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adsphd's Introduction

ADS PhD LaTeX template

This template is the result of an ongoing group effort by a number of volunteers. Help your fellow PhD researcher in the Issues section and contribute updates if you can. If you are fluent in TeX and can help monitoring this repository, ask Wannes Meert for admin rights.

If you want to share tips, tricks, updates, questions or problems: add them as a GitHub issue or a GitHub pull request.

Information

This package provides a template when submitting a Phd dissertation to the Arenberg Doctoral School at KU Leuven.

Latest version of the ADS PhD template is available at github.com/wannesm/adsphd.

Questions and issues can be submitted to the ADS PhD issues component at Github.

Directory structure

The directory structure looks like this

  • thesis.tex: Main tex file for the final booklet.
  • run.py: Simple compilation script.
  • Makefile
  • Makefile.settings: This file contains file names and other settings used by make.
  • chapters
    • chapter1: Per chapter a directory with
      • chapter1.tex: Tex file with identical name
      • image/: Images directory. Note that to include a figure in chapter1.tex, you should NOT include the relative path, i.e., \includegraphics{myfigure} and not {image/myfigure}!

Using Latex directly

The adsphd.cls class can be used directly by latex:

pdflatex thesis
bibtex thesis
# biber thesis
makeindex thesis.glo -s thesis.ist -t thesis.glg -o thesis.gls
makeindex thesis.nlo -s nomencl.ist -o thesis.nls
pdflatex thesis
pdflatex thesis

Any other Latex build tool like latexmk, rubber, SCons, TeXShop or TeXWorks should also work out of the box (makeindex might not run by default in which case you will not see the glossary).

Using the simple Python compile script

There is a simple and naive Python compilation script supplied which should work cross-platform.

python3 run.py             # Compile to pdf
python3 run.py clean       # Clean auxiliary files
python3 run.py realclean   # Clean everything
python3 run.py newchapter  # Set up files for a new chapter
python3 run.py --help      # Help and more options

Some settings are available at the top of the run.py file.

Using make and other utility scripts

Some convenient Makefile targets:

In the main directory [./]:

make                       # create the full booklet thesis.pdf
make clean
make realclean             # cleanup all mess, including leftover
                           # {dvi,pdf,ps} files of main file or the
                           # chapters
make damnthatsreallyclean  # brutally remove all possible temporary
                           # files

In a chapter directory [./chapters/chapterX]:

For this to work you need to generate the chapter directory using the makeemptychapter.sh script which also generates a custom Makefile for the new chapter.

make                       # Creates chapterX.pdf containing the
                           # TOC, the contents of only chapterX and
                           # the bibliography.
make bare                  # Create chapterX.pdf containing only the 
                           # chapter text (no TOC, no bibliography).
make clean                 # remove temporary files left from
                           # compilation
make realclean             # clean + also remove {ps,pdf} files
make figurelist            # Print out the names of all figures that are
                             effectively used in ./chapters/chapterX/chapterX.tex
make cover                 # Generate a separate pdf the cover

Creating a chapter directory:

./chapters/makeemptychapter.sh # Create the directory structure for a new
                               # chapter.

Settings:

Settings for the Makefile script can be found in the makefile.settings file.

Options for the adsphd class

faculty               : faculty
                          [firw] Faculty of Engineering Science
                          [fbiw] Faculty of Bioscience Engineering
                          [fw]   Faculty of Science
                          [fa]   Faculty of Architecture
                          [fiiw] Faculty of Engineering Technology
		      [hiw]  Institute of Philosophy

department            : department
                          [aow] Department of Earth and Environmental Sciences
                          [arc] Department of Architecture
                          [bio] Department of Biology
                          [bsy] Department of Biosystems
                          [bwk] Department of Civil Engineering
                          [che] Department of Chemistry
                          [cit] Department of Chemical Engineering
                          [cws] Department of Computer Science
                          [elt] Department of Electrical Engineering
                          [mtk] Department of Materials Engineering
                          [mms] Department of Microbial and Molecular Systems
                          [nat] Department of Physics and Astronomy
                          [wtk] Department of Mechanical Engineering
                          [wis] Department of Mathematics
                          [cespp]   Centre for Ethics, Social and Political Philosophy
                          [clps]    Centre for Logic and Philosophy of Science
                          [cmprpc]  Centre for Metaphysics, Philosophy of Religion and Philosophy of Culture
                          [dwmc]    De Wulf-Mansion Centre for Ancient, Medieaval and Renaissance Philosophy
                          [hua]     Husserl-Archives: Centre for Phenomenology and Continental Philosophy

phddegree             : official PhD degree on diploma (only for the
                        faculties of Engineering Science and Science)

