1 \chapter{Description of programs and tools}
4 Some selected programs and tools utilized within this study are introduced in the following.
5 The source code is available for download\footnote{http://www.physik.uni-augsburg.de/\~{}zirkelfr/posic}.
6 The \textsc{vasp} utilities reside in the {\em vasp\_tools} subdirectory included within the \textsc{posic} source.
8 \section[Contents of the {\normalfont\textsc{posic}} program suite]{Contents of the POSIC program suite}
10 \subsection{The molecular dynamics application}
12 \paragraph{mdrun.\{c,h\}}
13 constitutes the actual, executable molecular dynamics application program.
14 \paragraph{config.default}
15 is a sample configuration file that is parsed by the {\em mdrun} application.
16 \paragraph{moldyn.\{c,h\}}
17 includes all the molecular dynamics routines.
18 \paragraph{potentials/albe.\{c,h\}}
19 implements the energy and force evaluation of the potential.
20 \paragraph{list/list.\{c,h\}}
21 contains code for the management of linked lists.
22 \paragraph{random/random.\{c,h\}}
23 deals with random numbers and distributions.
24 \paragraph{math/math.h}
25 provides inlined mathematical functions.
26 \paragraph{runmd, runmd\_rx200}
27 script starting the {\em mdrun} application and postprocessing.
29 \subsection{Postprocessing tools}
31 \paragraph{calc\_delta\_e}
32 determines defect formation energies using SiC as a particle reservoir.
33 \paragraph{pair\_correlation\_calc.c}
34 computes the radial dsitribution function.
35 \paragraph{display\_atom\_data.c}
36 displays atom specific information.
37 \paragraph{bond\_analyze.c}
38 counts the amount of C atoms that have four Si neighbors.
39 \paragraph{bond\_analyze\_script}
40 performs bond analysis on a large quantity of data.
41 \paragraph{search\_bonds.c}
42 prints out pairs of atoms featuring specific bond properties.
43 \paragraph{visual\_atoms.c}
44 creates a detailed atomic datafile.
46 creates images of atomic configurations.
47 \paragraph{parcasconv}
48 converts \textsc{parcas} output to \textsc{posic} format.
50 converts \textsc{posic} output to \textsc{parcas/rasmol} format.
52 extracts (modified) {\em xyz} data from \textsc{posic} save files.
54 creates a movie out of atomic configuration images.
56 \section[{\normalfont\textsc{vasp}} utilities]{VASP utilities}
58 \subsection[Operating {\normalfont\textsc{vasp}}]{Operating VASP}
60 \paragraph{create\_lattice.c}
61 create the lattice in \textsc{vasp} POSCAR fomat.
62 \paragraph{runvasp\_rx200}
63 executing \textsc{vasp} on the Augsburg Linux Compute Cluster.
64 \paragraph{sd\_rot\_all-atoms.patch}
65 enables selected dynamics in a user-defined basis for every atom.
66 \paragraph{mig\_fullct.sh}
67 calculates a series of configurations within a migration path.
69 \subsection{Postprocessing utilities}
72 prints out the configurational energies within a migration path.
74 calculates the cohesive energy.
75 \paragraph{e\_form\_tersoff}
76 calculates defect formation energies using SiC as a particle reservoir.
78 calculates the binding energy of a defect pair.
79 \paragraph{get\_ks\_levels}
80 creates the Kohn-Sham level diagram.
82 creates images of atomic configurations.