Phonons

The vibrational modes are read from the CRYSTAL output when it contains a frequency calculation, and are listed in the Phonons panel.

The list of modes

Each mode is listed with its frequency and, when the output reports the selection rules, its infrared and Raman activity. The list can be restricted to the active modes.

Animation

A mode selected in the list is animated with the Play button. Bonds, coordination polyhedra and hydrogen bonds follow the displacements.

The Amplitude is defined as the largest displacement of any atom, so that one value is appropriate for structures of different size, and the Speed sets the rate of the animation.

A mode gives one displacement per atom, so it describes the structure the calculation was run on and no other. Moving an atom or changing its element leaves the modes in place, but adding or deleting one sets them aside and the panel says so; undoing that edit brings them back.

Above: MOF-5 seen down a cube axis, in the lowest optical mode at 17 cm⁻¹, the terephthalate linkers twisting between the Zn₄O clusters. The crystallographic cell is shown: 424 atoms, animated live.

Exporting an animation

File → Export phonon animation… writes the animation of the selected mode.

Format	Requirement
GIF, or a sequence of numbered frames	none
MP4, MOV, WebM	pip install CRYSTALLine[video]

The resolution, the number of frames and the frame rate are set in the dialog.

Modes away from Γ

A dispersion calculation (DISPERSI) computes modes at several points of the Brillouin zone. The q points are listed above the mode list, and a mode chosen at one of them is animated as a travelling wave: each cell drawn carries its own phase, in the crystallographic cell, in a supercell and after completion of the molecules at the boundary alike.

The Tile button repeats the cell over one period of the wave, and restores the original cell when pressed again.

Above: diamond at q = (0, 0, ½), the transverse acoustic mode at 537 cm⁻¹, with the cell repeated six times along c: three wavelengths of the wave.

In a static image the displacement arrows can be scaled by the magnitude of the displacement and coloured by the phase of the cell in which they are drawn, which repeats once per wavelength. The amplitude is the same in every cell, and the phase is what distinguishes them.

Phonon band structures

Phonon band structures and densities of states are plotted by Plot → Phonon bands & DOS…; see Property plots.