matterviz 0.3.6 → 0.3.7

package/dist/src/lib/rdf/RdfPlot.svelte

@@ -1,247 +0,0 @@
-<script lang="ts">
-  import { PLOT_COLORS } from '$lib/colors'
-  import { get_electro_neg_formula } from '$lib/composition'
-  import { StatusMessage } from '$lib/feedback'
-  import { create_file_drop_handler } from '$lib/io'
-  import type { DataSeries } from '$lib/plot'
-  import { ScatterPlot } from '$lib/plot'
-  import type { Crystal, Pbc } from '$lib/structure'
-  import { parse_any_structure } from '$lib/structure/parse'
-  import { is_crystal } from '$lib/structure/validation'
-  import type { ComponentProps, Snippet } from 'svelte'
-  import { calculate_all_pair_rdfs, calculate_rdf, type RdfEntry } from './index'
-
-  let {
-    patterns,
-    structures,
-    mode = `element_pairs`,
-    show_reference_line = true,
-    x_axis = {},
-    y_axis = {},
-    cutoff = 15,
-    n_bins = 75,
-    pbc = [true, true, true],
-    enable_drop = false,
-    on_file_drop,
-    loading = $bindable(false),
-    error_msg = $bindable(),
-    children,
-    drag_dropped = $bindable([]),
-    dragging = $bindable(false),
-    ...rest
-  }: {
-    patterns?: RdfEntry | RdfEntry[]
-    structures?: Crystal | Crystal[] | Record<string, Crystal>
-    mode?: `element_pairs` | `full`
-    show_reference_line?: boolean
-    x_axis?: ComponentProps<typeof ScatterPlot>[`x_axis`]
-    y_axis?: ComponentProps<typeof ScatterPlot>[`y_axis`]
-    cutoff?: number
-    n_bins?: number
-    pbc?: Pbc
-    enable_drop?: boolean
-    on_file_drop?: (content: string | ArrayBuffer, filename: string) => void
-    loading?: boolean
-    error_msg?: string
-    children?: Snippet<[{ drag_dropped: Crystal[] }]>
-    drag_dropped?: Crystal[]
-    dragging?: boolean
-  } & ComponentProps<typeof ScatterPlot> = $props()
-
-  function format_structure_label(struct: Crystal, label_base: string): string {
-    const formula = get_electro_neg_formula(struct)
-    return formula && label_base ? `${formula}: ${label_base}` : formula || label_base
-  }
-
-  const compute_and_add = (content: string | ArrayBuffer, filename: string) => {
-    try {
-      const text = content instanceof ArrayBuffer
-        ? new TextDecoder().decode(content)
-        : content
-      const parsed_struct = parse_any_structure(text, filename)
-      if (is_crystal(parsed_struct)) {
-        drag_dropped = [...drag_dropped, parsed_struct]
-      } else {
-        error_msg = `Crystal has no lattice or sites; cannot compute RDF`
-      }
-    } catch (exc) {
-      error_msg = `Failed to process structure: ${
-        exc instanceof Error ? exc.message : String(exc)
-      }`
-    }
-  }
-
-  const handle_drop = create_file_drop_handler({
-    allow: () => enable_drop,
-    on_drop: (content, filename) =>
-      (on_file_drop || compute_and_add)(content, filename),
-    on_error: (msg) => {
-      error_msg = msg
-    },
-    set_loading: (val) => {
-      loading = val
-      if (val) [error_msg, dragging] = [undefined, false]
-    },
-  })
-
-  function handle_dragover(ev: DragEvent) {
-    ev.preventDefault()
-    if (ev.dataTransfer) ev.dataTransfer.dropEffect = `copy`
-    dragging = true
-  }
-
-  const entries = $derived.by(() => {
-    const result: RdfEntry[] = []
-
-    // Add patterns
-    if (patterns) {
-      if (Array.isArray(patterns)) result.push(...patterns)
-      else result.push(patterns)
-    }
-
-    // Add structures
-    const struct_list: { struct: Crystal; label: string }[] = []
-    if (structures) {
-      if (Array.isArray(structures)) {
