matterviz 0.1.12 → 0.1.13

package/dist/rdf/calc-rdf.js

@@ -0,0 +1,107 @@
+import { calc_lattice_params, euclidean_dist, matrix_inverse_3x3, pbc_dist, } from '../math';
+import { make_supercell } from '../structure/supercell';
+// Calculate radial distribution function
+export function calculate_rdf(structure, options = {}) {
+    const { center_species, neighbor_species, cutoff = 15, n_bins = 75, auto_expand = true, expansion_factor = 2.0, } = options;
+    let { pbc = [true, true, true] } = options;
+    if (cutoff <= 0 || n_bins <= 0) {
+        throw new Error(`cutoff and n_bins must be positive`);
+    }
+    // Validate structure has lattice
+    if (!structure.lattice?.matrix) {
+        throw new Error(`Structure must have a lattice for RDF calculation`);
+    }
+    let lattice = structure.lattice.matrix;
+    let { sites } = structure;
+    // Expand structure if needed to ensure shortest lattice vector is expansion_factor× the cutoff
+    // This prevents artificial close contacts at cell boundaries when using PBC
+    // Standard practice uses 2.0-2.5× to eliminate finite-size effects
+    if (auto_expand) {
+        const { a, b, c } = calc_lattice_params(lattice);
+        const min_size = cutoff * expansion_factor;
+        const [n_a, n_b, n_c] = [a, b, c].map((len) => Math.ceil(min_size / len));
+        if (n_a > 1 || n_b > 1 || n_c > 1) {
+            const expanded_structure = make_supercell(structure, [n_a, n_b, n_c], false);
+            sites = expanded_structure.sites;
+            lattice = expanded_structure.lattice.matrix;
+            pbc = [false, false, false]; // Disable PBC since we explicitly expanded the structure
+        }
+    }
+    const bin_size = cutoff / n_bins;
+    const r = Array.from({ length: n_bins }, (_, idx) => (idx + 0.5) * bin_size);
+    const g_r = new Array(n_bins).fill(0);
+    if (sites.length === 0)
+        return { r, g_r };
+    // Note: Sites with mixed occupancy are treated as the first species only.
+    // TODO For proper occupancy support, contributions should be weighted by species occupancy.
+    const elements = sites.map((s) => s.species[0].element);
+    const centers = center_species
+        ? sites.filter((_, idx) => elements[idx] === center_species)
+        : sites;
+    const neighbors = neighbor_species
+        ? sites.filter((_, idx) => elements[idx] === neighbor_species)
+        : sites;
+    if (centers.length === 0 || neighbors.length === 0) {
+        const element_pair = center_species && neighbor_species
+            ? [center_species, neighbor_species]
+            : undefined;
+        return { r, g_r, element_pair };
+    }
+    // Calculate distances and bin them
+    const use_pbc = pbc.some((flag) => flag);
+    // Pre-compute lattice inverse once to avoid O(P) inversions in inner loop
+    const lattice_inv = use_pbc ? matrix_inverse_3x3(lattice) : undefined;
+    for (const center of centers) {
+        for (const neighbor of neighbors) {
+            if (center === neighbor)
+                continue;
+            const dist = use_pbc
+                ? pbc_dist(center.xyz, neighbor.xyz, lattice, lattice_inv, pbc)
+                : euclidean_dist(center.xyz, neighbor.xyz);
+            if (dist > 0 && dist < cutoff) {
+                g_r[Math.min(Math.floor(dist / bin_size), n_bins - 1)]++;
+            }
+        }
+    }
+    // Normalize
+    const n_pairs = center_species === neighbor_species
+        ? centers.length * (neighbors.length - 1)
+        : centers.length * neighbors.length;
+    if (n_pairs > 0) {
+        const volume = calc_lattice_params(lattice).volume;
+        for (let idx = 0; idx < n_bins; idx++) {
+            g_r[idx] /= n_pairs * ((4 * Math.PI * r[idx] ** 2 * bin_size) / volume);
+        }
+    }
+    const element_pair = center_species && neighbor_species
+        ? [center_species, neighbor_species]
+        : undefined;
+    return { r, g_r, element_pair };
+}
+// Calculate RDF for all element pairs
+export function calculate_all_pair_rdfs(structure, options = {}) {
+    const elems = [...new Set(structure.sites.map((s) => s.species[0].element))].sort();
+    // If auto_expand is true, expand the structure once and reuse it for all pairs
+    // to avoid repeated supercell computations
+    let structure_to_use = structure;
+    if (options.auto_expand !== false) {
+        const { cutoff = 15, expansion_factor = 2.0 } = options;
+        const lattice = structure.lattice?.matrix;
+        if (lattice) {
+            const { a, b, c } = calc_lattice_params(lattice);
+            const min_size = cutoff * expansion_factor;
+            const [n_a, n_b, n_c] = [a, b, c].map((len) => Math.ceil(min_size / len));
+            if (n_a > 1 || n_b > 1 || n_c > 1) {
+                structure_to_use = make_supercell(structure, [n_a, n_b, n_c], false);
+            }
+        }
+    }
+    // Pass auto_expand=false since we've already expanded, and pbc=false for expanded structure
+    const pbc = [false, false, false];
+    const rdf_options = { ...options, auto_expand: false, pbc };
+    return elems.flatMap((el1, idx1) => elems.slice(idx1).map((el2) => calculate_rdf(structure_to_use, {
+        ...rdf_options,
+        center_species: el1,
+        neighbor_species: el2,
+    })));
+}

