vasp.bonds: Generates a data.frame containing the start- and the...

In theGreatWhiteShark/vasp2R: R package to import and plot results obtained by the DFT program VASP.

Usage

vasp.bonds(x, distance)

Arguments

x	A data.frame containing the x, y and z position of the atoms in Cartesian coordinates as named columns and a fourth column names "type" containing a character specifying the atom species or an object of class "vasp". See vasp.import$atoms.
distance	Vector of length unique( atoms$type ) containing the bonding distances between the individual atoms. To establish a bond two atoms must be closer together than this value. The order in this distances vector has to be the same as in unique( atoms$type ).

Details

Two atoms share a bond if they a closer than a specified minimum distance. Since this function was originally written for a layered system the bonds are only created within one type of atoms. But it is quite easily extendable to bonds between several kinds of atoms.

Value

A data.frame with seven named columns "x.begin", "y.begin", "z.begin", "x.end", "y.end", "z.end" and "type" containing the start- and endpoints of the bonds in the system as well as the type of atoms between which the bond is established. The later is necessary for the correct coloring and can be easily extended to bonds of many different atom types.

Author(s)

Philipp Mueller

See Also

Other vasp: vasp.diff, vasp.import, vasp.reproduce, vasp.rotate.cell

theGreatWhiteShark/vasp2R documentation built on May 31, 2019, 9:10 a.m.