                          faculty=firw
                            [arc] Doctor of Engineering Science (PhD): Architecture
                            [bwk] Doctor of Engineering Science (PhD): Civil Engineering
                            [cit] Doctor of Engineering Science (PhD): Chemical Engineering
                            [cws] Doctor of Engineering Science (PhD): Computer Science
                            [elt] Doctor of Engineering Science (PhD): Electrical Engineering
                            [mtk] Doctor of Engineering Science (PhD): Materials Engineering
                            [wtk] Doctor of Engineering Science (PhD): Mechanical Engineering
                            [gen] Doctor of Engineering Science (PhD)

                          faculty=fw
                            [ste] Doctor of Science (PhD): Astronomy and Astrophysics
                            [bct] Doctor of Science (PhD): Biochemistry and Biotechnology
                            [bio] Doctor of Science (PhD): Biology
                            [bfy] Doctor of Science (PhD): Biophysics
                            [che] Doctor of Science (PhD): Chemistry
                            [ggr] Doctor of Science (PhD): Geography
                            [glo] Doctor of Science (PhD): Geology
                            [inf] Doctor of Science (PhD): Informatics
                            [mat] Doctor of Science (PhD): Mathematics
                            [fys] Doctor of Science (PhD): Physics
                            [sta] Doctor of Science (PhD): Statistics
                            [tou] Doctor of Science (PhD): Tourism
                            [gen] Doctor of Science (PhD)

10pt, 11pt, 12pt      : text point size
oneside, twoside
showgit               : when showing extra info (with [info] or
                        [frame] option), also show git version.
                        You need to run latex with '-shell-escape'
                        for this to work! (default in Makefile)

british               : Use British spelling in cover (i.e.
                        fulfilment instead of fulfillment)

showinstructions      : show instructions provided by the
                        faculty. These can be included anywhere
                        in the tex by commands of the form
                        \instructionsabstract,
                        \instructionsintroduction, ...  

info                  : put logical page on physical A4 paper and
                        show some info (compilation time, ...)
draft                 : show info and compile the document as a
                        draft
tothejury             : generate a version of the document
                        suitable to send to the jury. This means
                        that the logical page is put on an A4
                        without info, frame, ... 
final                 : generate true size (cropped!) pdf without
                        info, frame, ...
print                 : generate true size (cropped!) pdf without
                        info, frame, ... suitable for
                        printing (basically equal to final, but
                        forcing uncolored links, even when this
                        option is given explicitly)
online                : generate true size (cropped!) pdf without
                        info, frame, ... suitable for
                        printing (basically equal to final, but
                        forcing colored links)
croppedpdf            : generate true size pdf
frame                 : put frame around the logical page and
                        place the result on an A4 page
cam                   : instead of a frame, use cropmarks
cropmarks             : identical to cam
epub                  : use a small page size that works better on an
                        epub reader (e.g. Kindle)

covershowcommittee    : show the committee also on the cover.
coverfontpercent=<int>: change the cover title font size. Should
                        be an integer number between 1 and 100.

Most of the useful commands provided by this class can be found in the provided example file thesis.tex.

Chapters

Inclusion of normal chapters

Use the command \includechapter{.}, e.g.,

\includechapter{introduction}

includes ./chapters/introduction/introduction.tex.

If the chapter is an appendix, use \includeappendix{.}!

Inclusion of 'special' chapters

The term 'special' chapters refers to the

  • preface (preface)
  • dutch preface (prefacenl)
  • abstract (abstract)
  • dutch abstract (abstractnl)
  • list of publications (publications)
  • curriculum vitae (cv)

To include any of the above, use the command

\includeXXX{filename}

where XXX stands for the name indicated in between brackets above, and filename is as in the \includechapter command. For instance,

\includeappendix{myappendix} % includes ./chapters/myappendix/myappendix.tex as an appendix

Other special chapters are

  • list of figures
  • list of tables
  • table of contents
  • bibliography

but these different from the above as they are generated using standard commands (\listoffigures, \listoftables, \tableofcontents, \includebibliography).

For typical usage, see the provided file thesis.tex.

Loaded packages

The following packages are loaded automatically by the adsphd.cls class:

  • babel
  • calc
  • datatool
  • etoolbox
  • fancyhdr
  • fontenc
  • framed
  • geometry
  • hyperref
  • ifpdf
  • iftex
  • ifthen
  • kvoptions
  • listings
  • lmodern
  • microtype
  • placeins
  • rotating
  • setspace
  • showlabels
  • textpos
  • xcolor

Generating the cover page

Most printing services will create their own cover page based on the details you send them (title, name, affiliation, ...). The template generates only a front and back cover for the version you want to distribute online, not for the version you send to the printing service.

However, the template has some support to create a separate cover page. Use make cover or python run.py cover to generate cover.tex and run.

Troubleshooting

  • To be able to make the chapter compilation work, you should make sure that the desired chapter is included in thesis.tex (e.g., using \includechapter{introduction})!!
  • If you get spurious empty pages when compiling a single chapter, this is probably due to the combination of \cleardoublepage and \includeonly. To avoid it, make sure you end all included chapters (and appendices) with \cleardoublepage (if you use makeemptychapter.sh to generate the chapter skeleton this is automatically done!)

