clean up

01-title.tex

@@ -1,70 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Title Page
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\pagestyle{empty}
-
-\begin{center}
-
-\phantom{} \\  \vspace{2cm}
-
-  \includegraphics[width=0.6\textwidth]{images/trex-logo.png}
-
-  \vspace{2cm}
-
-    {\Huge \DelNumber{} -- \DelTitle}\\\vspace{1cm}
-    {Version \DelVersion}
-
- \vspace*{\fill}
-
-  {\Huge {GA no 952165}}
-  \vspace{1cm}
-
-
-\end{center}
-\noindent
-  Dissemination Level\\[5mm]
-\newcommand{\Dissemination}{PU}    % TODO   <------
-  \begin{tabular*} {\textwidth}{rl}
-$\boxtimes$  & PU: Public  \\      % TODO   <------
-$\Box$       & PP: Restricted to other programme participants (including the Commission) \\
-$\Box$       & RE: Restricted to a group specified by the consortium (including the Commission) \\
-$\Box$       & CO: Confidential, only for members of the consortium (including the Commission)
-  \end{tabular*} \\
-
-
-
-\clearpage
-
-\pagestyle{fancy}
-\fancyhf{}
-\rhead{Overleaf}
-\lhead{Guides and tutorials}
-
-
-\renewcommand{\footrulewidth}{1pt}
-
-\lhead{ \includegraphics[width=1in]{images/trex-logo.png} }
-\rhead{ \DelNumber -- \DelTitle }
-
-\lfoot{
-%\setlength{\tabcolsep}{0.3em}
-\begin{tabular*}{0.9\textwidth}{l @{\extracolsep{\fill}}l}
-\begin{tabular}{c}                                             
-\includegraphics[width=0.1\textwidth]{images/EU_flag.png} \\
-\end{tabular}
-& 
-\begin{tabular}{p{0.75\textwidth}}
-  \footnotesize
-TREX: Targeting Real Chemical Accuracy at the Exascale project  has received
-funding from the European Union Horizon 2020 research and       innovation program
-under Grant Agreement No. 952165.
-\end{tabular} 
-\end{tabular*}
-}
-
-\rfoot{ \thepage\ of \pageref{LastPage}}
-
-
-
-

02-info.tex

@@ -1,61 +0,0 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Second Page 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\section*{Document Information}
-
-
-\renewcommand{\arraystretch}{1.5}
-
-\begin{tabular*}{\textwidth}{l p{12cm}}
-    Project Title    &   Targeting Real Chemical accuracy at the EXascale \\
-    Project Acronym & TREX \\
-    Grant Agreement No & 952165 \\
-    Instrument & Call: H2020-INFRAEDI-2019-1 \\
-    Topic & INFRAEDI-05-2020 Centres of Excellence in EXascale computing \\
-    Start Date of Project & 01-10-2020 \\
-    Duration of Project & 36 Months \\
-    Project Website & \url{https://trex-coe.eu/} \\
-& \\
-    Deliverable Number & \DelNumber \\
-    Deliverable title & \DelNumber{} -- \DelTitle, as seen in GA \\
-    Due Date & \DueDate (from GA) \\
-    Actual Submission Date & \SubDate \\
-& \\
-    Work Package & WP\WorkPackage{} -- \WorkPackageTitle \\
-    Lead Author (Org) & \LeadAuthor \\
-    Contributing Author(s) (Org) & \Contributors \\
-    Reviewers (Org) & \Reviewers \\
-    Version & \DelVersion \\
-& \\
-    Dissemination level & \Dissemination \\
-    Nature & Report \\
-    Draft / final & \DraftOrFinal \\  
-    No. of pages including cover & \pageref{LastPage} \\
-\end{tabular*}
-
-
-\clearpage
-\section*{Disclaimer}
-
-\setlength{\tabcolsep}{0.3em}
-\begin{tabular*}{\textwidth}{l @{\extracolsep{\fill}}l}
-
-\begin{tabular}{c}
-\includegraphics[width=0.15\textwidth]{images/EU_flag.png} \\
-\end{tabular}
-& 
-\begin{tabular}{p{0.8\textwidth}}
-TREX: Targeting Real Chemical Accuracy at the Exascale project has received
-funding from the European Union Horizon 2020 research and innovation program
-under Grant Agreement No. 952165.
-\end{tabular}
-\end{tabular*}
-
-\noindent The content of this document does not represent the opinion of the European
-Union, and the European Union is not responsible for any use that might be made
-of such content.
-
-
-\clearpage
-

