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 = 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 and .
For carbon-carbon bonds, the sigma electrons are placed at the bond midpoint, with = 1.258 bohr.
For carbon-hydrogen bonds, the sigma electrons are placed closer to the hydrogen atom, using the expression