-        structures.forEach((struct, idx) =>
-          struct_list.push({
-            struct,
-            label: format_structure_label(struct, `Crystal ${idx + 1}`),
-          })
-        )
-      } else if (is_crystal(structures)) {
-        struct_list.push({
-          struct: structures,
-          label: format_structure_label(structures, ``),
-        })
-      } else {
-        Object.entries(structures).forEach(([label, struct]) =>
-          struct_list.push({ struct, label: format_structure_label(struct, label) })
-        )
-      }
-    }
-    drag_dropped.forEach((struct, idx) =>
-      struct_list.push({
-        struct,
-        label: format_structure_label(struct, `Dropped ${idx + 1}`),
-      })
-    )
-
-    for (const { struct, label } of struct_list) {
-      if (mode === `element_pairs`) {
-        const pairs = calculate_all_pair_rdfs(struct, { cutoff, n_bins, pbc })
-        result.push(...pairs.map((pair) => ({
-          label: pair.element_pair ? `${pair.element_pair[0]}-${pair.element_pair[1]}` : label,
-          legend_group: label, // Group by structure name for multi-structure plots
-          pattern: pair,
-        })))
-      } else {
-        const pattern = calculate_rdf(struct, { cutoff, n_bins, pbc })
-        result.push({ label, pattern })
-      }
-    }
-    return result
-  })
-
-  const max_r = $derived(Math.max(...entries.flatMap((entry) => entry.pattern.r), 0))
-  const max_g = $derived(Math.max(1.2, ...entries.flatMap((entry) => entry.pattern.g_r)))
-
-  const series = $derived<DataSeries[]>(
-    entries.map((ent, idx) => ({
-      x: ent.pattern.r,
-      y: ent.pattern.g_r,
-      label: ent.label,
-      legend_group: ent.legend_group,
-      visible: mode === `element_pairs` ? idx < 3 : true,
-      markers: `line` as const,
-      line_style: {
-        stroke: ent.color ?? PLOT_COLORS[idx % PLOT_COLORS.length],
-        stroke_width: 2,
-      },
-    })),
-  )
-</script>
-
-<StatusMessage bind:message={error_msg} type="error" dismissible />
-
-{#if enable_drop && drag_dropped.length > 0}
-  <div class="dropped-info">
-    {drag_dropped.length} structure{drag_dropped.length > 1 ? `s` : ``} loaded
-    <button onclick={() => (drag_dropped = [])}>Clear</button>
-  </div>
-{/if}
-
-{#if series.length === 0}
-  <!-- svelte-ignore a11y_no_static_element_interactions -->
-  <div
-    class="empty-drop {dragging ? `dragging` : ``}"
-    ondragover={enable_drop ? handle_dragover : undefined}
-    ondragleave={enable_drop ? () => (dragging = false) : undefined}
-    ondrop={enable_drop ? handle_drop : undefined}
-  >
-    <StatusMessage
-      message={enable_drop
-      ? `Drag and drop structure files here to visualize RDFs`
-      : `No RDF data to display`}
-      style="border: none"
-    />
-  </div>
-{:else}
-  <ScatterPlot
-    {...rest}
-    {series}
-    x_axis={{ label: `r (Å)`, range: [0, max_r], ...x_axis }}
-    y_axis={{ label: `g(r)`, range: [0, max_g * 1.05], ...y_axis }}
-    styles={{ show_lines: true, show_points: false }}
-    class="{rest.class ?? ``} {dragging ? `dragging` : ``}"
-    style={rest.style ?? `height: 400px;`}
-    ondragover={enable_drop ? handle_dragover : undefined}
-    ondragleave={enable_drop ? () => (dragging = false) : undefined}
-    ondrop={enable_drop ? handle_drop : undefined}
-  >
-    {#snippet user_content({ width, y_scale_fn, pad })}
-      {#if show_reference_line}
-        {@const y1 = y_scale_fn(1)}
-        {#if isFinite(y1)}
-          {@const [x1, x2] = [pad.l, width - pad.r]}
