\chapter{Description of programs and tools}
\label{app:code}

Some selected programs and tools utilized within this study are introduced in the following.
The source code is available for download\footnote{http://www.physik.uni-augsburg.de/\~{}zirkelfr/posic}.
The \textsc{vasp} utilities reside in the {\em vasp\_tools} subdirectory included within the \textsc{posic} source.

\section[Contents of the {\normalfont\textsc{posic}} program suite]{Contents of the POSIC program suite}

\subsection{The molecular dynamics application}

\textbf{mdrun.\{c,h\}}
constitutes the actual, executable molecular dynamics application program.\\
\textbf{config.default}
is a sample configuration file that is parsed by the {\em mdrun} application.\\
\textbf{moldyn.\{c,h\}}
includes all the molecular dynamics routines.\\
\textbf{potentials/albe.\{c,h\}}
implements the energy and force evaluation of the potential.\\
\textbf{list/list.\{c,h\}}
contains code for the management of linked lists.\\
\textbf{random/random.\{c,h\}}
deals with random numbers and distributions.\\
\textbf{math/math.h}
provides inlined mathematical functions.\\
\textbf{runmd, runmd\_rx200}
starts the {\em mdrun} application and postprocessing.

\subsection{Postprocessing tools}

\textbf{calc\_delta\_e}
determines defect formation energies using SiC as a particle reservoir.\\
\textbf{pair\_correlation\_calc.c}
computes the radial distribution function.\\
\textbf{display\_atom\_data.c}
displays atom specific information.\\
\textbf{bond\_analyze.c}
counts the amount of C atoms that have four Si neighbors.\\
\textbf{bond\_analyze\_script}
performs bond analysis on a large quantity of data.\\
\textbf{search\_bonds.c}
prints out pairs of atoms featuring specific bond properties.\\
\textbf{visual\_atoms.c}
creates a detailed atomic data file.\\
\textbf{visualize}
creates images of atomic configurations.\\
\textbf{parcasconv}
converts \textsc{parcas} output to \textsc{posic} format.\\
\textbf{povconv}
converts \textsc{posic} output to \textsc{parcas/rasmol} format.\\
\textbf{s2xyz.c}
extracts (modified) {\em xyz} data from \textsc{posic} save files.\\
\textbf{ppm2avi}
creates a movie out of atomic configuration images.

\section[{\normalfont\textsc{vasp}} utilities]{VASP utilities}

\subsection[Operating {\normalfont\textsc{vasp}}]{Operating VASP}

\textbf{create\_lattice.c}
creates the lattice in \textsc{vasp} POSCAR format.\\
\textbf{runvasp\_rx200}
executes \textsc{vasp} on the Augsburg Linux Compute Cluster.\\
\textbf{sd\_rot\_all-atoms.patch}
enables selected dynamics in a user-defined basis for every atom.\\
\textbf{mig\_fullct.sh}
calculates a series of configurations within a migration path.

\subsection{Postprocessing utilities}

\textbf{mig\_calc}
prints out the configurational energies within a migration path.\\
\textbf{e\_coh}
calculates the cohesive energy.\\
\textbf{e\_form\_tersoff}
calculates defect formation energies using SiC as a particle reservoir.\\
\textbf{e\_fc}
calculates the binding energy of a defect pair.\\
\textbf{get\_ks\_levels}
creates the Kohn-Sham level diagram.\\
\textbf{visualize}
creates images of atomic configurations.

