matterviz 0.3.6 → 0.3.7

package/dist/src/lib/trajectory/TrajectoryInfoPane.svelte

@@ -1,313 +0,0 @@
-<script lang="ts">
-  import type { InfoItem } from '$lib/layout'
-  import InfoPaneCards from '$lib/overlays/InfoPaneCards.svelte'
-  import { format_num } from '$lib/labels'
-  import DraggablePane from '$lib/overlays/DraggablePane.svelte'
-  import { get_electro_neg_formula } from '$lib/composition'
-  import { SETTINGS_CONFIG } from '$lib/settings'
-  import type { AnyStructure } from '$lib/structure'
-  import type { ComponentProps } from 'svelte'
-  import type { TrajectoryType } from './index'
-
-  let {
-    trajectory,
-    current_step_idx,
-    current_filename,
-    current_file_path,
-    file_size,
-    file_object,
-    pane_open = $bindable(false),
-    toggle_props,
-    pane_props,
-    ...rest
-  }: Omit<ComponentProps<typeof DraggablePane>, `children`> & {
-    trajectory: TrajectoryType
-    current_step_idx: number
-    current_filename?: string | null
-    current_file_path?: string | null
-    file_size?: number | null
-    file_object?: File | null
-    pane_open?: boolean
-    toggle_props?: ComponentProps<typeof DraggablePane>[`toggle_props`]
-    pane_props?: ComponentProps<typeof DraggablePane>[`pane_props`]
-  } = $props()
-
-  // Helper functions
-  const format_size = (bytes: number) =>
-    bytes > 1024 * 1024
-      ? `${format_num(bytes / (1024 * 1024), `.2~f`)} MB`
-      : `${format_num(bytes / 1024, `.2~f`)} KB`
-
-  const is_valid_number = (val: unknown): val is number =>
-    typeof val === `number` && isFinite(val)
-
-  const extract_numeric_array = (frames: typeof trajectory.frames, prop: string) =>
-    frames.map((frame) => frame.metadata?.[prop]).filter(is_valid_number)
-
-  const format_range = (values: number[], unit = ``, decimals = `.2~f`) => {
-    if (!values.length) return null
-    if (values.length === 1) {
-      return `${format_num(values[0], decimals)} ${unit}`.trim()
-    }
-    const [min, max] = [Math.min(...values), Math.max(...values)]
-    return `${format_num(min, decimals)} - ${format_num(max, decimals)} ${unit}`
-      .trim()
-  }
-
-  const safe_item = (
-    label: string,
-    value: string | null,
-    key?: string,
-    tooltip?: string,
-  ): InfoItem | null => value ? { label, value, key, tooltip } : null
-
-  const is_info_item = (item: unknown): item is InfoItem => Boolean(item)
-
-  const safe_formula = (structure: AnyStructure) => {
-    try {
-      return get_electro_neg_formula(structure)
-    } catch {
-      return null
-    }
-  }
-
-  // Get trajectory info organized by sections
-  let info_pane_data = $derived.by(() => {
-    if (
-      (!trajectory?.frames?.length && !trajectory?.total_frames) ||
-      current_step_idx < 0 ||
-      current_step_idx >= (trajectory.total_frames ?? trajectory.frames?.length ?? 0)
-    ) return []
-
-    // For indexed trajectories, we might not have the current frame loaded
-    const current_frame = trajectory.frames?.[current_step_idx]
-    const total_frames = trajectory.total_frames ?? trajectory.frames?.length ?? 0
-
-    const sections: { title: string; items: InfoItem[] }[] = []
-
-    // File info section
-    const file_items = [
-      current_filename &&
-      safe_item(
-        `Name`,
-        current_filename,
-        `file-name`,
-        current_file_path || undefined,
-      ),
-      file_size && file_size > 0 &&
-      safe_item(`File Size`, format_size(file_size), `file-size`),
-      file_object?.lastModified &&
-      safe_item(
-        `Modified`,
-        new Date(file_object.lastModified).toLocaleString(),
-        `file-modified`,
-      ),
