matterviz 0.3.4 → 0.3.6

package/dist/src/lib/constants.ts

@@ -0,0 +1,134 @@
+// Shared keyword constants for file type detection across the codebase
+
+// compression formats and their file extensions
+export const COMPRESSION_FORMATS = {
+  gzip: [`.gz`, `.gzip`] as const,
+  deflate: [`.deflate`] as const,
+  'deflate-raw': [`.z`] as const,
+  zip: [`.zip`] as const, // Browser DecompressionStream doesn't support ZIP
+  xz: [`.xz`] as const, // Browser DecompressionStream doesn't support XZ
+  bz2: [`.bz2`] as const, // Browser DecompressionStream doesn't support BZ2
+} as const satisfies Record<string, readonly string[]>
+
+// All detectable compression extensions
+export const COMPRESSION_EXTENSIONS = Object.freeze(
+  Object.values(COMPRESSION_FORMATS).flat(),
+) as readonly string[]
+
+// Keywords that indicate a file is likely a trajectory file
+export const TRAJ_KEYWORDS = Object.freeze([
+  `trajectory`,
+  `traj`,
+  `relax`,
+  `npt`,
+  `nvt`,
+  `nve`,
+  `qha`,
+  `md`,
+  `dynamics`,
+  `simulation`,
+])
+
+// Keywords that indicate a file is likely a structure file
+export const STRUCT_KEYWORDS = Object.freeze([
+  `structure`,
+  `phono`,
+  `vasp`,
+  `crystal`,
+  `material`,
+  `lattice`,
+  `geometry`,
+  `unit_cell`,
+  `unitcell`,
+  `atoms`,
+  `sites`,
+  `data`,
+  `phono3py`,
+  `phonopy`,
+])
+
+// More restrictive keywords for JSON/YAML files (excludes generic terms like "data")
+export const STRUCT_KEYWORDS_STRICT = Object.freeze([
+  `structure`,
+  `phono`,
+  `vasp`,
+  `crystal`,
+  `material`,
+  `lattice`,
+  `geometry`,
+  `unit_cell`,
+  `unitcell`,
+  `atoms`,
+  `sites`,
+  `phono3py`,
+  `phonopy`,
+])
+
+// Regex patterns for keyword matching
+export const TRAJ_KEYWORDS_REGEX = new RegExp(
+  `(^|[-_.])(${TRAJ_KEYWORDS.join(`|`)})([-_.]|$)`,
+  `i`,
+)
+
+export const STRUCT_KEYWORDS_REGEX = new RegExp(`(${STRUCT_KEYWORDS.join(`|`)})`, `i`)
+
+export const STRUCT_KEYWORDS_STRICT_REGEX = new RegExp(
+  `(${STRUCT_KEYWORDS_STRICT.join(`|`)})`,
+  `i`,
+)
+
+export const TRAJ_KEYWORDS_SIMPLE_REGEX = new RegExp(`(${TRAJ_KEYWORDS.join(`|`)})`, `i`)
+
+// File extensions for different file types
+export const TRAJ_EXTENSIONS = Object.freeze([`.traj`, `.xtc`, `.lammpstrj`])
+export const TRAJ_EXTENSIONS_REGEX = new RegExp(
+  `\\.(${TRAJ_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
+  `i`,
+)
+export const STRUCTURE_EXTENSIONS = Object.freeze([
+  `.cif`,
+  `.mcif`,
+  `.poscar`,
+  `.vasp`,
+  `.cube`,
+  `.lmp`,
+  `.data`,
+  `.dump`,
+  `.pdb`,
+  `.mol`,
+  `.mol2`,
+  `.sdf`,
+  `.mmcif`,
+])
+export const STRUCTURE_EXTENSIONS_REGEX = new RegExp(
+  `\\.(${STRUCTURE_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
+  `i`,
+)
+export const TRAJ_FALLBACK_EXTENSIONS = Object.freeze([
+  `.dat`,
+  `.data`,
+  `.log`,
+  `.out`,
+  `.json`,
+])
+export const TRAJ_FALLBACK_EXTENSIONS_REGEX = new RegExp(
+  `\\.(${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)$/i
+export const XYZ_EXTXYZ_REGEX = /\.(xyz|extxyz)$/i
+
+// Compression extensions regex (shared across files)
+export const COMPRESSION_EXTENSIONS_REGEX = new RegExp(
+  `\\.(${COMPRESSION_EXTENSIONS.map((ext) => ext.slice(1)).join(`|`)})$`,
+  `i`,
+)