-          {@const [x, y] = [width - pad.r - 5, y1 - 5]}
-          <line {x1} {x2} {y1} y2={y1} stroke="gray" stroke-dasharray="4" opacity="0.5" />
-          <text {x} {y} text-anchor="end" fill="gray" font-size="0.8em">
-            g(r) = 1
-          </text>
-        {/if}
-      {/if}
-    {/snippet}
-
-    {@render children?.({ drag_dropped })}
-  </ScatterPlot>
-{/if}
-
-<style>
-  :global(.dragging) {
-    outline: 2px dashed #4e79a7;
-    outline-offset: 4px;
-  }
-  .empty-drop {
-    outline: 2px dashed #ccc;
-    border-radius: var(--border-radius, 3pt);
-    text-align: center;
-  }
-  .dropped-info {
-    padding: 0.5em;
-    margin-bottom: 0.5em;
-    background: #f0f0f0;
-    border-radius: 4px;
-  }
-  button {
-    margin-left: 1em;
-    padding: 0.25em 0.75em;
-    background: #e0e0e0;
-    border: 1px solid #ccc;
-    border-radius: 3px;
-    cursor: pointer;
-  }
-  button:hover {
-    background: #d0d0d0;
-  }
-</style>

package/dist/src/lib/rdf/calc-rdf.ts

@@ -1,167 +0,0 @@
-import type { Matrix3x3, Vec3 } from '$lib/math'
-import {
-  calc_lattice_params,
-  create_lattice_converters,
-  euclidean_dist,
-  pbc_dist,
-} from '$lib/math'
-import type { Crystal, Pbc } from '$lib/structure'
-import { make_supercell } from '$lib/structure/supercell'
-import type { RdfOptions, RdfPattern } from './index'
-
-const get_occu = (site: Crystal[`sites`][number], elem: string | undefined) =>
-  elem ? (site.species.find((spec) => spec.element === elem)?.occu ?? 0) : 1
-const has_species = (site: Crystal[`sites`][number], elem: string | undefined) =>
-  !elem || site.species.some((spec) => spec.element === elem)
-const sum_occu = (sites: Crystal[`sites`], elem: string | undefined) =>
-  sites.reduce((sum, site) => sum + get_occu(site, elem), 0)
-
-// Calculate radial distribution function
-export function calculate_rdf(structure: Crystal, options: RdfOptions = {}): RdfPattern {
-  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(`Crystal must have a lattice for RDF calculation`)
-  }
-
-  let lattice: Matrix3x3 = 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] as Vec3,
-        false, // Don't fold back to unit cell
-      )
-      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 = Array(n_bins).fill(0)
-
-  if (sites.length === 0) return { r, g_r }
-
-  // Get occupancy weight for a site-species pair (supports mixed occupancy)
-  const centers = sites.filter((site) => has_species(site, center_species))
-  const neighbors = sites.filter((site) => has_species(site, neighbor_species))
-
-  if (centers.length === 0 || neighbors.length === 0) {
-    const element_pair =
-      center_species && neighbor_species
-        ? ([center_species, neighbor_species] as [string, string])
-        : undefined
-    return { r, g_r, element_pair }
-  }
-
-  // Calculate distances and bin them with occupancy weighting
-  const use_pbc = pbc.some((flag) => flag)
-  const converters = use_pbc ? create_lattice_converters(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, converters, pbc)
-        : euclidean_dist(center.xyz, neighbor.xyz)
-
-      if (dist > 0 && dist < cutoff) {
-        // Weight by product of occupancies for the species pair
-        const weight = get_occu(center, center_species) * get_occu(neighbor, neighbor_species)
-        g_r[Math.min(Math.floor(dist / bin_size), n_bins - 1)] += weight
-      }
-    }
-  }
-
-  // Normalize using occupancy-weighted pair count (excludes self-interactions for same species)
-  const center_weight = sum_occu(centers, center_species)