-      trajectory.metadata?.source_format &&
-      safe_item(`Format`, String(trajectory.metadata.source_format), `file-format`),
-    ].filter(is_info_item)
-
-    if (file_items.length > 0) {
-      sections.push({ title: `File`, items: file_items })
-    }
-
-    // Trajectory info section (always show this)
-    const traj_items = [
-      safe_item(
-        `Total Frames`,
-        `${format_num(total_frames, `.3~s`)} (current: ${
-          format_num(current_step_idx + 1, `.3~s`)
-        })`,
-        `total-frames`,
-      ),
-      trajectory.is_indexed &&
-      safe_item(
-        `Indexed`,
-        `Yes`,
-        `indexed-mode`,
-        SETTINGS_CONFIG.trajectory.use_indexing.description,
-      ),
-      trajectory.indexed_frames &&
-      safe_item(
-        `Index Points`,
-        `${trajectory.indexed_frames.length}`,
-        `index-points`,
-        `Number of frames indexed for fast seeking`,
-      ),
-      trajectory.plot_metadata &&
-      safe_item(
-        `Plot Metadata`,
-        `${trajectory.plot_metadata.length} frames`,
-        `plot-metadata`,
-        `Pre-extracted metadata for plotting`,
-      ),
-    ].filter(is_info_item)
-
-    if (traj_items.length > 0) {
-      sections.push({ title: `Trajectory`, items: traj_items })
-    }
-
-    // Structure info section (only if we have the current frame)
-    if (current_frame?.structure?.sites) {
-      const { structure } = current_frame
-      const lattice = `lattice` in structure ? structure.lattice : null
-      const { volume, a, b, c, alpha, beta, gamma } = lattice || {}
-      const formula = safe_formula(structure)
-
-      const structure_items = [
-        safe_item(`Atoms`, `${structure.sites.length}`, `atoms`),
-        formula && safe_item(`Formula`, String(formula), `formula`),
-        is_valid_number(volume) && volume > 0 &&
-        safe_item(`Volume`, `${format_num(volume, `.3~s`)} ų`, `volume`),
-        is_valid_number(volume) && volume > 0 && structure.sites.length > 0 &&
-        safe_item(
-          `Density`,
-          `${format_num(structure.sites.length / volume, `.4~s`)} atoms/ų`,
-          `density`,
-        ),
-        [a, b, c].every(is_valid_number) &&
-        safe_item(
-          `Cell Lengths`,
-          `${format_num(a as number, `.3~f`)}, ${format_num(b as number, `.3~f`)}, ${
-            format_num(c as number, `.3~f`)
-          } Å`,
-          `cell-lengths`,
-        ),
-        [alpha, beta, gamma].every(is_valid_number) &&
-        safe_item(
-          `Cell Angles`,
-          `${format_num(alpha as number, `.2~f`)}°, ${
-            format_num(beta as number, `.2~f`)
-          }°, ${format_num(gamma as number, `.2~f`)}°`,
-          `cell-angles`,
-        ),
-      ].filter(is_info_item)
-
-      if (structure_items.length > 0) {
-        sections.push({ title: `Structure`, items: structure_items })
-      }
-    } else if (trajectory.is_indexed) {
-      // For indexed trajectories, show a note that frame data is loaded on demand
-      const structure_items = [
-        safe_item(
-          `Frame Loading`,
-          `On-demand`,
-          `frame-loading`,
-          `Structure data loaded when frame is accessed`,
-        ),
-      ].filter(is_info_item)
-
-      if (structure_items.length > 0) {
-        sections.push({ title: `Structure`, items: structure_items })
-      }
-    }
-
-    // Energy section (only for regular trajectories with multiple frames)
-    if (!trajectory.is_indexed && trajectory.frames.length > 1) {
-      const energies = extract_numeric_array(trajectory.frames, `energy`)
-      if (energies.length > 1) {