03-versioning.tex

@@ -1,34 +0,0 @@
-\section*{Versioning and contribution history}
-
-\begin{tabular*}{\textwidth}{|l|@{\extracolsep{\fill}}l|p{2.2in}|p{2.2in}|}
-\hline
-Version & Date & Authors & Notes \\
-\hline
-  % Version
-    0.5
-  &
-  % Date
-    DD.MM.YYYY
-  &
-  % Contributor
-    Contributor (Institution)
-  &
-  % Description
-    Description
-  \\
-\hline
-  % Version
-    0.6
-  &
-  % Date
-    DD.MM.YYYY
-  &
-  % Contributor
-    Contributor (Institution)
-  &
-  % Description
-    Description
-  \\
-\hline
-\end{tabular*}
-\clearpage

04-abbreviations.tex

@@ -1,64 +0,0 @@
-%% COMMANDS
-%%
-%% \acresetall	flushes the ’memory’ of the macro \ac (ie all "used" marks flushed)
-%%
-%% \ac{label}	singular (first time Full Name + (ACRO) and mark as used)
-%% \acp{label}	plural (as \ac but makes short and/or long forms into plurals)
-%%
-%% \acs{lable}	short (ACRO)
-%% \acf{lable}	“full acronym” (Full Name + (ACRO))
-%% \acl{lable}	long (_without_ ACRO)
-%%
-%% \acsp{label}	short plural (ACROs)
-%% \acfp{label}	“full acronym” plural (Full Names + (ACROs))
-%% \aclp{label}	long plural (_without_ ACRO)
-%%
-%% \acrodef{label}[acronym]{written out form}	definition
-%%		for example \acrodef{etacar}[$\eta$ Car]{Eta Carinae},
-%%		with the restriction that the label should be simple ASCII
-
-
-%% PACKAGE & OPTIONS
-%% acronym package must be loaded (in the preamble):
-%%    \usepackage[option1,option2,etc.]{acronym}
-%% OPTIONS:
-%%    footnote		The option footnote makes the full name appear as a
-%%			footnote.
-%%    nohyperlinks	If hyperref is loaded, all acronyms will link to their
-%%			glossary entry. With the option nohyperlinks these
-%%			linkscan be suppressed.
-%%    printonlyused	Only list used acronyms
-%%    withpage		In printonlyused-mode show the page number where
-%%			each acronym was first used.
-%%    smaller		Make the acronym appear smaller.
-%%    dua			The option dua stands for “don’t use acronyms”. It
-%%			leads to a redefinition of \ac and \acp, making the
-%%			full name appear all the time and suppressing all
-%%			acronyms but the explicity requested by \acf or \acfp.
-%%    nolist		The option nolist stands for “don’t write the list of
-%%			acronyms”.
-
-
-%% INCLUSION
-%%
-\section*{Abbreviations}
-\label{sec:abbrev}
-
-\begin{acronym}[TRUST-IT] %width of the longest acronym should be matched here
-
-\acro{UT}{Universiteit Twente}
-\acro{CNRS}{Centre National de la Recherche Scientifique}
-\acro{SISSA}{Scuola Internazionale Superiore di Studi Avanzati di trieste}
-\acro{CINECA}{Consorzio Interuniversitario del Nord Est italiano per il Calcolo Automatico}
-\acro{FZJ}{Forschungszentrum Jülich GmbH}
-\acro{MPG}{Max Planck Gesellschaft zur forderung der wissenschaften}
-\acro{UVSQ}{Université de Versailles Saint-Quentin-en-yvelines}
-\acro{Megware}{Megware computer vertrieb und service GmbH}
-\acro{STUBA}{Slovenská technická univerzita v Bratislave}
-\acro{UNIVIE}{Universität Wien}
-\acro{TUL}{Politechnika Łódzka}
-\acro{TRUST-IT}{TRUST-IT SRL}
-
-
-\end{acronym}
-\clearpage

