CRYSTALLine 0.1.2

A desktop app for building, editing and visualising CRYSTAL structures and their vibrational (phonon) modes — built on CRYSTALClear.

Features

Structure viewer

• Interactive 3D view (PyVista/VTK): ball-and-stick atoms, bonds, hydrogen bonds (dashed D–H···A contacts), coordination polyhedra (VESTA-style, shown by default), the unit-cell wireframe and an a/b/c gizmo.
• One-click view alignment down the a, b or c axis.
• A rich, dockable Display panel: atom size/opacity, per-element colours, bond radius/tolerance, hydrogen bonds, cell & axes, polyhedra, measurement colours, background colour, projection, an orientation marker and element labels.
• Crystallographic Info panel, dimensionality-aware: space group(3D) or layer group(2D slabs), point group, lattice parameters, cell volume/area, density and formula — recomputed live as you edit — plus CRYSTAL-computed properties (total energy, band gap, Fermi energy) read from the output.

Geometry & measurements

• Measure a selection: distance (2 atoms), angle (3), dihedral (4) or a least-squares plane (3+); mark single-atom points.
• Overlay measurements in 3D and colour them per item or by type default.

Phonons

• Loads vibrational modes automatically when the CRYSTAL output has them.
• Animate any mode in place — bonds, polyhedra and hydrogen bonds follow the motion; export the animation as GIF / MP4 / PNG frames with configurable resolution, frame count and frame rate.

Editing

• Select atoms (click / Ctrl-click), drag them in 3D (periodic images move together), drag a whole selection as one piece, or nudge with the arrow keys.
• Add, delete, duplicate, translate and re-element atoms — with a visual periodic-table, element picker — and full undo / redo.
• Cell tools: conventional cell, supercells, boundary completion and editable lattice parameters.

Import / export

• Open CRYSTAL .out / .gui / .f34 files and .cif** structures.
• Import atoms from .xyz / .pdb / .cif into the current structure.
• Save the structure as .gui or .cif (symmetry-reduced).
• Export the 3D view as an image (PNG/JPEG/TIFF/SVG/PDF/EPS) with resolution and transparency options.

Input builder

• Write a ready-to-run CRYSTAL .d12 deck for the current structure, with a live preview of the exact input before you save it.
• Geometry is derived from the structure — space group and asymmetric unit for a crystal, and the right coordinate convention for slabs, polymers and molecules.
• Choose the method (HF or DFT, one functional keyword or separate exchange and correlation), basis set, SCF settings and the calculation: single point, geometry optimisation, frequencies with IR/Raman, phonon dispersion, QHA, equation of state, elastic constants, CPHF, anharmonic runs and spin–orbit coupling.

Property plots (via CRYSTALClear, shown in a dockable tabbed panel)

• IR & Raman spectra, elastic surfaces (Young's modulus, linear compressibility, shear, Poisson), equation of state.
• Electronic & phonon band structures and densities of states, simulated XRD.

Screenshots

The main window — crystallographic info, the interactive 3D view and the phonon-mode list (brucite, Mg(OH)₂).

A computed Raman spectrum beside the structure, with the phonon-animation export dialog (thiourea).

The Display panel and coordination polyhedra on a 2×2×2 supercell, with a Young's modulus elastic surface.

Architecture

The package is deliberately layered so the domain logic stays independent of the Qt UI — and therefore unit-testable without a display:

src/crystalline/
├── core/        domain model — Structure, phonons, cells, bonds, undo (no Qt)
├── crystalio/   thin adapter over CRYSTALClear (load/save, property plots)
├── viz/         PyVista/VTK rendering, phonon animation, image/movie export (no Qt)
├── ui/          PySide6 widgets: 3D viewport, dockable panels, main window
└── resources/   bundled assets (logo)

Only ui/ (and the viewport that embeds the VTK interactor) imports Qt. Adding a new property (a new plot, panel, …) is a matter of dropping a widget into ui/panels/ and wiring its signals in MainWindow.

Usage

python -m crystalline
# or, after install, just:
crystalline

Use File → Open to load a CRYSTAL .out/.gui/.34 file or a .cif. If a CRYSTAL output contains a vibrational calculation, the phonon modes are loaded too — pick one in the Phonons panel and press Play. Otherwise the geometry is shown on its own. Tweak the look from the Display panel, measure geometry from the Geometry panel, and build property plots from the Plot menu.

Enable Edit → Editing mode (Ctrl+E) to edit atoms: click to select, drag or arrow-key the selection to move it, Del to delete, and pick elements from the visual periodic table.

CRYSTALLine runs on Linux, macOS and Windows — anywhere PySide6 and a working OpenGL/VTK stack are available.

Testing

pytest

The suite runs headless and exercises the Qt-free core, the renderer (via an off-screen PyVista plotter), the plotting adapter and the file I/O.

License

GNU General Public License v3.0 or later.

Acknowledgements

Built on the CRYSTALClear I/O and plotting framework for the CRYSTAL quantum chemistry code.

This software was developed with the assistance of Claude (Anthropic), using Claude Code.