Generating hydrocarbons

The xyz2cfg script takes as input the .xyz nuclear coordinates of a saturated hydrocarbon, and generates as output a .cfg file containing nuclear and electron positions, and electron sizes:

  xyz2cfg [.xyz file, no extension]

An example of the script's use was given in Section 2.4.

The script estimates the electron positions as follows. First, it places core electrons at the nuclear positions with size $s_{\textbf{core}}$ = 0.333 bohr. Then, it finds the carbon-carbon and carbon-hydrogen bonds by computing at the pairwise distances between nuclei, and using the bond distance thresholds $d_{\mathrm{CH}} < 1.2\ \mathrm{\AA}$ and $d_{\mathrm{CC}} < 1.6\ \mathrm{\AA}$.

For carbon-carbon bonds, the sigma electrons are placed at the bond midpoint, with $s_{\sigma-\mathrm{CC}}$ = 1.258 bohr.

For carbon-hydrogen bonds, the sigma electrons are placed closer to the hydrogen atom, using the expression

$$\mathbf{r} = 0.293 \cdot \mathbf{r_{\mathrm{H}}} + (1 - 0.293) \cdot \mathbf{r_{\mathrm{C}}}$$

with $s_{\sigma-\mathrm{CH}}$ = 1.543 bohr.