-        const current_energy = current_frame?.metadata?.energy
-        const energy_range = format_range(energies, `eV`, `.3~s`)
-
-        const energy_items = [
-          is_valid_number(current_energy) &&
-          safe_item(
-            `Current Energy`,
-            `${format_num(current_energy, `.3~s`)} eV`,
-            `energy-current`,
-          ),
-          energy_range && safe_item(`Energy Range`, energy_range, `energy-range`),
-        ].filter(is_info_item)
-
-        if (energy_items.length > 0) {
-          sections.push({ title: `Energy`, items: energy_items })
-        }
-      }
-    }
-
-    // Forces section (only for regular trajectories with multiple frames)
-    if (!trajectory.is_indexed && trajectory.frames.length > 1) {
-      const forces = extract_numeric_array(trajectory.frames, `force_max`)
-      if (forces.length > 1) {
-        const current_force = current_frame?.metadata?.force_max
-        const force_range = format_range(forces, `eV/Å`, `.3~s`)
-
-        const force_items = [
-          is_valid_number(current_force) &&
-          safe_item(
-            `Max Force`,
-            `${format_num(current_force, `.3~s`)} eV/Å`,
-            `force-current`,
-          ),
-          force_range && safe_item(`Force Range`, force_range, `force-range`),
-        ].filter(is_info_item)
-
-        if (force_items.length > 0) {
-          sections.push({ title: `Forces`, items: force_items })
-        }
-      }
-    }
-
-    // Volume change section (only for regular trajectories)
-    if (
-      !trajectory.is_indexed && current_frame?.structure &&
-      trajectory.frames.length > 1
-    ) {
-      const lattice = `lattice` in current_frame.structure
-        ? current_frame.structure.lattice
-        : null
-      if (lattice) {
-        const volumes = trajectory.frames.map((
-          { structure },
-        ) => (`lattice` in structure && structure.lattice?.volume))
-          .filter(is_valid_number)
-          .filter((volume) => volume > 0)
-
-        if (volumes.length > 1) {
-          const vol_change = (Math.max(...volumes) - Math.min(...volumes)) /
-            Math.min(...volumes)
-          if (Math.abs(vol_change) > 0.1 && is_valid_number(vol_change)) {
-            const vol_items = [safe_item(
-              `Volume Change`,
-              `${format_num(vol_change, `.2~%`)}`,
-              `vol-change`,
-            )].filter(is_info_item)
-
-            if (vol_items.length > 0) {
-              sections.push({ title: `Volume`, items: vol_items })
-            }
-          }
-        }
-      }
-    }
-    return sections
-  })
-
-  let info_cards = $derived(
-    info_pane_data.map(({ title, items }) => ({ title, rows: items })),
-  )
-  let n_info_items = $derived(
-    info_pane_data.reduce((count, { items }) => count + items.length, 0),
-  )
-</script>
-
-<DraggablePane
-  bind:show={pane_open}
-  max_width="24em"
-  toggle_props={{
-    title: pane_open ? `` : `Trajectory info`,
-    ...toggle_props,
-    class: `trajectory-info-toggle ${toggle_props?.class ?? ``}`,
-  }}
-  open_icon="Cross"
-  closed_icon="Info"
-  pane_props={{ ...pane_props, class: `trajectory-info-pane ${pane_props?.class ?? ``}` }}
-  {...rest}
->
-  <h4 style="margin-top: 0">Trajectory Info</h4>
-  <InfoPaneCards
-    cards={info_cards}
-    filter_placeholder="Filter trajectory info"
-    empty_label="trajectory info"
-    show_filter={n_info_items > 5}
-  />
-</DraggablePane>

package/dist/src/lib/trajectory/constants.ts

@@ -1,7 +0,0 @@
-// Constants for trajectory parsing and large file handling
-export const MAX_SAFE_STRING_LENGTH = 0x1fffffe8 * 0.5 // 50% of JS max string length as safety
