Trajectories & Molecular Dynamics

Playback, analysis, and export of molecular dynamics trajectories from multiple file formats.

Source: src/lib/trajectory/

Supported Formats

Format	Extensions	Description
XYZ	.xyz	Multi-frame XYZ (frames separated by headers)
Extended XYZ	.extxyz	Multi-frame with lattice and properties
ASE Trajectory	.traj	ASE native binary format
XDATCAR	XDATCAR	VASP molecular dynamics output
HDF5	.hdf5, .h5	Hierarchical Data Format (multi-frame)

Key Functions

Loading

// Load trajectory from file
load_trajectory_file(content, filename): Trajectory

// Validate trajectory data
validate_trajectory(trajectory): ValidationResult

// Get trajectory metadata
get_trajectory_stats(trajectory): TrajectoryStats

Streaming & Indexing

For large trajectory files (>100 MB), the module supports indexed access:

// Build index for random frame access (avoids reading entire file)
build_frame_index(content, format): FrameIndex[]

// FrameIndex contains byte offsets for fast seeking
interface FrameIndex {
  byte_offset: number
  estimated_size: number
}

Components

Component	Description
Trajectory.svelte	Main trajectory player with animation controls
TrajectoryInfoPane.svelte	Frame count, duration, and property metadata
TrajectoryExportPane.svelte	Export individual frames or sub-ranges
TrajectoryError.svelte	Error display for invalid trajectories

Playback Controls

• Play/Pause — animate through frames
• Frame slider — scrub to any frame
• FPS control — adjustable playback speed
• Step forward/backward — single frame advance
• Loop mode — continuous playback

Visualization Modes

The trajectory viewer can display alongside analysis plots:

• Structure + Scatter — 3D structure with per-frame property scatter plot
• Structure + Histogram — 3D structure with property distribution histogram

Properties that can be plotted:

• Energy per frame
• Forces (max, mean)
• Temperature
• Stress/pressure
• Custom per-frame properties (from EXTXYZ)

Settings

Setting	Type	Default	Description
trajectory_fps	number	10	Playback speed (frames per second)
trajectory_auto_play	boolean	false	Start playing on load
trajectory_display_mode	string	"structure"	Display layout mode

Performance

• Frame indexing enables random access into GB-scale trajectory files
• Binary formats (.traj, .h5) are more memory-efficient than text (.xyz)
• Lazy decompression for gzip-compressed trajectories
• Only the current frame's atom positions are sent to the GPU