "temperature" | "display" | "fullscreen" | "color_mode" | "color_scale" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "info_pane_open" | "legend_pane_open" | "wrapper" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
+declare const ConvexHull2D: import("svelte").Component<$$ComponentProps, {}, "temperature" | "display" | "color_scale" | "fullscreen" | "color_mode" | "show_stable" | "show_unstable" | "show_stable_labels" | "show_unstable_labels" | "max_hull_dist_show_phases" | "max_hull_dist_show_labels" | "info_pane_open" | "legend_pane_open" | "wrapper" | "energy_source_mode" | "stable_entries" | "unstable_entries" | "phase_stats" | "highlighted_entries" | "selected_entry" | "gas_pressures">;
 type ConvexHull2D = ReturnType<typeof ConvexHull2D>;
 export default ConvexHull2D;