package/dist/rdf/index.d.ts

@@ -0,0 +1,22 @@
+import type { Pbc } from '../structure';
+export { calculate_all_pair_rdfs, calculate_rdf } from './calc-rdf';
+export { default as RdfPlot } from './RdfPlot.svelte';
+export type RdfPattern = {
+    r: number[];
+    g_r: number[];
+    element_pair?: [string, string];
+};
+export interface RdfEntry {
+    label: string;
+    pattern: RdfPattern;
+    color?: string;
+}
+export interface RdfOptions {
+    center_species?: string;
+    neighbor_species?: string;
+    cutoff?: number;
+    n_bins?: number;
+    pbc?: Pbc;
+    auto_expand?: boolean;
+    expansion_factor?: number;
+}

package/dist/rdf/index.js

@@ -0,0 +1,2 @@
+export { calculate_all_pair_rdfs, calculate_rdf } from './calc-rdf';
+export { default as RdfPlot } from './RdfPlot.svelte';

package/dist/settings.d.ts

@@ -1,10 +1,11 @@
+import type { D3SymbolName } from './labels';
 import type { Vec3 } from './math';
-import type { D3SymbolName, Markers, Orientation } from './plot';
+import type { Orientation } from './plot';
 import type { BondingStrategy } from './structure/bonding';
 export interface SettingType<T = unknown> {
     value: T;
     description: string;
-    enum?: readonly string[];
+    enum?: Readonly<Record<Extract<T, string>, string>>;
     minimum?: number;
     maximum?: number;
     minItems?: number;
@@ -13,6 +14,64 @@ export interface SettingType<T = unknown> {
 }
 export declare const show_bonds_options: readonly ["never", "always", "crystals", "molecules"];
 export type ShowBonds = (typeof show_bonds_options)[number];
+export type CameraProjection = `perspective` | `orthographic`;
+type DisplayConfigType = {
+    x_grid: SettingType<boolean>;
+    y_grid: SettingType<boolean>;
+    y2_grid: SettingType<boolean>;
+    x_zero_line: SettingType<boolean>;
+    y_zero_line: SettingType<boolean>;
+};
+type BarStyleType = {
+    color: SettingType<string>;
+    opacity: SettingType<number>;
+    stroke_width: SettingType<number>;
+    stroke_color: SettingType<string>;
+    stroke_opacity: SettingType<number>;
+};
+type PointStyleType = {
+    size: SettingType<number>;
+    color: SettingType<string>;
+    opacity: SettingType<number>;
+    stroke_width: SettingType<number>;
+    stroke_color: SettingType<string>;
+    stroke_opacity: SettingType<number>;
+};
+type LineStyleType = {
+    width: SettingType<number>;
+    color: SettingType<string>;
+    opacity: SettingType<number>;
+    dash: SettingType<string>;
+};
+type SimpleBarStyleType = {
+    color: SettingType<string>;
+    opacity: SettingType<number>;
+};
+type SimpleLineStyleType = {
+    width: SettingType<number>;
+    color: SettingType<string>;
+};
+type PhaseDiagramCommonType = {
+    camera_zoom: SettingType<number>;
+    camera_center_x: SettingType<number>;
+    camera_center_y: SettingType<number>;
+    color_mode: SettingType<`stability` | `energy`>;
+    color_scale: SettingType<string>;
+    show_stable: SettingType<boolean>;
+    show_unstable: SettingType<boolean>;
+    show_stable_labels: SettingType<boolean>;
+    show_unstable_labels: SettingType<boolean>;
+    max_hull_dist_show_phases: SettingType<number>;
+    max_hull_dist_show_labels: SettingType<number>;
+    fullscreen: SettingType<boolean>;
+    info_pane_open: SettingType<boolean>;
+    legend_pane_open: SettingType<boolean>;
+};
