initial commit

paper/.latexmk

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+#!/bin/env perl
+
+# Shebang is only to get syntax highlighting right across GitLab, GitHub and IDEs.
+# This file is not meant to be run, but read by `latexmk`.
+
+# ======================================================================================
+# Perl `latexmk` configuration file
+# ======================================================================================
+
+# ======================================================================================
+# PDF Generation/Building/Compilation
+# ======================================================================================
+
+@default_files=('dehaeze24_nano_active_stabilization_system.tex');  
+
+# PDF-generating modes are:
+# 1: pdflatex, as specified by $pdflatex variable (still largely in use)
+# 2: postscript conversion, as specified by the $ps2pdf variable (useless)
+# 3: dvi conversion, as specified by the $dvipdf variable (useless)
+# 4: lualatex, as specified by the $lualatex variable (best)
+# 5: xelatex, as specified by the $xelatex variable (second best)
+$pdf_mode = 1;
+
+# Treat undefined references and citations as well as multiply defined references as
+# ERRORS instead of WARNINGS.
+# This is only checked in the *last* run, since naturally, there are undefined references
+# in initial runs.
+# This setting is potentially annoying when debugging/editing, but highly desirable
+# in the CI pipeline, where such a warning should result in a failed pipeline, since the
+# final document is incomplete/corrupted.
+#
+# However, I could not eradicate all warnings, so that `latexmk` currently fails with
+# this option enabled.
+# Specifically, `microtype` fails together with `fontawesome`/`fontawesome5`, see:
+# https://tex.stackexchange.com/a/547514/120853
+# The fix in that answer did not help.
+# Setting `verbose=silent` to mute `microtype` warnings did not work.
+# Switching between `fontawesome` and `fontawesome5` did not help.
+$warnings_as_errors = 0;
+
+# Show used CPU time. Looks like: https://tex.stackexchange.com/a/312224/120853
+$show_time = 1;
+
+# Default is 5; we seem to need more owed to the complexity of the document.
+# Actual documents probably don't need this many since they won't use all features,
+# plus won't be compiling from cold each time.
+$max_repeat=7;
+
+# --shell-escape option (execution of code outside of latex) is required for the
+#'svg' package.
+# It converts raw SVG files to the PDF+PDF_TEX combo using InkScape.
+#
+# SyncTeX allows to jump between source (code) and output (PDF) in IDEs with support
+# (many have it). A value of `1` is enabled (gzipped), `-1` is enabled but uncompressed,
+# `0` is off.
+# Testing in VSCode w/ LaTeX Workshop only worked for the compressed version.
+# Adjust this as needed. Of course, only relevant for local use, no effect on a remote
+# CI pipeline (except for slower compilation, probably).
+#
+# %O and %S will forward Options and the Source file, respectively, given to latexmk.
+#
+# `set_tex_cmds` applies to all *latex commands (latex, xelatex, lualatex, ...), so
+# no need to specify these each. This allows to simply change `$pdf_mode` to get a
+# different engine. Check if this works with `latexmk --commands`.
+set_tex_cmds("--shell-escape -interaction=nonstopmode --synctex=1 %O %S");
+
+# Use default pdf viewer
+$pdf_previewer = 'zathura';
+
+# option 2 is same as 1 (run biber when necessary), but also deletes the
+# regeneratable bbl-file in a clenaup (`latexmk -c`). Do not use if original
+# bib file is not available!
+$bibtex_use = 2;  # default: 1
+
+# Change default `biber` call, help catch errors faster/clearer. See
+# https://web.archive.org/web/20200526101657/https://www.semipol.de/2018/06/12/latex-best-practices.html#database-entries
+$biber = "biber --validate-datamodel %O %S";
+
+# ======================================================================================
+# Auxiliary Files
+# ======================================================================================
+
+# Let latexmk know about generated files, so they can be used to detect if a
+# rerun is required, or be deleted in a cleanup.
+# loe: List of Examples (KOMAScript)
+# lol: List of Listings (`listings` and `minted` packages)
+# run.xml: biber runs
+# glg: glossaries log
+# glstex: generated from glossaries-extra
+push @generated_exts, 'loe', 'lol', 'run.xml', 'glg', 'glstex';
+
+# Also delete the *.glstex files from package glossaries-extra. Problem is,
+# that that package generates files of the form "basename-digit.glstex" if
+# multiple glossaries are present. Latexmk looks for "basename.glstex" and so
+# does not find those. For that purpose, use wildcard.
+# Also delete files generated by gnuplot/pgfplots contour plots
+# (.dat, .script, .table).
+$clean_ext = "%R-*.glstex %R_contourtmp*.*";
+