Contributors

Wannes Meert, Yves Frederix, Bart Vandewoestyne, Nele Famaey, Tias Guns, Jan Hendrik Becker, Steven Op de beeck, Frederik Colle, Dominique Devriese, Marko van Dooren, Rutger Claes, Dirk Van Hertem, Anthony Van Herrewege, Tassos Natsakis, Till Nagel, Job Noormal, Jesper Cockx, Laurens Sion, Felipe Morales, Pieter Maene, Roel Van Beeumen.

adsphd's People

Contributors

dcbr avatar dominiquedevriese avatar fmoralesc avatar giulioben avatar laurenss avatar markovandooren avatar pmaene avatar rutgerclaes avatar stevenodb avatar trldp avatar vincentcp avatar wannesm avatar

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adsphd's Issues

Chapter-specific preamble defs.tex not working

makeemptychapter.sh tells you to put chapter-specific preamble in defs.tex in the same folder as the chapter's tex file. However, this preamble is not loaded during compilation.

Does anybody have a workaround?

Do not load hyperref (maybe optionally)

Since the class loads hyperref, it is difficult to configure hyperref to ones needs from the document. The only way to do so seems to be to use \PassOptionsToPackage before the \documentclass which is kind of hacky.

I propose to either remove all the hyperref code from the class file or to add an option (e.g. nohyperref) to make the class not load hyperref. I'm willing to create a pull request implementing either of these options if it would be accepted.

Suggestion: improve breaking of long urls (e.g. in references)

The hyperref package loads the url package for the \url{} command. However, long latex does not play well with long urls, especially in the references. To improve layout, I suggest adding the line

\PassOptionsToPackage{hyphens}{url}

just before loading the hyperref package, which allows line breaks at hyphens in urls.

co-tutorship layout

Good Morning!
I am compiling in Latex a `joint phd diploma' thesis, hence there must be the logos and names of the two institutions (in my case, Bicocca University of Milan and KUL), + both names of faculties and deparments, and supervisor 7 co-supervisor, of course.
I've made a cover by myself, however I wonder if there are common guidelines already available with regard to co-tutored phd thesis.

Thanks a lot and in advance for any suggestion and help,
best wishes
sofia p.

maxcite=?

Hi,

Would anyone know how to change the number of named authors from the current 2 to 3? I use the standard template (i.e. I haven't changed any of the default options)

References in the text

My promoter want to see the references in the text like authoryear
for example: (Berckmans, 2013).

default of ASDPHD is numbers.

How can i change it?

Error caused by a float in a specific position

I'm experiencing a frustrating error I've never encountered.
Frustrating because I can't locate the actual error in the .log and because it seems to be caused by the simple placement of a specific figure environment (the error doesn't occur if I use a different figure?!) in a specific place (the error doesn't occur if I comment out all the text and just leave the figure in the chapter?!).

I can't really post an MWE because the error seems to be dependent on the specific order of all the sections I am inputting; although I'm not sure how much this might help, I can upload the logs coming from the error-free and error-containing compilation, hoping that someone can spot something I've missed:

gb_phd_dissert_error.txt
gb_phd_dissert_OK.txt

The specific figure I'm talking about is the following:

cmp_PB_KF_AF_diff_vs_musigma_IR_ha42_0dB.pdf

if needed I can post the tikz code used to generate it.

published chapters references

Each Chapter starts with an opening page. Is it possible to indicated on this page a note that the chapter has been published as a journal paper, with the reference?

Issues with tikz image externalization

Hi guys,
I'm using the tikz package for my images, but it seems that the template creates some problems when externalizing (i.e. creating a PDF file from the tikz image to speed up the inclusion when compiling the whole template) tikz images.

You can see the correct and wrong outcomes here:

Correct.pdf
Wrong.pdf

Do you have any idea of what causes this clash?

Typo in README.md

In the "special chapters" section it says "dutch abstract (prefacenl)" while it should be "dutch preface (prefacenl)".

Example for chapter with previous publication

For a PhD by publication it would be great if your template supports handling multiple bibliographies, i.e. for each publication chapter.

(As you already kindly provide an commented example on how to cite a chapter as your own previous publication in "introduction.tex", I thought it would be useful to include a full example for this.)

Glossary

Hello,

Thanks very much for the template, it has been quite useful. There is one issue I cannot seem te resolve: I'm having problems with the glossary.