05-content.tex

@@ -1,9 +0,0 @@
-\section{Introduction}
-
-This repository contains the \Latex template for TREX reports.
-To use it, you should first create a 
-
-\section{Example}
-
-
-I am testing the acronyms of \ac{TUL} and \ac{CNRS}.

LICENSE

@@ -1,121 +0,0 @@
-Creative Commons Legal Code
-
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-    REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS
-    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
-    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
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-
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-applied by Affirmer to the Work. Should any part of the License for any
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-partial invalidity or ineffectiveness shall not invalidate the remainder
-of the License, and in such case Affirmer hereby affirms that he or she
-will not (i) exercise any of his or her remaining Copyright and Related
-Rights in the Work or (ii) assert any associated claims and causes of
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-express Statement of Purpose.
-
-4. Limitations and Disclaimers.
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- a. No trademark or patent rights held by Affirmer are waived, abandoned,
-    surrendered, licensed or otherwise affected by this document.
- b. Affirmer offers the Work as-is and makes no representations or
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-    this CC0 or use of the Work.

Makefile

@@ -1,20 +0,0 @@
-WP=2
-NUMBER=1
-TITLE=main
-
-NAME=D$(WP).$(NUMBER)-$(TITLE)
-TEX=$(NAME).tex
-PDF=$(NAME).pdf
-
-default: $(TEX) references.bib
-	pdflatex $(TEX)
-	pdflatex $(TEX)
-	bibtex $(TEX)
-	pdflatex $(TEX)
-
-create:
-	@test -f $(TEX) && \
-	echo  "File $(TEX) already exists" ||\
-        cp main.tex $(TEX)
-
-