paper/config.tex

@@ -0,0 +1 @@
+

paper/dehaeze24_nano_active_stabilization_system.bib

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+@inproceedings{dehaeze18_sampl_stabil_for_tomog_exper,
+  author          = {Thomas Dehaeze and M. Magnin Mattenet and Christophe
+                  Collette},
+  title           = {Sample Stabilization For Tomography Experiments In Presence
+                  Of Large Plant Uncertainty},
+  booktitle       = {MEDSI'18},
+  year            = 2018,
+  number          = 10,
+  pages           = {153--157},
+  doi             = {10.18429/JACoW-MEDSI2018-WEOAMA02},
+  url             = {https://doi.org/10.18429/JACoW-MEDSI2018-WEOAMA02},
+  address         = {Geneva, Switzerland},
+  isbn            = {978-3-95450-207-3},
+  keywords        = {nass, esrf},
+  language        = {english},
+  month           = {Dec},
+  publisher       = {JACoW Publishing},
+  series          = {Mechanical Engineering Design of Synchrotron Radiation
+                  Equipment and Instrumentation},
+  venue           = {Paris, France},
+}
+
+
+
+@inproceedings{dehaeze21_mechat_approac_devel_nano_activ_stabil_system,
+  author          = {Dehaeze, T. and Bonnefoy, J. and Collette, C.},
+  title           = {Mechatronics Approach for the Development of a
+                  Nano-Active-Stabilization-System},
+  booktitle       = {MEDSI'20},
+  year            = 2021,
+  language        = {english},
+  publisher       = {JACoW Publishing},
+  series          = {Mechanical Engineering Design of Synchrotron Radiation
+                  Equipment and Instrumentation},
+  venue           = {Chicago, USA},
+  keywords        = {nass, esrf},
+}
+

