From a812d191e3b5f031b2227a3bbb40ec3b4be79b3a Mon Sep 17 00:00:00 2001 From: hackbard Date: Thu, 4 Aug 2011 18:38:51 +0200 Subject: [PATCH] some more steps to final version --- posic/thesis/ack.tex | 2 +- posic/thesis/code.tex | 114 ++++++++++++++++++------------------- posic/thesis/d_tersoff.tex | 2 +- posic/thesis/thesis.tex | 28 +++++---- posic/thesis/title.tex | 10 ++-- 5 files changed, 82 insertions(+), 74 deletions(-) diff --git a/posic/thesis/ack.tex b/posic/thesis/ack.tex index 608c741..b3440ee 100644 --- a/posic/thesis/ack.tex +++ b/posic/thesis/ack.tex @@ -1,6 +1,6 @@ \newpage \addcontentsline{toc}{chapter}{Acknowledgment} -\chapter*{Acknowledgment} +\chapter*{Acknowledgment\markboth{Acknowledgment}{}} First of all, I would like to thank my official advisers Prof. Dr. Bernd Stritzker and Prof. Dr. Kai Nordlund for accepting me as a doctoral candidate at their chairs at the University of Augsburg and the University of Helsinki. I am grateful to Prof. Dr. Bernd Stritzker who, although being an experimental scientist, gave me the opportunity to work on a rather theoretical field. 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. diff --git a/posic/thesis/d_tersoff.tex b/posic/thesis/d_tersoff.tex index 8492963..92b421f 100644 --- a/posic/thesis/d_tersoff.tex +++ b/posic/thesis/d_tersoff.tex @@ -185,7 +185,7 @@ Concerning $b_{ij}$, in addition to the angular term, the derivative of the cut- \subsection{Code realization} -The implementation of the force evaluation shown in the following is applied to the potential designed by Erhard and Albe \cite{albe_sic_pot}. +The implementation of the force evaluation shown in the following is applied to the potential designed by Erhart and Albe \cite{albe_sic_pot}. There are slight differences compared to the original potential by Tersoff: \begin{itemize} \item Difference in sign of the attractive part. diff --git a/posic/thesis/thesis.tex b/posic/thesis/thesis.tex index dd3eacc..82dc58d 100644 --- a/posic/thesis/thesis.tex +++ b/posic/thesis/thesis.tex @@ -3,8 +3,10 @@ %\documentclass[twoside,a4paper,11pt,draft]{book} \usepackage[activate]{pdfcprot} \usepackage{verbatim} -\usepackage{a4} -\usepackage{a4wide} +%\usepackage{layout} +%\usepackage{a4} +%\usepackage{a4wide} +\usepackage[a4paper,textheight=636pt,textwidth=442pt,includeheadfoot]{geometry} \usepackage[english,german]{babel} \usepackage[latin1]{inputenc} \usepackage[T1]{fontenc} @@ -20,6 +22,9 @@ \usepackage{rotating} \usepackage{fancyhdr} +% custom sections +\usepackage{titlesec} + % cites \usepackage[numbers,sort,compress]{natbib} @@ -70,17 +75,17 @@ %} \pagestyle{fancy} -\fancyhf{} -\fancyhead[EL]{\thepage} -\fancyhead[ER]{\leftmark} -\fancyhead[OL]{\rightmark} -\fancyhead[OR]{\thepage} -\renewcommand{\sectionmark}[1]{ - \markboth{\thesection{} #1}{\thesection{} #1} + +\renewcommand{\chaptermark}[1]{ + \markboth{\thechapter.\ #1}{} } -\renewcommand{\subsectionmark}[1]{ - \markright{\thesubsection{} #1} +\renewcommand{\sectionmark}[1]{ + \markright{\thesection.\ #1} } +\fancyhf{} +\fancyhead[LE,RO]{\thepage} +\fancyhead[LO]{\nouppercase\rightmark} +\fancyhead[RE]{\nouppercase\leftmark} % hyphenation \hyphenation{} @@ -131,6 +136,7 @@ \backmatter{} \include{literature} +\include{cv} \include{publications} \include{ack} diff --git a/posic/thesis/title.tex b/posic/thesis/title.tex index e0f0a73..e4f0149 100644 --- a/posic/thesis/title.tex +++ b/posic/thesis/title.tex @@ -44,19 +44,21 @@ \vspace{60pt} {\large - Augsburg, Juli 2011 + Augsburg, August 2011 } \end{center} \newpage -\raisebox{600pt}{ } +%\raisebox{600pt}{ } +\raisebox{586pt}{ } \begin{tabular}{ll} Erstgutachter: & Prof. Dr. Bernd Stritzker \\ -Zweitgutachter: & Prof. Dr. Kai Nordlund \\ -Tag der m"undlichen Pr"ufung: & 27. Juli 2011 \\ +Zweitgutachter: & Priv.-Doz. Dr. habil. Volker Eyert \\ +Drittgutachter: & Prof. Dr. Kai Nordlund \\ +Tag der m"undlichen Pr"ufung: & \underline{\hspace*{0.7cm}}. Oktober 2011\\ \end{tabular} % switch back to english -- 2.20.1