README.org

@@ -1,123 +0,0 @@
-#+TITLE: TREX Reports latex template
-
-* Installation
-
-  To use this template, create a new GitHub repository by using this one
-  as a template.
-
-  #+begin_important
-  Make sure that both the /draft/ and /final/ branches are imported by checking
-  the box when you create your repository. 
-  #+end_important
-
-
-  In your new repository, start working on the /draft/ branch. When you submit
-  the pdf for review, create a pull request to the /final/ branch from
-  the /draft/ branch.
-
-  The reviewers can then use the GitHub code-review system to make
-  reviews of the document. When all the reviews are accepted, the pull
-  request is accepted to the /final/ branch.
-
-  #+begin_important
-  When the versions of the file are changed, be sure that you create a
-  git tag accordingly.
-  #+end_important
-
-
-** List of required LaTex Packages
-
-   - lastpage
-   - graphicx
-   - fancyhdr
-   - amsmath
-   - amssymb
-   - titlesec
-   - colortbl
-   - acronym
-   - tocloft
-   - hyperref
-   - xcolor
-   - xparse
-
-   
-* Manual
-
-** Initialization
-   
-   Edit the ~Makefile~ and provide:
-
-   - the Work Package (~WP~) number
-   - the ~NUMBER~ of the deliverable
-   - a ~TITLE~
-
-   Create the main file with the adapted name:
-   #+BEGIN_SRC sh
-   make create
-   #+END_SRC sh
-
-   This will create a file named =D$(WP).$(NUMBER)-$(TITLE).tex=,
-   which will be the main \LaTeX file.
-
-   Now, you can compile the example provided using 
-   #+BEGIN_SRC sh
-   make 
-   #+END_SRC sh
-
-   The output =pdf= file will contain a starting example of the report.
-  
-   
-** Meta-data
-
-   Open the main =tex= file (=D$(WP).$(NUMBER)-$(TITLE).tex=), and
-   fill in the macros in the prepared block. This information will be
-   re-used in multiple places in the document.
-  
-** Title Page
-
-   Search for the string ~TODO~ in the =01-title.tex= file.
-   You will need to change the ~\Dissemination~ macro according to the
-   chosen dissemination level. Default is /PU/.
-
-   You will also need to check the appropriate box of the front page.
-   Use ~$\boxtimes$~ for the checked box and ~$\Box$~ for the empty boxes.
-
-** The main document
-
-   The main text of your report will be written in the
- =05-content.tex= file.
-
-   The references can be handled with bibtex in the =references.bib=
-   file.
-
-   The appendices should be written in the =appendix.tex= file.
-
-   The images and figures should be put in the =images= directory.
-
-** Versioning
-
-   When the version changes, please create a git tag associated with
-   the commit containing the change.
-   
-** Abbreviations
-
-   Every time you use an abbreviation, don't do it inline in the
-   text. We use the [[http://mirrors.ctan.org/macros/latex/contrib/acronym/acronym.pdf][acronym]] \LaTeX package which allows to define the
-   acronym the 1st time it occurs in the text, and to create
-   automatically a list of acronyms, keeping only the ones that were
-   used in the text.
-
-   To add a new acronym, add it in the =04-abbreviations.tex=
-   file. For example:
-
-   #+begin_src latex
-   \acro{QMC}{Quantum Monte Carlo}
-   #+end_src
-
-   and to use it in the text, use the =\ac= macro, for example
-
-   #+begin_src latex
-   Thanks to the \ac{TREX} \ac{CoE}, \ac{QMC} methods will produce amazing results.
-   #+end_src
-
-