paper/dehaeze24_nano_active_stabilization_system.org

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+#+TITLE:
+:DRAWER:
+#+LATEX_CLASS: iopconfser
+#+OPTIONS: toc:nil date:nil
+#+STARTUP: overview
+
+#+DATE:
+#+AUTHOR:
+
+# #+LATEX_HEADER: \input{config.tex}
+
+#+LATEX_HEADER_EXTRA: \usepackage[backend=biber,style=iopart-num]{biblatex}
+#+LATEX_HEADER_EXTRA: \addbibresource{dehaeze24_nano_active_stabilization_system.bib}
+:END:
+
+* LaTeX Config                                                      :noexport:
+#+begin_src latex :tangle config.tex
+
+#+end_src
+
+* Build                                                             :noexport:
+#+name: startblock
+#+BEGIN_SRC emacs-lisp :results none
+  (add-to-list 'org-latex-classes
+               '("iopconfser"
+                 "\\documentclass{iopconfser}"
+                 ("\\section{%s}" . "\\section*{%s}")
+                 ("\\subsection{%s}" . "\\subsection*{%s}")
+                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+               )
+
+  (setq org-latex-packages-alist nil)
+  (setq org-latex-default-packages-alist nil)
+
+  ;; Remove automatic org headings
+  (defun my-latex-filter-removeOrgAutoLabels (text backend info)
+    "Org-mode automatically generates labels for headings despite explicit use of `#+LABEL`. This filter forcibly removes all automatically generated org-labels in headings."
+    (when (org-export-derived-backend-p backend 'latex)
+      (replace-regexp-in-string "\\\\label{sec:org[a-f0-9]+}\n" "" text)))
+
+  (add-to-list 'org-export-filter-headline-functions
+               'my-latex-filter-removeOrgAutoLabels)
+
+  ;; Automatic delete org org-comments
+  (defun delete-org-comments (backend)
+    (loop for comment in (reverse (org-element-map (org-element-parse-buffer)
+                                      'comment 'identity))
+          do
+          (setf (buffer-substring (org-element-property :begin comment)
+                                  (org-element-property :end comment))
+                "")))
+
+  ;; add to export hook
+  (add-hook 'org-export-before-processing-hook 'delete-org-comments)
+
+  ;; Remove hypersetup
+  (setq org-latex-with-hyperref nil)
+
+  ;; Remove empty title as it is manually placed after "/begin{document}"
+  (defun my-org-latex-remove-title (str)
+    (replace-regexp-in-string "^\\\\title{}$" "" str))
+
+  (advice-add 'org-latex-template :filter-return 'my-org-latex-remove-title)
+
+  ;; Remove empty date
+  (defun my-org-latex-remove-date (str)
+    (replace-regexp-in-string "^\\\\date{}$" "" str))
+
+  (advice-add 'org-latex-template :filter-return 'my-org-latex-remove-date)
+#+END_SRC
+
+* Title                                                               :ignore:
+
+#+begin_export latex
+\title{The Nano Active Stabilization System - Results on the ESRF ID31 Beamline}
+
+\author{Thomas Dehaeze$^{1,2}$ and Christophe Collette$^{2}$}
+
+\affil{$^1$European Synchrotron Radiation Facility Grenoble, France}
+\affil{$^2$Precision Mechatronics Laboratory University of Liege, Belgium}
+
+\email{thomas.dehaeze@esrf.fr}
+#+end_export
+
+* Abstract                                                            :ignore:
+
+# The abstract must be a single paragraph providing concise information about the content of the
+# article, including the main results obtained and conclusions drawn. The abstract must not contain any
+# table numbers, figure numbers, references or displayed mathematics. Leave at least 10 mm space below
+# the abstract before starting the main text of your article on the same page.
+
+#+begin_abstract
+This paper investigates...
+#+end_abstract
+
+* Introduction
+<<sec:introduction>>
+
+Here is the introduction ...
+Some citation:
+[[cite:&dehaeze18_sampl_stabil_for_tomog_exper]]
+[[cite:&dehaeze21_mechat_approac_devel_nano_activ_stabil_system]]
+
+* Conclusion
+<<sec:conclusion>>
+
+Conclusion text
+
+* Acknowledgment
+:PROPERTIES:
+:UNNUMBERED: t
+:END:
+
+This research benefited from a FRIA grant from the French Community of Belgium.
+
+* Bibliography                                                        :ignore:
+\printbibliography

paper/dehaeze24_nano_active_stabilization_system.tex

@@ -0,0 +1,43 @@
+% Created 2024-08-05 Mon 15:57
+% Intended LaTeX compiler: pdflatex
+\documentclass{iopconfser}
+
+\usepackage[backend=biber]{biblatex}
+
+\addbibresource{dehaeze24_nano_active_stabilization_system.bib}
+
+
+\begin{document}
+
+
+\title{The Nano Active Stabilization System - Results on the ESRF ID31 Beamline}
+
+\author{Thomas Dehaeze$^{1,2}$ and Christophe Collette$^{2}$}
+
+\affil{$^1$European Synchrotron Radiation Facility Grenoble, France}
+\affil{$^2$Precision Mechatronics Laboratory University of Liege, Belgium}
+
+\email{thomas.dehaeze@esrf.fr}
+
+\begin{abstract}
+This paper investigates\ldots{}
+\end{abstract}
+
+\section{Introduction}
+\label{sec:introduction}
+
+Here is the introduction \ldots{}
+Some citation:
+\cite{dehaeze18_sampl_stabil_for_tomog_exper}
+\cite{dehaeze21_mechat_approac_devel_nano_activ_stabil_system}
+
+\section{Conclusion}
+\label{sec:conclusion}
+
+Conclusion text
+
+\section*{Acknowledgment}
+This research benefited from a FRIA grant from the French Community of Belgium.
+
+\printbibliography
+\end{document}

