\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}

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

\subsection{Postprocessing tools}

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

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

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

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

\subsection{Postprocessing utilities}

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