TREX.cls

@@ -1,110 +0,0 @@
-\ProvidesClass{TREX}
-\LoadClass[a4paper,twoside,final,12pt]{article}
-
-\usepackage[paper=a4paper,
-top=1.18in,bottom=1in,right=0.75in,left=0.75in]{geometry}% http://ctan.org/pkg/geometry
-\usepackage[utf8]{inputenc}
-\usepackage{lastpage}
-\usepackage{graphicx}
-\usepackage{fancyhdr}
-\usepackage{amsmath}
-\usepackage{amssymb}
-\usepackage{titlesec}
-\usepackage{colortbl}
-
-\renewcommand{\familydefault}{\sfdefault}
-
-\usepackage[printonlyused,nohyperlinks]{acronym}
-
-
-\usepackage[pdftex, pdfusetitle, hyperfigures, hyperindex,
-bookmarksnumbered,colorlinks, bookmarks, breaklinks,
-linktocpage, citecolor=blue, urlcolor=blue, linkcolor=black]{hyperref}
-
-\usepackage[titles]{tocloft}
-\renewcommand{\contentsname}{Table of Contents}
-\renewcommand{\cftsecfont}{\normalfont}% titles in bold
-\renewcommand{\cftsecpagefont}{\normalfont}% page numbers in bold
-\renewcommand{\cftdotsep}{1}
-\renewcommand{\cftsecleader}{\cftdotfill{\cftsecdotsep}}% dot leaders in bold
-
-\renewcommand{\cftsecdotsep}{\cftdotsep}
-
-
-
-\setlength{\headheight}{1cm}
-\setlength{\footskip}{2cm}
-\addtolength{\textheight}{-\footskip}
-
-
-%%--Set the section number depth.
-\setcounter{secnumdepth}{3}
-\setcounter{tocdepth}{4}
-\setcounter{page}{2}
-
-\bibliographystyle{IEEEtran}
-\sloppy
-
-%%-----------------------------------------------
-%%-- Float related environments and commands.
-%%-----------------------------------------------
-%%--Modify behavior of the figure and table environment.
-\def\fps@figure{hbt}
-\def\fnum@figure{\textbf{\figurename~\thefigure}}
-\def\fps@table{htb}
-\def\fnum@table{\textbf{\tablename~\thetable}}
-\def\mathfigure{\thesisfiguretrue\figure}
-\def\endmathfigure{\endfigure\thesisfigurefalse}
-
-% --------------------------------------------
-% Headers
-% --------------------------------------------
-\pagestyle{fancyplain}
-\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
-
-
-\usepackage{xcolor}
-\definecolor{myblue}{HTML}{2F5496}
-\titleformat{\section}
-{\color{myblue}\normalfont\Large}
-{\color{myblue}\thesection}{1em}{}
-
-
-\makeatletter
-\makeindex
-\makeglossary
-\setcounter{tocdepth}{4}
-\setcounter{secnumdepth}{1}
-
-% Table of contents with section*
-
-\usepackage{xparse}
-
-\let\oldsection\section
-\makeatletter
-\newcounter{@secnumdepth}
-\RenewDocumentCommand{\section}{s o m}{%
-  \IfBooleanTF{#1}
-    {\setcounter{@secnumdepth}{\value{secnumdepth}}% Store secnumdepth
-     \setcounter{secnumdepth}{0}% Print only up to \chapter numbers
-     \oldsection{#3}% \section*
-     \setcounter{secnumdepth}{\value{@secnumdepth}}}% Restore secnumdepth
-    {\IfValueTF{#2}% \section
-       {\oldsection[#2]{#3}}% \section[.]{..}
-       {\oldsection{#3}}}% \section{..}
-}
-\makeatother
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Floating figures
-\renewcommand\floatpagefraction{.9}
-\renewcommand\topfraction{.9}
-\renewcommand\bottomfraction{.9}
-\renewcommand\textfraction{.1}
-\setcounter{totalnumber}{50}
-\setcounter{topnumber}{50}
-\setcounter{bottomnumber}{50}
-
-\endinput
-
-

main.tex

@@ -1,72 +0,0 @@
-\documentclass{TREX}
-
-%------
-% TODO : Fill in this information
-
-% Work package number
-\newcommand{\WorkPackage}{2}
-
-% Work package title
-\newcommand{\WorkPackageTitle}{Code modularization and interfacing}  % 2
-
-% Deliverable number
-\newcommand{\DelID}{1}
-
-% Title of the Deliverable
-\newcommand{\DelTitle}{Title of this deliverable}
-
-% Due date
-\newcommand{\DueDate}{M06 -- 31-03-2021 (from GA)}
-
-% Actual submission date
-\newcommand{\SubDate}{21-12-2020}
-
-% Main author (Leader)
-\newcommand{\LeadAuthor}{Author (Institution)}
-
-% Contributing authors
-\newcommand{\Contributors}{Contributor (Institution), Contributor (Institution)}
-
-% Reviewers
-\newcommand{\Reviewers}{Reviewer (Institution), Reviewer (Institution)}
-
-% Deliverable version
-\newcommand{\DelVersion}{X.0}
-
-% Draft or final version?
-\newcommand{\DraftOrFinal}{Draft}
-
-%------
-
-\newcommand{\DelNumber}{D\WorkPackage.\DelID}
-
-
-\title{\DelNumber{} -- \DelTitle}
-\author{\LeadAuthor}
-
-
-\begin{document}
-
-\input{01-title}
-\input{02-info}
-\input{03-versioning}
-\input{04-abbreviations}
-
-\tableofcontents
-\clearpage
-\listoffigures
-\clearpage
-\listoftables  
-\clearpage
-
-\input{05-content}
-
-\bibliography{references}
-
-\appendix
-\input{appendix.tex}
-
-
-\end{document}
-
-