diff --git a/01-title.tex b/01-title.tex deleted file mode 100644 index 873f89d..0000000 --- a/01-title.tex +++ /dev/null @@ -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}} - - - - diff --git a/02-info.tex b/02-info.tex deleted file mode 100644 index eeeb59f..0000000 --- a/02-info.tex +++ /dev/null @@ -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 - diff --git a/03-versioning.tex b/03-versioning.tex deleted file mode 100644 index 295b65d..0000000 --- a/03-versioning.tex +++ /dev/null @@ -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 diff --git a/04-abbreviations.tex b/04-abbreviations.tex deleted file mode 100644 index 1fe790d..0000000 --- a/04-abbreviations.tex +++ /dev/null @@ -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 diff --git a/05-content.tex b/05-content.tex deleted file mode 100644 index c7e0ec0..0000000 --- a/05-content.tex +++ /dev/null @@ -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}. diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 0e259d4..0000000 --- a/LICENSE +++ /dev/null @@ -1,121 +0,0 @@ -Creative Commons Legal Code - -CC0 1.0 Universal - - CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE - LEGAL SERVICES. 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Affirmer understands and acknowledges that Creative Commons is not a - party to this document and has no duty or obligation with respect to - this CC0 or use of the Work. diff --git a/Makefile b/Makefile deleted file mode 100644 index 073afdd..0000000 --- a/Makefile +++ /dev/null @@ -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 $(TEX) - - diff --git a/README.org b/README.org deleted file mode 100644 index 8cd31c5..0000000 --- a/README.org +++ /dev/null @@ -1,123 +0,0 @@ -#+TITLE: TREX Reports latex template - -* Installation - - To use this template, create a new GitHub repository by using this one - as a template. - - #+begin_important - Make sure that both the /draft/ and /final/ branches are imported by checking - the box when you create your repository. - #+end_important - - - In your new repository, start working on the /draft/ branch. When you submit - the pdf for review, create a pull request to the /final/ branch from - the /draft/ branch. - - The reviewers can then use the GitHub code-review system to make - reviews of the document. When all the reviews are accepted, the pull - request is accepted to the /final/ branch. - - #+begin_important - When the versions of the file are changed, be sure that you create a - git tag accordingly. - #+end_important - - -** List of required LaTex Packages - - - lastpage - - graphicx - - fancyhdr - - amsmath - - amssymb - - titlesec - - colortbl - - acronym - - tocloft - - hyperref - - xcolor - - xparse - - -* Manual - -** Initialization - - Edit the ~Makefile~ and provide: - - - the Work Package (~WP~) number - - the ~NUMBER~ of the deliverable - - a ~TITLE~ - - Create the main file with the adapted name: - #+BEGIN_SRC sh - make create - #+END_SRC sh - - This will create a file named =D$(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 - - diff --git a/TREX.cls b/TREX.cls deleted file mode 100644 index ddb362e..0000000 --- a/TREX.cls +++ /dev/null @@ -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 - - diff --git a/appendix.tex b/appendix.tex deleted file mode 100644 index e69de29..0000000 diff --git a/images/EU_flag.png b/images/EU_flag.png deleted file mode 100644 index e33462c..0000000 Binary files a/images/EU_flag.png and /dev/null differ diff --git a/images/trex-logo.png b/images/trex-logo.png deleted file mode 100644 index c4b9b18..0000000 Binary files a/images/trex-logo.png and /dev/null differ diff --git a/main.tex b/main.tex deleted file mode 100644 index 7ac03b7..0000000 --- a/main.tex +++ /dev/null @@ -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} - - diff --git a/src/Makefile b/parser/Makefile similarity index 100% rename from src/Makefile rename to parser/Makefile diff --git a/src/README.md b/parser/README.md similarity index 100% rename from src/README.md rename to parser/README.md diff --git a/src/TZ_1M_15k.det b/parser/TZ_1M_15k.det similarity index 100% rename from src/TZ_1M_15k.det rename to parser/TZ_1M_15k.det diff --git a/src/TZ_1M_15k.orb b/parser/TZ_1M_15k.orb similarity index 100% rename from src/TZ_1M_15k.orb rename to parser/TZ_1M_15k.orb diff --git a/src/TZ_1M_500.det b/parser/TZ_1M_500.det similarity index 100% rename from src/TZ_1M_500.det rename to parser/TZ_1M_500.det diff --git a/src/benzene.xyz b/parser/benzene.xyz similarity index 100% rename from src/benzene.xyz rename to parser/benzene.xyz diff --git a/src/buckyball.xyz b/parser/buckyball.xyz similarity index 100% rename from src/buckyball.xyz rename to parser/buckyball.xyz diff --git a/src/build.sh b/parser/build.sh similarity index 100% rename from src/build.sh rename to parser/build.sh diff --git a/src/caffeine.xyz b/parser/caffeine.xyz similarity index 100% rename from src/caffeine.xyz rename to parser/caffeine.xyz diff --git a/src/cas1010.sym b/parser/cas1010.sym similarity index 100% rename from src/cas1010.sym rename to parser/cas1010.sym diff --git a/src/global.inp b/parser/global.inp similarity index 100% rename from src/global.inp rename to parser/global.inp diff --git a/src/iochamp.f90 b/parser/iochamp.f90 similarity index 100% rename from src/iochamp.f90 rename to parser/iochamp.f90 diff --git a/src/jastrow_good_b3lyp.0 b/parser/jastrow_good_b3lyp.0 similarity index 100% rename from src/jastrow_good_b3lyp.0 rename to parser/jastrow_good_b3lyp.0 diff --git a/src/m_keywords.F90 b/parser/m_keywords.F90 similarity index 100% rename from src/m_keywords.F90 rename to parser/m_keywords.F90 diff --git a/src/m_periodic_table.F90 b/parser/m_periodic_table.F90 similarity index 100% rename from src/m_periodic_table.F90 rename to parser/m_periodic_table.F90 diff --git a/src/old/.gitignore b/parser/old/.gitignore similarity index 100% rename from src/old/.gitignore rename to parser/old/.gitignore diff --git a/src/old/Config_Fortran/Makefile b/parser/old/Config_Fortran/Makefile similarity index 100% rename from src/old/Config_Fortran/Makefile rename to parser/old/Config_Fortran/Makefile diff --git a/src/old/Config_Fortran/README.md b/parser/old/Config_Fortran/README.md similarity index 100% rename from src/old/Config_Fortran/README.md rename to parser/old/Config_Fortran/README.md diff --git a/src/old/Config_Fortran/benzene.xyz b/parser/old/Config_Fortran/benzene.xyz similarity index 100% rename from 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