-  const neighbor_weight = sum_occu(neighbors, neighbor_species)
-  const self_weight =
-    center_species === neighbor_species
-      ? centers.reduce((sum, site) => sum + get_occu(site, center_species) ** 2, 0)
-      : 0
-  const n_pairs = center_weight * neighbor_weight - self_weight
-
-  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] as [string, string])
-      : undefined
-  return { r, g_r, element_pair }
-}
-
-// Calculate RDF for all element pairs
-export function calculate_all_pair_rdfs(
-  structure: Crystal,
-  options: Omit<RdfOptions, `center_species` | `neighbor_species`> = {},
-): RdfPattern[] {
-  // Collect all unique elements across all species (supports mixed occupancy)
-  const elems = [
-    ...new Set(structure.sites.flatMap((site) => site.species.map((spec) => spec.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] as Vec3,
-          false, // Don't fold back to unit cell
-        )
-      }
-    }
-  }
-
-  // Pass auto_expand=false since we've already expanded, and pbc=false for expanded structure
-  const pbc = [false, false, false] as Pbc
-  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/src/lib/rdf/index.ts

@@ -1,27 +0,0 @@
-import type { Pbc } from '$lib/structure'
-
-export * 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
-  legend_group?: string // Group name for legend grouping (e.g. structure name)
-}
-
-export interface RdfOptions {
-  center_species?: string
-  neighbor_species?: string
-  cutoff?: number
-  n_bins?: number
-  pbc?: Pbc
-  auto_expand?: boolean
-  expansion_factor?: number
-}

package/dist/src/lib/sanitize.ts

@@ -1,126 +0,0 @@
-import DOMPurify from 'dompurify'
-import { format_formula_html } from './phase-diagram/utils'
-
-const SAFE_TAGS = [`a`, `b`, `i`, `em`, `strong`, `sub`, `sup`, `br`, `span`, `code`, `small`]
-const SAFE_ATTRS = [`style`, `class`, `title`, `href`, `target`, `rel`]
-// only allow safe CSS properties for text formatting
-const SAFE_STYLE_RE =
-  /^\s*(color|font-weight|font-style|font-size|text-decoration|vertical-align)\s*:/
-
-// Add a token to a space-separated string if not already present
-const ensure_token = (value: string, token: string): string => {
-  const tokens = new Set(value.split(/\s+/).filter(Boolean))
-  tokens.add(token)
-  return [...tokens].join(` `)
-}
-
-// undefined = not yet checked, null = no DOM available, instance = ready
-let purify: ReturnType<typeof DOMPurify> | null | undefined
-
-function get_purify(): ReturnType<typeof DOMPurify> | null {
-  if (purify !== undefined) return purify
-  if (typeof globalThis.window === `undefined`) return (purify = null)
-  const instance = DOMPurify()
-  if (typeof instance.sanitize !== `function`) {
-    purify = null
-    return null
-  }
-  purify = instance
-  instance.addHook(`uponSanitizeAttribute`, (node, data) => {
-    if (data.attrName === `style`) {
-      const rules = data.attrValue.split(`;`).filter((rule) => SAFE_STYLE_RE.test(rule))
-      if (rules.length === 0) data.keepAttr = false
-      else data.attrValue = rules.join(`;`)
-    }
-    // force rel="noopener" on links to prevent window.opener attacks
-    if (data.attrName === `href`) {
-      node.setAttribute(`rel`, ensure_token(node.getAttribute(`rel`) ?? ``, `noopener`))
-    }
-    if (data.attrName === `rel`) {
-      data.attrValue = ensure_token(data.attrValue, `noopener`)
-    }
-  })
-  return instance
-}
-
-// Wrap in <svg>, sanitize with allowlist, then unwrap. Required because DOMPurify
-// needs the <svg> parent to parse children in the SVG namespace.
