more fixes

[lectures/latex.git] / posic / thesis / code.tex

diff --git a/posic/thesis/code.tex b/posic/thesis/code.tex
index 6118b9a..a420c39 100644 (file)
--- a/posic/thesis/code.tex
+++ b/posic/thesis/code.tex
@@ -1,26 +1,83 @@
 \chapter{Description of programs and tools}
 \label{app:code}
 
-Programs and tools utilized within this study are introduced in the following.
+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 \textsc{posic} program suite}
+\section[Contents of the {\normalfont\textsc{posic}} program suite]{Contents of the POSIC program suite}
 
-\begin{itemize}
- \item mdrun
- \item moldyn.\{c,h\}
- \item potentials/albe.\{c,h\}
- \item ...
- \item ...
-\end{itemize}
+\subsection{The molecular dynamics application}
 
-\section{\textsc{vasp} utilities}
+\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.
 
-\begin{itemize}
- \item mig\_fullct.sh, mig\_calc
- \item e\_form\_tersoff, e\_fc\_tersoff
- \item ...
- \item ...
- \item ...
-\end{itemize}
+\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.
 
-\ldots will be written out in full soon!