Property plots

The entries of the Plot menu draw the properties computed by CRYSTAL. The figures are produced by CRYSTALClear and appear in the Plots panel at the bottom of the window, one tab per figure. Most figures carry their options beside them, and are redrawn as these are changed.

Some entries use the output file already open; the others read the data files written by a properties run, and their names end with …. Those files are looked for, and asked for, in the folder of the open output; see working in the calculation’s folder. Plot → Plot font… sets the font of the figures drawn afterwards.

Electronic band structures and densities of states

Plot → Electronic bands & DOS… draws a band structure, a density of states, or the two side by side.

Silicon, along Γ-X-W-L-Γ.

The files. BAND.DAT, DOSS.DAT, *.BAND, *.DOSS, fort.25 and *.f25 are read. Those in the folder of the open output are listed, recognised by their contents rather than by their names, so that a charge-density map or a COOP file is not offered as a band structure. When a folder holds several runs, the band file and the density of states are paired by their Fermi energy, which identifies the SCF they come from; a disagreement is reported.

The energies. CRYSTAL writes them relative to the Fermi level. They can be plotted that way or as absolute energies, in which case the Fermi energy is added back and the line marking it moves with the data. Units are eV or Hartree. The window is taken from the contents of the file, from the first wide gap below the Fermi level, which separates the valence bands from the core levels to as far above, and Suggested window restores it.

The rest. The projections of the density of states, with their names and colours; the treatment of the spin-down component; the labels of the path; and the colours, styles and widths of the lines.

Phonon band structures and densities of states

Plot → Phonon bands & DOS… draws the phonon bands of a dispersion calculation (DISPERSI with BANDS), its phonon density of states (PDOS), or the two side by side, with the same layout and the same options beside the plot as the electronic ones.

ZnO, along Γ-K-M-Γ-A-H-K, from a 5×5×5 supercell.

The files. PHONBANDS.DAT, PHONDOS.DAT, fort.25 and *.f25 are read. They have the formats of the electronic files and are told apart from them by their contents, so each dialog lists only its own. The band file of the open output comes first: it is recognised by the frequencies at the first point of its path, which the output prints too.

The path. A fort.25 writes the corners of the path as integers without their denominator. The output states each segment with it, and so does the BANDS block of the input deck, and from these the corners are named (Γ, K, M…) against the special points of the structure.

The frequencies. In cm⁻¹ or THz. The window runs from zero, or from the lowest imaginary branch when there is one deeper than the numerical noise at Γ, to just above the highest branch, and Suggested window restores it.

A run along a path prints no eigenvectors unless asked to with MODES, so its output opens with the structure and no modes to animate; the bands are plotted from here.

Vibrational spectra

Plot → Vibrational spectra… lists the curves contained in the output: infrared, Raman with its polarisations, and their anharmonic (VSCF, VCI) counterparts where present.

Brucite: the harmonic spectrum and its VCI counterpart, which shows the anharmonic shift.

Several curves may be selected at once, which is the usual case: the single-crystal Raman components on the same axes show the anisotropy, and a harmonic curve under its anharmonic counterpart shows the shift. The broadening is chosen in the same dialog (pseudo-Voigt, Lorentzian, Gaussian or a stick spectrum), and only the widths used by the chosen lineshape are enabled.

Anharmonic calculations

• VCI states…: the states of a VCI calculation, as a heatmap or a Sankey diagram.

• Anharmonic scan…: the scanned potential.

• Anharmonic PES…: one- and two-dimensional cuts of the potential energy surface, with the wavefunctions and probability densities of a double well.

Elastic properties

Plot → Elastic properties draws the directional elastic properties of an elastic-constants run (ELASTCON) from its elastic tensor: Young’s modulus, the linear compressibility, the shear modulus and Poisson’s ratio. The entries are enabled when the open output contains the tensor.

Coesite: Young’s modulus in every direction.

Coesite: the linear compressibility in the three principal planes.

Two views. A property is drawn as a surface over all directions, coloured by its value, or as sections through the principal planes xy, xz and yz. The entries of Elastic properties open the surfaces, those of Elastic properties (2D) the sections.

Beside the plot. The tensor is read once, and the property, the view, the planes shown, the colour map and the resolution are changed beside the plot, which is redrawn from the tensor in memory. The shear modulus and Poisson’s ratio depend on a second direction, perpendicular to the first, and are shown as their average, minimum or maximum over it. The moduli are in GPa, the linear compressibility in TPa⁻¹.

The values are computed by CRYSTALClear, whose notebooks work through each kind of plot in detail, what it is computed from and what can be varied.

Equation of state and XRD patterns

Plot → Equation of state draws the energy against the volume of an EOS run, from the open output. Plot → Simulated XRD pattern… draws the pattern written by a properties run.

Crystalline orbitals

Plot → Crystalline orbitals… reads the files written by the ORBITALS keyword and draws the orbital in the 3D view rather than in the plot panel; Clear orbital removes it.

The highest occupied orbital of graphite at k = (1/9, 0, 0), over three cells by three. The lobes change sign from cell to cell with the phase of the Bloch sum; at Γ they would all be alike.

Electron density and electrostatic potential

Plot → Electron density & potential… draws the grids written by ECH3 and POT3 over the structure, in the 3D view; Clear field removes them.

Urea: the charge density at 0.058 e/bohr³, coloured by the electrostatic potential.

The CUBE files and fort.31 are found in the folder of the open output and recognised by their content, with the grids of the open structure offered first. A field is drawn either as an isosurface, which opens at a level that clears the drawn atoms, or on a lattice plane given by its Miller indices in the conventional cell; the crystal in front of the plane is cut away and the atoms lying in it are marked. A colour bar can be added. A second field either colours the surface, as with the potential on the density above, or is subtracted from the first.