X-Git-Url: https://hackdaworld.org/gitweb/?p=lectures%2Flatex.git;a=blobdiff_plain;f=posic%2Fthesis%2Fcode.tex;h=bb6dc610877a1bb4dd80cc5383ce89663aa9fb93;hp=37039f8008bbb2b8171dd78826368a0146c1c465;hb=a812d191e3b5f031b2227a3bbb40ec3b4be79b3a;hpb=55e8012443a5732bca95a44b287662670944b661

diff --git a/posic/thesis/code.tex b/posic/thesis/code.tex
index 37039f8..bb6dc61 100644
--- a/posic/thesis/code.tex
+++ b/posic/thesis/code.tex
@@ -9,75 +9,75 @@ The \textsc{vasp} utilities reside in the {\em vasp\_tools} subdirectory include
 
 \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.
+\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}
 
-\paragraph{calc\_delta\_e}
-determines defect formation energies using SiC as a particle reservoir.
-\paragraph{pair\_correlation\_calc.c}
-computes the radial distribution 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 data file.
-\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}
+\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}
 
-\paragraph{create\_lattice.c}
-create the lattice in \textsc{vasp} POSCAR format.
-\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}
+\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}
 
-\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}
+\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.