This is the code in the thesis.tex file. However, the glossary does not show up. Any suggestions how this could be resolved?
Many thanks.
Joris

% To avoid problems, do NOT change the layout of the following two
% commands
\let\printglossaryorig\printglossary
\renewcommand{\printglossary}{%
\renewcommand{\glossaryname}{\glossname}
\cleardoublepage%
\printglossaryorig\chaptermark{\glossname}}

\usepackage{glossary}
\makeglossary
\glossary{name=MD,description=molecular dynamics}

% Specify the .bib file
\bibliography{allpapers}

% Bibtex style
\bibstyle{abbrv}
\bibstyle{acm}

% Own commands
\InputIfFileExists{defs} % defs.tex, contains own preamble settings

% }{}}} <-- Preamble

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%\makefrontcover
\makefrontcoverXII

\maketitle

\frontmatter % to get \pagenumbering{roman}

%\includepreface{preface}
%\includeabstract{abstract}
%\includeabstractnl{abstractnl}

% To create a list of abbreviations, there are 2 options
% 1. manual creation and inclusion of this file
% \includeabbreviations{abbreviations}
% 2. automatic generation via the glossary package

%\printglossary

\printglossary

Bibliography back-references

Hello,
when I started to work on my thesis I decided to enter manually the bibliography in each chapter.
Now the thesis is ready and corrected, but I noticed utterly annoying back-references after compilation.
For example:
[1] Y. Taur, and E. Nowak CMOS devices below 0.1 μm: how high will
performance go? IEEE Proc. IEDM, 215-218 (1997) pages 3

I have been trying for days to get rid of this awful thing, but couldn't find any command.
Please help.

! LaTeX Error: File `mfirstuc.sty' not found.

I just downloaded the whole thing today and only changed the names on the front page but when I try to compile I get this error:
! LaTeX Error: File `mfirstuc.sty' not found.

Can anyone help me with this?

Thanks

make bare

The documentation states:

To create a bare document containing just the chapter text (i.e., NO TOC and
references), use the 'bare' target.

For me, it does the exact opposite. It creates a document with ONLY the TOC and the references.

Package "glossary" is deprecated

It is currently advised to use "glossaries" instead.

ftp://ftp.dante.de/tex-archive/macros/latex/contrib/glossaries/glossary2glossaries.pdf

Rasterization of some of the template fonts

I noticed that the pdf produced compiling the template presents some rasterized fonts; specifically, the titles of each chapter, section, subsection, the disclaimer at page 4 etc...

Is that supposed to be normal?

make index

Dear,
I am concerning how to make indeces under adsphd.
It have been trying doing myself but I am stuck.
Can anyone help me this?
Thanks in advance,
Hieu

image not displayed in curriculum

Hi,
I tried to add an image in the 'curriculum' chapter. For some reason it doesn't show up. Could you help fix this issue? I'm using TexWorks on Windows 7.

the code:
\chapter{Curriculum Vitae}\label{ch:curriculum}

%\ldots

%\instructionscv
\begin{figure}[H]
\centering
\medskip
\includegraphics[width=0.9\textwidth]{photo1}
\caption{Vijay}
\label{fig:photo1}
\end{figure}

\textbf{2003--2005} Master of Science (Physics)

\textbf{2010--2014} Doctor of Philosophy (Physics) at KU Leuven

Includegraphics in appendix chapter

Using includegraphics inside an appendix chapter always results in a "file not found" error

However, in "thesis.tex", if I use includechapter{appendix} instead of includeappendix{appendix}, the figure is successfully included.

What could be the problem here? I'm using version 1.2 of the adsphd template

error while converting .ps to .pdf

Hi,
I found the latex template through the site of the ADS. After spending some time reading and copy-paste-editing files, I managed to get something out of the Make.

Unfortunately during the conversion from .ps to .pdf ps2pdf encounters an error. I'll copy-paste it below. Can anybody help me out, please ?

Thanks for your help (and for the latex-template) !!

grtz
jo

ps2pdf -dMaxSubsetPct=100 -dSubsetFonts=true -dEmbedAllFonts=true -dPDFSETTINGS=/printer -dCompatibilityLevel=1.4 thesis.ps thesis.pdf
GPL Ghostscript 9.05: Set UseCIEColor for UseDeviceIndependentColor to work properly.
Error: /undefined in ���
Operand stack:

Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1910 1 3 %oparray_pop 1909 1 3 %oparray_pop 1893 1 3 %oparray_pop 1787 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval--
Dictionary stack:
--dict:1168/1684(ro)(G)-- --dict:1/20(G)-- --dict:93/200(L)-- --dict:213/300(L)-- --dict:85/200(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 1183609
GPL Ghostscript 9.05: Unrecoverable error, exit code 1
GPL Ghostscript 9.05: ERROR: A pdfmark destination page 20 points beyond the last page 19.
make: *** [thesis.pdf] Error 1

Bump chapter headings to next page of TOC if they are alone

What I have in the TOC is:

CHAPTER W
...
...

CHAPTER X
----------- Latex inserts page break here -------

chapter x subheading 1 chapter x subheading 2

And this is what I want to happen:

Table of Contents

... some stuff here ....

CHAPTER W
...
...

CHAPTER X
chapter x subheading 1
chapter x subheading 2

Somebody knows how to fix this?

