Density Visualization

Visualize volumetric data from CUBE files with 3D isosurfaces and 2D slice planes.

Source: src/lib/cube/

Overview

The density visualization module reads Gaussian/VASP CUBE files containing volumetric data (electron density, molecular orbitals, electrostatic potential) and renders them as interactive 3D isosurfaces or 2D cross-section planes overlaid on the atomic structure.

Components

Component	Description
CubeViewer.svelte	Main cube data viewer
CubeScene.svelte	Three.js scene for 3D density rendering
CubeControls.svelte	Isosurface threshold, opacity, color, and slice controls
IsosurfaceMesh.svelte	Renders the 3D isosurface mesh
SlicePlane.svelte	2D cross-section plane through the data

Key Functions

// Parse CUBE file format
parse_cube_file(content: string): CubeData

// Generate isosurface mesh at a given threshold
compute_isosurface(cube_data, isovalue): IsosurfaceMesh

// Extract 2D cross-section
create_slice_plane(cube_data, plane_origin, plane_normal): SliceData

CUBE File Format

The CUBE format contains:

• Atomic positions and elements
• 3D grid dimensions (nx, ny, nz)
• Volumetric data on the grid (one value per grid point)
• Origin and axis vectors defining the grid in space

Features

• Isosurface rendering — 3D surface at constant value (e.g., electron density = 0.05)
• Adjustable threshold — slider to change isosurface value
• Dual surfaces — show both positive and negative lobes (e.g., for orbitals)
• Opacity control — transparent to opaque isosurfaces
• Color control — customizable surface colors
• Slice planes — 2D color-mapped cross-sections through the data
• Overlay on structure — isosurfaces rendered alongside atoms and bonds

Integration

The CubePanel.svelte component in the structure viewer integrates density visualization directly into the main structure viewer, allowing simultaneous display of atomic structure and volumetric data.

Server API

The Python server provides additional CUBE file processing:

GET  /api/cube/parse     — Parse CUBE file on server
POST /api/cube/process   — Process volumetric data