-function sanitize_svg_content(
-  html: string,
-  allowed_tags: string[],
-  allowed_attrs: string[],
-): string {
-  const dp = get_purify()
-  if (!dp) return html
-  const wrapped = dp.sanitize(`<svg>${html}</svg>`, {
-    ALLOWED_TAGS: [...allowed_tags, `svg`],
-    ALLOWED_ATTR: allowed_attrs,
-  })
-  const open_end = wrapped.indexOf(`>`)
-  const close_start = wrapped.lastIndexOf(`</svg>`)
-  if (open_end < 0 || close_start < 0) return wrapped
-  return wrapped.slice(open_end + 1, close_start)
-}
-
-const stringify_html_input = (html: unknown): string => {
-  if (html == null) return ``
-  if (typeof html === `string`) return html
-  if (typeof html === `number`) return Number.isNaN(html) ? `NaN` : `${html}`
-  if (typeof html === `boolean` || typeof html === `bigint`) return `${html}`
-  if (typeof html !== `object`) return ``
-  try {
-    return JSON.stringify(html) ?? ``
-  } catch {
-    return ``
-  }
-}
-
-// Sanitize HTML string, allowing only safe formatting tags and links.
-// Two-pass: happy-dom promotes dangerous children when a non-allowed parent is
-// stripped (e.g. <div><script>…</script></div> → <script>…</script>). The first
-// pass explicitly removes dangerous tags so they can't survive promotion.
-export function sanitize_html(html: unknown): string {
-  const str = stringify_html_input(html)
-  const dp = get_purify()
-  if (!dp) return str
-  // oxfmt-ignore
-  const safe = dp.sanitize(str, { ADD_ATTR: [`target`], FORBID_TAGS: [
-    `script`, `style`, `iframe`, `object`, `embed`, `form`, `input`, `textarea`,
-    `select`, `button`, `meta`, `link`, `base`, `template`, `noscript`,
-  ] })
-  return dp.sanitize(safe, { ALLOWED_TAGS: SAFE_TAGS, ALLOWED_ATTR: SAFE_ATTRS })
-}
-
-export const compact_formula = (formula: string): string => formula.replaceAll(/\s+/g, ``)
-
-// Sanitize a chemical formula with optional subscript formatting
-export const sanitize_formula = (formula: string, use_subscripts = true): string =>
-  sanitize_html(format_formula_html(formula, use_subscripts))
-
-export const sanitize_compact_formula = (formula: string, use_subscripts = true): string =>
-  sanitize_formula(compact_formula(formula), use_subscripts)
-
-const SVG_TEXT_TAGS = [`tspan`, `title`]
-// oxfmt-ignore
-const SVG_TEXT_ATTRS = [`dx`, `dy`, `x`, `y`, `fill`, `font-size`, `font-weight`, `baseline-shift`]
-
-// Sanitize HTML intended for SVG text contexts (tspan, title)
-export const sanitize_svg = (html: string): string =>
-  sanitize_svg_content(html, SVG_TEXT_TAGS, SVG_TEXT_ATTRS)
-
-// oxfmt-ignore
-const SVG_ICON_TAGS = [
-  `path`, `circle`, `rect`, `line`, `polyline`, `polygon`, `g`, `ellipse`,
-  `clipPath`, `defs`, `mask`, `use`, `title`,
-]
-// oxfmt-ignore
-const SVG_ICON_ATTRS = [
-  `d`, `fill`, `stroke`, `stroke-width`, `stroke-linecap`, `stroke-linejoin`,
-  `cx`, `cy`, `r`, `rx`, `ry`, `x`, `y`, `x1`, `y1`, `x2`, `y2`,
-  `width`, `height`, `viewBox`, `points`, `transform`, `opacity`,
-  `clip-path`, `clip-rule`, `fill-rule`, `id`, `class`,
-]
-
-// Sanitize inline SVG markup (path, circle, rect, etc.) for icon rendering
-export const sanitize_icon_svg = (html: string): string =>
-  sanitize_svg_content(html, SVG_ICON_TAGS, SVG_ICON_ATTRS)