+type PhaseDiagramWith3DType = PhaseDiagramCommonType & {
+    show_hull_faces: SettingType<boolean>;
+    hull_face_color: SettingType<string>;
+    hull_face_opacity: SettingType<number>;
+};
 export interface SettingsConfig {
     color_scheme: SettingType<string>;
     background_color: SettingType<string>;
@@ -29,7 +88,7 @@ export interface SettingsConfig {
         bonding_strategy: SettingType<BondingStrategy>;
         show_gizmo: SettingType<boolean>;
         camera_position: SettingType<Vec3>;
-        camera_projection: SettingType<`perspective` | `orthographic`>;
+        camera_projection: SettingType<CameraProjection>;
         initial_zoom: SettingType<number>;
         fov: SettingType<number>;
         rotation_damping: SettingType<number>;
@@ -77,11 +136,6 @@ export interface SettingsConfig {
         text_file_threshold: SettingType<number>;
         use_indexing: SettingType<boolean>;
         chunk_size: SettingType<number>;
-        histogram_mode: SettingType<`overlay` | `single`>;
-        histogram_show_legend: SettingType<boolean>;
-        histogram_bin_count: SettingType<number>;
-        histogram_bar_opacity: SettingType<number>;
-        histogram_bar_stroke_width: SettingType<number>;
         step_label_format: SettingType<string>;
         property_value_format: SettingType<string>;
         tooltip_format: SettingType<string>;
@@ -107,10 +161,11 @@ export interface SettingsConfig {
         auto_fit_range: SettingType<boolean>;
         grid_lines: SettingType<boolean>;
         axis_labels: SettingType<boolean>;
-        show_zero_lines: SettingType<boolean>;
-        x_grid: SettingType<boolean>;
-        y_grid: SettingType<boolean>;
-        y2_grid: SettingType<boolean>;
+        show_x_zero_line: SettingType<boolean>;
+        show_y_zero_line: SettingType<boolean>;
+        show_x_grid: SettingType<boolean>;
+        show_y_grid: SettingType<boolean>;
+        show_y2_grid: SettingType<boolean>;
         x_format: SettingType<string>;
         y_format: SettingType<string>;
         y2_format: SettingType<string>;
@@ -120,84 +175,39 @@ export interface SettingsConfig {
         y_ticks: SettingType<number>;
     };
     scatter: {
-        point_size: SettingType<number>;
         show_legend: SettingType<boolean>;
-        markers: SettingType<Markers>;
-        point_color: SettingType<string>;
-        point_opacity: SettingType<number>;
-        point_stroke_width: SettingType<number>;
-        point_stroke_color: SettingType<string>;
-        point_stroke_opacity: SettingType<number>;
-        line_width: SettingType<number>;
-        line_color: SettingType<string>;
-        line_opacity: SettingType<number>;
-        line_dash: SettingType<string>;
         show_points: SettingType<boolean>;
         show_lines: SettingType<boolean>;
         symbol_type: SettingType<D3SymbolName>;
+        display: DisplayConfigType;
+        point: PointStyleType;
+        line: LineStyleType;
+    };
+    histogram: {
+        mode: SettingType<`overlay` | `single`>;
+        show_legend: SettingType<boolean>;
+        bin_count: SettingType<number>;
+        bar: BarStyleType;
+        display: DisplayConfigType;
+    };
+    bar: {
+        display: DisplayConfigType;
+        bar: SimpleBarStyleType;
+        line: SimpleLineStyleType;
     };
     composition: {