-export const MAX_METADATA_SIZE = 50 * 1024 * 1024 // 50MB limit for metadata
-export const LARGE_FILE_THRESHOLD = 400 * 1024 * 1024 // 400MB
-export const INDEX_SAMPLE_RATE = 100 // Default sample rate for frame indexing
-export const MAX_BIN_FILE_SIZE = 100 * 1024 * 1024 // 100MB default for ArrayBuffer files
-export const MAX_TEXT_FILE_SIZE = 50 * 1024 * 1024 // 50MB default for string files

package/dist/src/lib/trajectory/extract.ts

@@ -1,196 +0,0 @@
-// Data extraction functions for trajectory analysis and plotting
-import { get_density } from '$lib/structure/index'
-import type { TrajectoryDataExtractor, TrajectoryFrame, TrajectoryType } from './index'
-
-// Common data extractor that extracts energy and structural properties
-export const energy_data_extractor: TrajectoryDataExtractor = (
-  frame: TrajectoryFrame,
-): Record<string, number> => {
-  const data: Record<string, number> = {
-    Step: frame.step,
-  }
-
-  if (frame.metadata) {
-    // Extract energy-related properties
-    const energy_fields = [
-      `energy`,
-      `energy_per_atom`,
-      `potential_energy`,
-      `kinetic_energy`,
-      `total_energy`,
-    ]
-
-    for (const field of energy_fields) {
-      if (field in frame.metadata && typeof frame.metadata[field] === `number`) {
-        data[field] = frame.metadata[field]
-      }
-    }
-  }
-
-  return data
-}
-
-// Data extractor for forces and stresses
-export const force_stress_data_extractor: TrajectoryDataExtractor = (
-  frame: TrajectoryFrame,
-): Record<string, number> => {
-  const data: Record<string, number> = {
-    Step: frame.step,
-  }
-
-  if (frame.metadata) {
-    // Calculate force properties from forces array if available (preferred)
-    if (frame.metadata.forces && Array.isArray(frame.metadata.forces)) {
-      const forces = frame.metadata.forces as number[][]
-      if (forces.length > 0) {
-        const force_magnitudes = forces.map((force) => Math.hypot(...force))
-        data.force_max = Math.max(...force_magnitudes)
-        // Calculate RMS (root mean square) of force magnitudes
-        data.force_norm = Math.sqrt(
-          force_magnitudes.reduce((sum, f) => sum + f ** 2, 0) / force_magnitudes.length,
-        )
-      }
-    } else {
-      // Fallback to metadata values if forces array not available
-      if (frame.metadata.force_max && typeof frame.metadata.force_max === `number`) {
-        data.force_max = frame.metadata.force_max
-      }
-      // Prefer force_norm if available, fall back to force_rms
-      if (frame.metadata.force_norm && typeof frame.metadata.force_norm === `number`) {
-        data.force_norm = frame.metadata.force_norm
-      } else if (frame.metadata.force_rms && typeof frame.metadata.force_rms === `number`) {
-        data.force_norm = frame.metadata.force_rms // Use force_rms as fallback
-      }
-    }
-
-    // Extract other stress and pressure properties (no duplicates expected)
-    const other_stress_fields = [`stress_max`, `stress_frobenius`, `stress_trace`, `pressure`]
-    for (const field of other_stress_fields) {
-      if (field in frame.metadata && typeof frame.metadata[field] === `number`) {
-        data[field] = frame.metadata[field]
-      }
-    }
-  }
-
-  return data
-}
-
-// Data extractor for structural properties
-export const structural_data_extractor: TrajectoryDataExtractor = (
-  frame: TrajectoryFrame,
-): Record<string, number> => {
-  const data: Record<string, number> = {
-    Step: frame.step,
-  }
-
-  // Extract lattice properties (preferred source for volume)
-  if (`lattice` in frame.structure) {
-    const lattice = frame.structure.lattice