paper/iopconfser.cls

@@ -0,0 +1,99 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{iopconfser}[2022/11/30 IOP Conference Series LaTeX template]
+
+\LoadClass[a4paper]{article}
+
+
+% Margin settings
+\setlength{\hoffset}{0mm}
+\setlength{\marginparsep}{0mm}
+\setlength{\marginparwidth}{0mm}
+\setlength{\textwidth}{160mm}
+\setlength{\oddsidemargin}{-0.4mm}
+\setlength{\evensidemargin}{-0.4mm}
+\setlength{\voffset}{0mm}
+\setlength{\headheight}{8mm}
+\setlength{\headsep}{5mm}
+\setlength{\footskip}{0mm}
+\setlength{\textheight}{230mm}
+\setlength{\topmargin}{1.6mm}
+
+% More length definitions
+\setlength\maxdepth{.5\topskip}
+\setlength\@maxdepth\maxdepth
+\setlength\footnotesep{8.4\p@}
+\setlength{\skip\footins} {10.8\p@ \@plus 4\p@ \@minus 2\p@}
+\setlength\floatsep       {14\p@ \@plus 2\p@ \@minus 4\p@}
+\setlength\textfloatsep   {24\p@ \@plus 2\p@ \@minus 4\p@}
+\setlength\intextsep      {16\p@ \@plus 4\p@ \@minus 4\p@}
+\setlength\dblfloatsep    {16\p@ \@plus 2\p@ \@minus 4\p@}
+\setlength\dbltextfloatsep{24\p@ \@plus 2\p@ \@minus 4\p@}
+\setlength\@fptop{0\p@}
+\setlength\@fpsep{10\p@ \@plus 1fil}
+\setlength\@fpbot{0\p@}
+\setlength\@dblfptop{0\p@}
+\setlength\@dblfpsep{10\p@ \@plus 1fil}
+\setlength\@dblfpbot{0\p@}
+\setlength\partopsep{3\p@ \@plus 2\p@ \@minus 2\p@}
+
+% Set indent for front matter
+\renewenvironment{quote}%
+  {\list{}{\leftmargin=25mm}\item\relax}%
+  {\endlist}
+
+% Clear the header and footer
+
+\pagestyle{empty}
+
+% Styles for front matter
+
+\renewcommand{\title}[1]{\vspace*{25mm}{\exhyphenpenalty=10000\hyphenpenalty=10000 
+ \fontsize{18}{24}\selectfont\bf\noindent\raggedright
+        \textsf{#1}\par}}
+
+		
+\renewcommand{\author}[1]{\vspace*{1.5pc}%
+   \fontsize{11}{13}
+       \begin{quote}\raggedright \textbf{#1}\end{quote}}
+
+\newcommand{\affil}[1]{\fontsize{10}{11}\selectfont
+       \begin{quote}\raggedright #1\end{quote}
+	   \vspace*{-22pt}}
+
+\newcommand{\email}[1]{\vspace*{12pt}\fontsize{10}{11}\selectfont
+       \begin{quote}\raggedright E-mail: #1\end{quote}
+	   \vspace*{-22pt}}
+
+\renewenvironment{abstract}{%
+      \vspace{16pt plus3pt minus3pt}
+      \begin{quote}
+      \bfseries \abstractname.\quad\rm\ignorespaces} 
+      {\end{quote}\vspace{5mm}}
+
+% Section titles
+	
+\renewcommand\section{\@startsection {section}{1}{\z@}%
+                   {-3.25ex\@plus -1ex \@minus -.2ex}%
+                   {1sp}%
+                   {\reset@font\normalsize\bfseries\raggedright}}
+\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
+                   {-3.25ex\@plus -1ex \@minus -.2ex}%
+                   {1sp}%
+                   {\reset@font\normalsize\itshape\raggedright}}
+\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
+                                     {-3.25ex\@plus -1ex \@minus -.2ex}%
+                                     {-1em \@plus .2em}%
+                                     {\reset@font\normalsize\itshape}}
+\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
+                                    {3.25ex \@plus1ex \@minus.2ex}%
+                                    {-1em}%
+                                    {\reset@font\normalsize\itshape}}
+\renewcommand\subparagraph{\@startsection{subparagraph}{5}{\parindent}%
+                                       {3.25ex \@plus1ex \@minus .2ex}%
+                                       {-1em}%
+                                      {\reset@font\normalsize\itshape}}
+			
+
+
+
+\endinput