In-text references

Hi, I have some experience with latex, but not nearly enough to figure out this issue.

I would like to use some references in the body of my thesis (not just in the references part): the idea is that at the end of the first chapter (Introduction), I'd have a breakdown of the content of the following chapters, and here I'd also like to list the publications each chapter was based on.

For this I tried to use the \bibentry command from the bibentry package, which included nothing.
I also tried to use the \fullcite command from the biblatex package, but it seems that the biblatex package is not working with the acm bibiliography style, which I am using, so that's also not a viable solution.

And at this point I'm out of ideas, and was hoping someone more knowledgeable in latex could help me.
(BTW I'm using windows 7, texmaker, and the chain of commands I use to create my pdf is the following:

pdflatex -synctex=1 -interaction=nonstopmode %.tex
bibtex %
makeindex -s %.ist -t %.nlg -o %.nls -t %.glg -o %.gls %.nlo %.glo
pdflatex -synctex=1 -interaction=nonstopmode %.tex
makeindex %.nlo -s nomencl.ist -o %.nls
pdflatex -synctex=1 -interaction=nonstopmode %.tex
makeindex %.nlo -s nomencl.ist -o %.nls|pdflatex -synctex=1 -interaction=nonstopmode %.tex
"C:/Program Files (x86)/Adobe/Reader 11.0/Reader/AcroRd32.exe" %.pdf)

Thank you in advance for any help.

List of Symbols not showing in the pdf

Hi,

This is my first post here, so I hope I will be able to give all necessary details, so that someone can help me. My problem is that the List of symbols is not showing up in my pdf, even if I don't modify the downloaded package in any way, just unzip it, and compile it with a latex editor.

I'm using Windows 7, and a latex editor called TexMaker. The chain of commands I use to create the pdf is the following:

  1. pdflatex -synctex=1 -interaction=nonstopmode %.tex
  2. bibtex %
  3. makeindex -s %.ist -t %.nlg -o %.nls -t %.glg -o %.gls %.nlo %.glo
  4. pdflatex -synctex=1 -interaction=nonstopmode %.tex
  5. pdflatex -synctex=1 -interaction=nonstopmode %.tex

This is based on a description I found somewhere when I was trying to solve a problem of the List of Abbreviations not showing up. Now that list is in my pdf, but unfortunately the list of symbols is still not there. I hope there will be someone on this forum who can help me.

side-by-side figures

The adsphd template uses the deprecated packages subfig and subfigure. I tried to put figures side by side, but did not manage to. If I want to use the newer subcaption package, I get complaints about incompatibilities.

Is there a way to either:

  • simply put figures side by side using the adsphd as it is
  • use the subcaption package without errors

Many thanks
Rik

The option british is buggy

There are a lot of \selectlanguage{english} statements which should probably be \selectlanguage{british} when using the british option.

Undefined control sequence

Hi,
I just downloaded the ZIP-file and tried to compile the thesis.tex file as it is. I got many error messages, and the first ones are about line 50:

Line Message
line 50 ! Undefined control sequence.
line 50 ! LaTeX Error: Missing \begin{document}.
line 50 ! Extra }, or forgotten $.
line 50 ! LaTeX Error: Bad math environment delimiter.

Could anyone please help me? Thanks!

Todo notes are visible in the 'tothejury' version

When using the tothejury version for sending my thesis to the jury, I noticed that the todo notes were still visible, which is not consistent with what is written in the Readme. I fixed that in my fork (tassos@f63cc35), but as I am waiting for a pull request to be accepted, I will wait with making a new pull request with this one.

Just reporting it here, so that people that want to send their thesis to the jury are aware that their todo notes will be visible.

minus sign in equation is shown as space

when I try to write an equation with minus sign "-", the minus is shown as space instead. For example:
\begin{equation}
a - 1
\end{equation}
the output is :"a 1" instead of "a-1" in the output .pdf.
I use "make" to compile the document. I did not define any extra packages.

Thank you!

cover page

I have some troubles creating the cover page using the comand make cover.
I get the following error.
Class adsphd Error: Unsupported value '' for class option 'faculty'.

See the adsphd class documentation for explanation.
Type H for immediate help.
...

l.393 ...r class option 'faculty'}{\MessageBreak}}

Question (not an issue)

Dear,

Sorry in advance since this is probably not the right forum for questions, but this seems very specific to the adsphd template.

How do you get rid of the labels that are printed in the right margin (for example in the original version of thesis.pdf from github, the label '{ch:manual}' that appear on the upper right margin of p5)

Thanks in advance,

Not loading of glossary and nomenclature in Texstudio pdf (windows)

Hi,
I'm working with the thesis template, but I'm not super familiar with latex yet. At the moment the glossary and nomenclature doesn't show in the pdf. I read here that I need to use 'makeindex' for Linux. But I was wondering how I can fix it in windows7.

Hereunder is the main thesis. text file I use.