package/dist/src/lib/controls.ts

@@ -0,0 +1,42 @@
+// Controls visibility configuration for visualization components
+// Manages visibility of control buttons in Structure, Trajectory, BrillouinZone
+
+export type ControlsVisibility = `always` | `hover` | `never`
+
+export type ShowControlsConfig = {
+  mode?: ControlsVisibility
+  hidden?: string[]
+  style?: string
+}
+
+// Prop type: boolean shorthand, mode string, or full config
+export type ShowControlsProp = ControlsVisibility | ShowControlsConfig | boolean
+
+// Normalize show_controls prop into consistent config with helper methods
+export function normalize_show_controls(prop: ShowControlsProp | undefined) {
+  // Extract mode, hidden, style from various prop forms
+  let mode: ControlsVisibility = `hover`
+  let hidden_arr: string[] | undefined
+  let style: string | undefined
+
+  if (typeof prop === `boolean`) {
+    mode = prop ? `always` : `never`
+  } else if (typeof prop === `string`) {
+    mode = prop
+  } else if (prop) {
+    mode = prop.mode ?? `hover`
+    hidden_arr = prop.hidden
+    style = prop.style
+  }
+
+  const hidden = new Set(hidden_arr)
+  return {
+    mode,
+    hidden,
+    style,
+    // Helper: check if a control should be visible
+    visible: (name: string) => !hidden.has(name),
+    // CSS class for visibility mode
+    class: mode === `never` ? `` : `${mode}-visible`,
+  }
+}

package/dist/src/lib/convex-hull/ConvexHull.svelte

@@ -0,0 +1,157 @@
+<script lang="ts">
+  import { extract_formula_elements } from '$lib/composition/parse'
+  import type { AxisConfig } from '$lib/plot'
+  import { DEFAULTS } from '$lib/settings'
+  import type { Component } from 'svelte'
+  import { SvelteSet } from 'svelte/reactivity'
+  import ConvexHull2D from './ConvexHull2D.svelte'
+  import ConvexHull3D from './ConvexHull3D.svelte'
+  import ConvexHull4D from './ConvexHull4D.svelte'
+  import type { BaseConvexHullProps, Hull3DProps } from './index'
+  import type { GasSpecies, GasThermodynamicsConfig } from './types'
+
+  // Union type combining all possible props from 2D, 3D, and 4D components
+  // each specific component will only use its relevant props from this super set
+  type ConvexHullProps = BaseConvexHullProps & Hull3DProps & {
+    x_axis?: AxisConfig
+    y_axis?: AxisConfig
+    // Gas thermodynamics config - enables atmosphere-controlled phase diagrams
+    gas_config?: GasThermodynamicsConfig
+    // Gas pressure binding - enables two-way binding for atmosphere control
+    gas_pressures?: Partial<Record<GasSpecies, number>>
+  }
+
+  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: hull_face_opacity_prop = $bindable(
+      undefined as number | 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
+  }: ConvexHullProps = $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(
+    hull_entries: { composition: Record<string, number> }[],
+  ): string[] {
+    const elements = new SvelteSet<string>()
+    for (const entry of hull_entries) {
+      for (const key of Object.keys(entry.composition)) {
+        // Extract valid element symbols, stripping oxidation states
+        for (const elem of extract_formula_elements(key, { unique: false })) {
+          elements.add(elem)
+        }
+      }
+    }
+    return Array.from(elements).toSorted()
+  }
+
+  // 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)
+  const ConvexHullComponent = $derived(
+    { 2: ConvexHull2D, 3: ConvexHull3D, 4: ConvexHull4D }[element_count] ??
+      null,
+  ) as Component<ConvexHullProps> | null
+</script>
+
+{#if ConvexHullComponent}
+  <ConvexHullComponent
+    {entries}
+    {...rest}
+    bind:fullscreen
+    bind:wrapper
+    bind:show_stable
+    bind:show_unstable
+    bind:show_hull_faces
+    bind:hull_face_opacity
+    bind:color_mode
+    bind:color_scale
+    bind:info_pane_open
+    bind:legend_pane_open
+    bind:max_hull_dist_show_phases
+    bind:max_hull_dist_show_labels
+    bind:show_stable_labels
+    bind:show_unstable_labels
+    bind:energy_source_mode
+    bind:phase_stats
+    bind:display
+    bind:stable_entries
+    bind:unstable_entries
+    bind:highlighted_entries
+    bind:selected_entry
+    bind:temperature
+    bind:gas_pressures
+  />
+{:else}
+  <!-- Error state for unsupported dimensionalities -->
+  <div class="convex-hull-error">
+    <div
+      style="text-align: center; padding: 2em; color: var(--convex-hull-text-color, #666)"
+    >
+      <h3 style="margin: 0 0 1em 0">Unsupported Chemical System</h3>
+      <p style="margin: 0">
+        Convex hulls require 2, 3, or 4 elements. Found {element_count} element{
+          element_count === 1 ? `` : `s`
+        }:
+      </p>
+      <p style="margin: 0.5em 0 0 0; font-weight: bold">
+        {elements.join(`, `)}
+      </p>
+    </div>
+  </div>
+{/if}
+
+<style>
+  .convex-hull-error {
+    display: flex;
+    align-items: center;
+    justify-content: center;
+    box-sizing: border-box;
+    height: var(--convex-hull-height, 500px);
+    border: 1px solid var(--convex-hull-border-color, #ccc);
+    border-radius: var(--border-radius, 3pt);
+    background: var(--convex-hull-bg, transparent);
+  }
+</style>