-    data.volume = lattice.volume // Use consistent lowercase naming
-    data.a = lattice.a
-    data.b = lattice.b
-    data.c = lattice.c
-    data.alpha = lattice.alpha
-    data.beta = lattice.beta
-    data.gamma = lattice.gamma
-  }
-
-  if (frame.metadata) {
-    // Extract other structural properties, avoiding volume duplicate
-    const structural_fields = [`temperature`]
-
-    for (const field of structural_fields) {
-      if (field in frame.metadata && typeof frame.metadata[field] === `number`)
-        data[field] = frame.metadata[field]
-    }
-
-    // Handle density separately - prefer metadata, but calculate if not available
-    if (frame.metadata.density && typeof frame.metadata.density === `number`) {
-      data.density = frame.metadata.density
-    } else if (`lattice` in frame.structure) {
-      try {
-        data.density = get_density(frame.structure)
-      } catch (error) {
-        console.warn(`Failed to calculate density for frame ${frame.step}:`, error)
-      }
-    }
-
-    // Only use metadata volume if lattice volume is not available
-    if (!data.volume && frame.metadata.volume && typeof frame.metadata.volume === `number`) {
-      data.volume = frame.metadata.volume
-    }
-
-    // Note: pressure is handled by force_stress_data_extractor to avoid duplication
-  } else if (`lattice` in frame.structure) {
-    // Calculate density even when no metadata is available
-    try {
-      data.density = get_density(frame.structure)
-    } catch (error) {
-      console.warn(`Failed to calculate density for frame ${frame.step}:`, error)
-    }
-  }
-
-  return data
-}
-
-// Helper function to check if a property varies across trajectory frames
-function property_varies(
-  trajectory: TrajectoryType,
-  property_key: string,
-  tolerance = 1e-10,
-): boolean {
-  if (trajectory.frames.length <= 1) return false
-
-  const values: number[] = []
-  for (const frame of trajectory.frames) {
-    // Check both direct structure properties and metadata
-    let value: number | undefined
-
-    if (`lattice` in frame.structure) {
-      const lattice_value = (frame.structure.lattice as Record<string, unknown>)[property_key]
-      if (typeof lattice_value === `number`) value = lattice_value
-    }
-
-    if (value === undefined && frame.metadata && property_key in frame.metadata) {
-      const metadata_value = frame.metadata[property_key]
-      if (typeof metadata_value === `number`) {
-        value = metadata_value
-      }
-    }
-
-    if (value !== undefined) {
-      values.push(value)
-    }
-  }
-
-  if (values.length <= 1) return false
-
-  const first_value = values[0]
-  return values.some((value) => Math.abs(value - first_value) > tolerance)
-}
-
-// Combined data extractor that extracts all common properties
-export const full_data_extractor: TrajectoryDataExtractor = (
-  frame: TrajectoryFrame,
-  trajectory: TrajectoryType,
-): Record<string, number> => {
-  const base_data = {
-    ...energy_data_extractor(frame, trajectory),
-    ...force_stress_data_extractor(frame, trajectory),
-    ...structural_data_extractor(frame, trajectory),
-  }
-
-  // Check which lattice parameters vary
-  const lattice_params = [`a`, `b`, `c`, `alpha`, `beta`, `gamma`]
-  const result = { ...base_data }
-
-  // Add metadata to specify which properties don't vary
-  for (const param of lattice_params) {
-    if (!property_varies(trajectory, param)) {
-      // Mark individual lattice parameters as constant
-      result[`constant_${param}`] = 1
-    }
-  }
-
-  return result
-}

package/dist/src/lib/trajectory/format-detect.ts

@@ -1,96 +0,0 @@