Sincerely,
Daan
..............................
\documentclass[pagebackref,showinstructions,showlabels,coverfontpercent=100]{adsphd}
%\documentclass[pagebackref,showinstructions,showlabels,biblatex,biber,biblatexstyle=authoryear]{adsphd}
%\documentclass[croppedpdf,pagebackref,showinstructions]{adsphd}
%\documentclass[online]{adsphd}
%\documentclass[print]{adsphd}

% To use biblatex:
%\documentclass[biblatex,biblatexstyle=authoryear,showinstructions,showlabels]{adsphd}

% Preamble {{{}{

\usepackage[english,dutch]{babel}

\usepackage{nomencl} % For nomenclature
\usepackage[style=long,number=none]{glossary} % For list of abbreviations

% !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
% !! !!
% !! WARNING: do not remove the following lines between !!
% !! "%%% COVER: Settings %%%" and "%%% COVER: End settings %%%" !!
% !! !!
% !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

%%% COVER: Settings %%%
\title{First principle study of defects in III-V on oxide ($GaAsO_4$)}
%\subtitle{Multiscale computing for Dummies}

\author{Daan}{Lipkens}

\supervisor{Prof.~Dr.~Michel Houssa}{}
%\cosupervisor{Prof.~dr.~ir.~R.Cools}{}
%\president{Prof.~dr.~ir.DeVoorzitter}
%\jury{Prof.~dr.~ir.DenEne
% Prof.~dr.~ir.~Den Andere
%}
%\externaljurymember{Prof.dr.Hetexternjurylid}{Ver weg}

\phddegree{Physics} % "Doctor of ..."
\faculty{Faculty of Science}
\department{Department of Physics and Astronomy}
\researchgroup{Semiconductor Physics Laboratory}
\address{Celestijnenlaan 200D, B-3001, Leuven, Belgium}
% \addresscity{B-3001 Heverlee} % This is the default value. Note
% that 'B-3001 Leuven' is incorrect!!
% /[http://www.kuleuven.be/communicatie/schrijven/taalgebruik.html]
\email{[email protected]} % Leave empty to hide
\website{} % Leave empty to hide

\date{June 2014}
\copyyear{2014}
%\udc{XXX.XX} % UDC is no longer necessary.
\depot{XXXX/XXXX/XX} % Leave out the initial D/ (it is added
% automatically)
\isbn{XXX-XX-XXXX-XXX-X}

% Set spine width:
\setlength{\adsphdspinewidth}{9mm}

%% Set bleeds
%\setlength{\defaultlbleed}{7mm}
%\setlength{\defaultrbleed}{7mm}

% Set custom cover page
\setcustomcoverpage{mycoverpage.tex} % mycoverpage.tex is the default Masterproef_NL_2012.tex

%%% COVER: End settings %%%

% for the nomenclature
\renewcommand{\nomname}{List of Symbols}
\makeatletter
\let@printnomenclatureorig@printnomenclature
\def@printnomenclature[#1]{%
\cleardoublepage%
\chaptermark{\nomname}
@printnomenclatureorig[#1]
}
\makeatother
\makenomenclature

% for the list of abbreviations.
\newcommand{\glossname}{Abbreviations}
\makeglossary

% To avoid problems, do NOT change the layout of the following two
% commands
\let\printglossaryorig\printglossary
\renewcommand{\printglossary}{%
\renewcommand{\glossaryname}{\glossname}
\cleardoublepage%
\printglossaryorig\chaptermark{\glossname}}

% Specify the .bib file
\bibliography{allpapers}
% For biblatex include the extension
%\bibliography{allpapers.bib}
%\addbibresource{allpapers.bib}

% Bibtex style
%\bibstyle{abbrv}
\bibstyle{acm}
%\bibstyle{ieeetr}

% Own commands
\InputIfFileExists{defs}{}{} % defs.tex, contains own preamble settings

% }{}}} <-- Preamble

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%\makefrontcoverX
\makefrontcoverXII

\maketitle

\frontmatter % to get \pagenumbering{roman}

\includepreface{preface}
\includeabstract{abstract}
\includeabstractnl{abstractnl}

% To create a list of abbreviations, there are 2 options
% 1. manual creation and inclusion of this file
% \includeabbreviations{abbreviations}
% 2. automatic generation via the glossary package
% \usepackage{glossary}
% \makeglossary
% \glossary{name=MD,description=molecular dynamics}
% \printglossary
\printglossary

% To create a list of symbols, there are 2 options
% 1. include a manually created nomenclature as a chapter
% \includenomenclature{nomenclaturechapter}
% 2. automatic generation via the nomencl package
% \usepackage{nomencl}
% \makenomenclature
% \nomenclature[cB]{$c_B(\vec{x})$}{Characteristic function of $B$}
% \printnomenclature[3cm]
\printnomenclature[3cm]

\tableofcontents
\listoffigures
\listoftables

% Show an overview of todos with page numbers...
\listoftodos

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\mainmatter % to get \pagenumbering{arabic}

% Show instructions on a separate page
\instructionschapters\cleardoublepage

\includechapter{introduction}
\includechapter{manual} % Remove this chapter

% Insert here your own chapters
% Chapters are expected to be in a tex-file with the given name dot
% tex and in a directory with the given name in the chapters
% directory.

