Visualization

The electron densities, molecular orbitals, and potentials are output to files in a Gaussian cube format. Figure 11 shows examples of isosurface maps visualized by using gOpenMol [48]. These data are output in a form of the Gaussian cube. So, many softwares, such as gOpenMol [48], Molekel [49], and XCrysDen [50], can be used for the visualization. You can find the details of files output in the cube format in the Section 'Output files'. It should be noted that current gOpenMol does not support a cube file of orthorhombic cell, while XCrysDen supports any cube file of both orthogonal and orthorhombic cells.

Figure: (a) Isosurface map of the total electron density of a C$_{60}$ molecule where 0.13 was used as an isovalue of total electron density. (b) Isosurface map of the highest occupied molecular orbital (HOMO) of a L-leucine molecule where $\vert.05\vert$ was used as an isovalue of the molecular orbital. (b) Isosurface map of the spin electron density of a molecular magnet (Mn$_{12}$O$_{12}$(CH$_3$COO)$_{16}$(H$_2$O)$_4$ [51]) where $\vert.02\vert$ was used as an isovalue of the spin electron density.