         display_mode: SettingType<`pie` | `bubble` | `bar`>;
         color_scheme: SettingType<string>;
     };
     phase_diagram: {
-        binary: {
-            camera_zoom: SettingType<number>;
-            camera_center_x: SettingType<number>;
-            camera_center_y: SettingType<number>;
-            color_mode: SettingType<`stability` | `energy`>;
-            color_scale: SettingType<string>;
-            show_stable: SettingType<boolean>;
-            show_unstable: SettingType<boolean>;
-            show_stable_labels: SettingType<boolean>;
-            show_unstable_labels: SettingType<boolean>;
-            energy_threshold: SettingType<number>;
-            label_energy_threshold: SettingType<number>;
-            fullscreen: SettingType<boolean>;
-            info_pane_open: SettingType<boolean>;
-            legend_pane_open: SettingType<boolean>;
-        };
-        ternary: {
+        binary: PhaseDiagramCommonType;
+        ternary: PhaseDiagramWith3DType & {
             camera_elevation: SettingType<number>;
             camera_azimuth: SettingType<number>;
-            camera_zoom: SettingType<number>;
-            camera_center_x: SettingType<number>;
-            camera_center_y: SettingType<number>;
-            color_mode: SettingType<`stability` | `energy`>;
-            color_scale: SettingType<string>;
-            show_stable: SettingType<boolean>;
-            show_unstable: SettingType<boolean>;
-            show_stable_labels: SettingType<boolean>;
-            show_unstable_labels: SettingType<boolean>;
-            energy_threshold: SettingType<number>;
-            label_energy_threshold: SettingType<number>;
-            show_hull_faces: SettingType<boolean>;
-            hull_face_color: SettingType<string>;
-            hull_face_opacity: SettingType<number>;
-            fullscreen: SettingType<boolean>;
-            info_pane_open: SettingType<boolean>;
-            legend_pane_open: SettingType<boolean>;
         };
-        quaternary: {
+        quaternary: PhaseDiagramWith3DType & {
             camera_rotation_x: SettingType<number>;
             camera_rotation_y: SettingType<number>;
-            camera_zoom: SettingType<number>;
-            camera_center_x: SettingType<number>;
-            camera_center_y: SettingType<number>;
-            color_mode: SettingType<`stability` | `energy`>;
-            color_scale: SettingType<string>;
-            show_stable: SettingType<boolean>;
-            show_unstable: SettingType<boolean>;
-            show_stable_labels: SettingType<boolean>;
-            show_unstable_labels: SettingType<boolean>;
-            show_hull_faces: SettingType<boolean>;
-            hull_face_color: SettingType<string>;
-            hull_face_opacity: SettingType<number>;
-            energy_threshold: SettingType<number>;
-            label_energy_threshold: SettingType<number>;
-            fullscreen: SettingType<boolean>;
-            info_pane_open: SettingType<boolean>;
-            legend_pane_open: SettingType<boolean>;
         };
     };
 }
@@ -213,3 +223,4 @@ export declare const DEFAULTS: DefaultSettings;
 export declare const merge: (user?: Partial<DefaultSettings>) => DefaultSettings;
 export type PhaseDiagramDefaults = DefaultSettings[`phase_diagram`];
 export declare const PD_DEFAULTS: PhaseDiagramDefaults;
+export {};