\includechapter{conclusion}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\appendix

\includeappendix{myappendix}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\backmatter

\includebibliography
\instructionsbibliography

%\includecv{curriculum}

%\includepublications{publications}

%\makebackcoverX
\makebackcoverXII

\end{document}

% vim: tw=70 nocindent expandtab foldmethod=marker foldmarker={{{}{,}{}}}

All the entries in the glossary link to the coverpage

I changed the way the glossary works in my template, in order to have different subsections describing math notation, acronyms etc..

However, every entry of each of the different glossaries points always to page a, which is the first page of the coverpage. Any idea of why this happens?

Here's the MWE, where I define four entries of math notation, each pointing to a

\documentclass[showinstructions,faculty=firw,department=cws,phddegree=cws]{adsphd}
%\documentclass[showinstructions,showlabels,coverfontpercent=100,faculty=firw,department=cws,phddegree=cws]{adsphd}
%\documentclass[croppedpdf,showinstructions,faculty=firw,department=cws,phddegree=cws]{adsphd}
%\documentclass[online,faculty=firw,department=cws,phddegree=cws]{adsphd}
%\documentclass[print,bleed,cropmarks,faculty=firw,department=cws,phddegree=cws]{adsphd} % include bleed for the print service
%\documentclass[print,faculty=firw,department=cws,phddegree=cws]{adsphd}
%\documentclass[final,faculty=firw,department=cws,phddegree=cws]{adsphd}

\usepackage[acronym,shortcuts,style=alttree,nopostdot,nolist,section]{glossaries}
\glssetwidest{mylongstring}% widest name

% !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
% !!                                                               !!
% !!  WARNING: do not remove the following lines between           !!
% !!  "%%% COVER: Settings %%%" and "%%% COVER: End settings %%%"  !!
% !!                                                               !!
% !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

%%% COVER: Settings %%%
\title{The Title of Your PhD Dissertation}
%\subtitle{Multiscale computing for Dummies}

\author{Your}{Name}

\supervisor{Prof.~dr.~ir.~B.~Leader}{}
\supervisor{Prof.~dr.~ir.~S.~Second-Leader}{}
\president{Prof.~dr.~ir.~The~Chairman}
\jury{Prof.~dr.~ir.~The~One\\
      Prof.~dr.~ir.~The~Other
}
\externaljurymember{Prof.~dr.~External~Jurymember}{Far Away}

% Your research group within the department
% e.g. iMinds-DistriNet, Scientific Computing Group, ...
\researchgroup{XXXXX}
\website{http://www.XXXXX.cs.kuleuven.be} % Leave empty to hide
\email{[email protected]} % Leave empty to hide

\address{Celestijnenlaan 200A box 2402}
% \addresscity{B-3001 Leuven} % This is the default value. Note
                              % that 'B-3001 Heverlee' is _incorrect_!!
                              % /[https://www.kuleuven.be/communicatie/marketing/intranet/huisstijl/taalgebruik.html]

\date{January 2016}
\copyyear{2016}
%\udc{XXX.XX}            % UDC, deposit number and ISBN are no longer necessary.
%\depot{XXXX/XXXX/XX}    % Leave out the initial D/ (it is added
                         % automatically)
%\isbn{XXX-XX-XXXX-XXX-X}


\makeatletter
\def\cleartextposbox{\global\setbox\TP@holdbox\vbox{}}
\makeatother

% Set spine width:
\setlength{\adsphdspinewidth}{9mm}

%% Set bleeds
%\setlength{\defaultlbleed}{7mm}
%\setlength{\defaultrbleed}{7mm}

% Set custom cover page
% \setcustomcoverpage{mycoverpage.tex} % mycoverpage.tex is the default

%%% COVER: End settings %%%

% Definition of new glossaries ----------------------------------------
% Define math notation glossary
\newglossary[nlg]{notation}{not}{ntn}{Mathematical notation}
% Define abbreviation glossary
%\newglossary[abb]{abbrev}{abr}{abv}{Abbreviations}
\makeglossaries
% --------------------------------------------------------------------

\newglossaryentry{not:scalar}{
% This entry goes in the ‘notation’ glossary:
    type=notation,
    name={\ensuremath{b}},
    description={scalar},
    sort={aaa}
}
\newglossaryentry{not:vector}{
% This entry goes in the ‘notation’ glossary:
    type=notation,
    name={\ensuremath{\mathbf{b}}},
    description={vector},
    sort={aab}
}
\newglossaryentry{not:matrix}{
% This entry goes in the ‘notation’ glossary:
    type=notation,
    name={\ensuremath{\mathbf{B}}},
    description={matrix},
    sort={aac}
}
\newglossaryentry{not:Imatrix}{
% This entry goes in the ‘notation’ glossary:
    type=notation,
    name={\ensuremath{\mathbf{I}_M}},
    description={Identity matrix},
    sort={aad}
}
\glsaddall