-// Format detection for trajectory files
-import {
-  COMPRESSION_EXTENSIONS_REGEX,
-  CONFIG_DIRS_REGEX,
-  MD_SIM_EXCLUDE_REGEX,
-  TRAJ_EXTENSIONS_REGEX,
-  TRAJ_FALLBACK_EXTENSIONS_REGEX,
-  TRAJ_KEYWORDS_SIMPLE_REGEX,
-  XDATCAR_REGEX,
-} from '$lib/constants'
-import { count_xyz_frames } from './helpers'
-
-export function strip_compression_extensions(filename: string): string {
-  let base_name = filename.toLowerCase()
-  while (COMPRESSION_EXTENSIONS_REGEX.test(base_name)) {
-    base_name = base_name.replace(COMPRESSION_EXTENSIONS_REGEX, ``)
-  }
-  return base_name
-}
-
-// Unified format detection
-export const FORMAT_PATTERNS = {
-  ase: (data: unknown, filename?: string) => {
-    const base_name = filename ? strip_compression_extensions(filename) : undefined
-    if (!base_name?.endsWith(`.traj`) || !(data instanceof ArrayBuffer)) {
-      return false
-    }
-    const view = new Uint8Array(data.slice(0, 24))
-    return [0x2d, 0x20, 0x6f, 0x66, 0x20, 0x55, 0x6c, 0x6d].every(
-      (byte, idx) => view[idx] === byte,
-    )
-  },
-
-  hdf5: (data: unknown, filename?: string) => {
-    const base_name = filename ? strip_compression_extensions(filename) : undefined
-    const has_ext = base_name?.match(/\.(h5|hdf5)$/)
-    if (!has_ext || !(data instanceof ArrayBuffer) || data.byteLength < 8) return false
-    const signature = new Uint8Array(data.slice(0, 8))
-    return [0x89, 0x48, 0x44, 0x46, 0x0d, 0x0a, 0x1a, 0x0a].every(
-      (b, idx) => signature[idx] === b,
-    )
-  },
-
-  vasp: (data: string, filename?: string) => {
-    const basename = filename?.toLowerCase().split(`/`).pop() || ``
-    if (basename === `xdatcar` || basename.startsWith(`xdatcar`)) return true
-    const lines = data.trim().split(/\r?\n/)
-    return (
-      lines.length >= 10 &&
-      lines.some((line) => line.includes(`Direct configuration=`)) &&
-      !isNaN(parseFloat(lines[1])) &&
-      lines.slice(2, 5).every((line) => line.trim().split(/\s+/).length === 3)
-    )
-  },
-
-  xyz_multi: (data: string, filename?: string) => {
-    const base = filename ? strip_compression_extensions(filename) : ``
-    if (!/\.(xyz|extxyz)$/.test(base)) return false
-    return count_xyz_frames(data) >= 2
-  },
-
-  lammpstrj: (data: string, filename?: string) => {
-    const base = filename ? strip_compression_extensions(filename) : ``
-    if (!base.endsWith(`.lammpstrj`)) return false
-    return data.includes(`ITEM: TIMESTEP`) && data.includes(`ITEM: ATOMS`)
-  },
-} as const
-
-// Check if file is a trajectory (supports both filename-only and content-based detection)
-export function is_trajectory_file(filename: string, content?: string): boolean {
-  if (CONFIG_DIRS_REGEX.test(filename)) return false
-  const base_name = strip_compression_extensions(filename)
-
-  // For xyz/extxyz files, use content-based detection if available
-  if (/\.(xyz|extxyz)$/i.test(base_name)) {
-    if (content) return count_xyz_frames(content) >= 2
-    return TRAJ_KEYWORDS_SIMPLE_REGEX.test(base_name)
-  }
-
-  // Always detect these specific trajectory formats
-  if (TRAJ_EXTENSIONS_REGEX.test(base_name) || XDATCAR_REGEX.test(base_name)) return true
-
-  // Special exclusion for generic md_simulation pattern with certain extensions
-  if (MD_SIM_EXCLUDE_REGEX.test(base_name)) return false
-
-  // For .h5/.hdf5 files, require trajectory keywords
-  if (/\.(h5|hdf5)$/i.test(base_name)) {
-    return TRAJ_KEYWORDS_SIMPLE_REGEX.test(base_name)
-  }
-
-  // For other extensions, require both keywords and specific extensions
-  return (
-    TRAJ_KEYWORDS_SIMPLE_REGEX.test(base_name) &&
-    TRAJ_FALLBACK_EXTENSIONS_REGEX.test(base_name)
-  )
-}