% Fonts
\usepackage{microtype}
\usepackage[T1]{fontenc}
\usepackage{lmodern}  % to make pdf searchable
\usepackage{textcomp} % nice greek alphabet
\usepackage{pifont}   % Dingbats
\usepackage{booktabs}
\usepackage{amssymb,amsthm}
\usepackage{amsmath}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\makefrontcoverXII

\maketitle

\frontmatter % to get \pagenumbering{roman}

\chapter*{List of Terms and Acronyms}
\printglossary[title={Abbreviations},type={abbrev}] %
\printglossary[type=\acronymtype]
\printglossary[title={Mathematical notation},type={notation}] %

\tableofcontents
\listoffigures
\listoftables

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\mainmatter % to get \pagenumbering{arabic}

% Show instructions on a separate page
\instructionschapters\cleardoublepage


% Clear boxes used on the front page as they should have been printed by now
\cleartextposbox

%\includechapter{introduction}
%\includechapter{manual} % Remove this chapter

% Insert here your own chapters
% Chapters are expected to be in a tex-file with the given name dot
% tex and in a directory with the given name in the chapters
% directory.

\includechapter{conclusion}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\appendix

\includeappendix{myappendix}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\backmatter

\includebibliography
% BibTex
\bibliographystyle{acm}
\bibliography{allpapers}
% BibLatex (comment lines above and comment out biblatex lines in preamble)
%\printbibliography[title=\bibname]
\instructionsbibliography

\includecv{curriculum}

\includepublications{publications}

\makebackcoverXII

\end{document}

Glossary: using entries failed

Dear,

I want to use the defined glossary "MD" in the example of this template as follows,
----------------- latex -------------------------
\glossary{name=MD,description=molecular dynamics}
\

\gls{MD}

But the \gls{MD} did not work.

Is this the correct way to use the glossary?

Many thanks guys,

Elber

Margin settings and line spacing

Hello,

I'm writing my masters thesis, but they didn't give much guidelines for LaTex.
Word-guidelines specify a line spacing of exactly 18pt. Using 18pt leading however seems huge. Can anyone tell me how to mimic the 18pt in Word?

Also, I'd like to change the margins of my document. What are the standard margins ADS recommends?

Regarding lay out, I currently use:

\documentclass[12pt]{article}
\usepackage[font={small}]{caption}
\usepackage{leading}
\leading{12pt}

\begin{document}
\setlength{\parskip}{0.12cm plus2mm minus1mm}

Thanks for your time!

Hyperref footnotes broken by setspace

Hyperref's footnote links refer to the title page. This seems to be caused by the package setspace, which is loaded after the hyperref in adsphd.cls.

Suggested solution: move the following from lines 684-685 to lines 487-488 in adsphd.cls.
% To easily change line spacing
\RequirePackage{setspace}

In-text citations

Hi, I am new in this latex templates so, my question might be basic.

I would like to use the template, but I want to use in-text citations instead of numbers, like this:

'Latex is difficult (Someone et al., 1914).'

and then list them in the References section.

Is it possible to achieve it using the current template, I tried to use the natbib package but I am not clear how to adapt it.

List of symbols not appearing in table of content

I have this part in the main file of the thesis:

\includepreface{preface}
\includeabstract{abstract}
\includeabstractnl{abstractnl}
\tableofcontents
\listoffigures
\listoftables
\includenomenclature{nomenclaturechapter}

\mainmatter
...

The list of symbols itself appears in the text but it is not shown in the table of content. Does anyone know why that is and how to solve it?

Thanks!

adsphd-master - glossaries don't show up

Hello,

I'm having some issues using the glossaries package. When I run the sample downloaded today (23September) from the git-hub and run it, I also don't get the example glossary.

This problem may be related with the latest update of my latex version (I updated to the latest version yesterday). Does anyone know how to correct this?

Thanks.

Manually generated list of symbols included twice

I have my own (manually generated) list of symbols in "symbols.tex", which I put in the directory "/chapters/symbols/". As a test, this file contains only one symbol and is given by:

\chapter{List of Symbols}
\nomenclature[B]{$a$}{test}
\cleardoublepage

When I start from the current adsphd-template and try to add my list of symbols by commenting out the line:
\includenomenclature{symbols}

then, thesis.pdf contains 2 lists of symbols: 1 empty list of two pages having only "List of Symbols" as header followed by my actual "symbols.tex" symbol list (result: see attached file).
In addition, there is only one entry in the table of contents for "List of Symbols" and the page refers to the empty list of symbols.
Any idea what I am doing wrong ?
thesis.pdf

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