Version sent for printing the book

config_extra.tex

@@ -26,6 +26,8 @@
 \usepackage{floatrow}
 \floatsetup[table]{font={footnotesize,sf},capposition=top}
 
+ % \usepackage[bottom=2.5cm]{geometry}
+
 \clubpenalty         = 10000
 \widowpenalty        = 10000
 \displaywidowpenalty = 10000

phd-thesis.org

@@ -10,8 +10,9 @@
 #+DATE: {{{time(%Y-%m-%d)}}}
 
 #+LATEX_CLASS: scrreprt
-#+LaTeX_CLASS_OPTIONS: [a4paper, 10pt, DIV=12, parskip=full, bibliography=totoc]
+# #+LaTeX_CLASS_OPTIONS: [a4paper, twoside, headings=openright, 10pt, DIV=12, BCOR=1cm, parskip=full, bibliography=totoc, usegeometry]
-# #+LATEX_CLASS_OPTIONS: [a4paper, twoside, 11pt, onecolumn, bibliography=totoc, openright, appendixprefix=true]
+#+LaTeX_CLASS_OPTIONS: [a4paper, twoside, headings=openright, 10pt, DIV=13, BCOR=1cm, parskip=full, bibliography=totoc]
+# #+LaTeX_CLASS_OPTIONS: [a4paper, 10pt, DIV=12, parskip=full, bibliography=totoc]
 
 #+OPTIONS: num:t toc:nil ':t *:t -:t ::t <:nil author:t date:t tags:nil todo:nil |:t H:5 title:nil
 
@@ -276,12 +277,16 @@ This approach represents a modest contribution towards a more open, reliable, an
 
 * Grants                                                              :ignore:
 
-#+begin_export latex
+#+latex: \vspace*{\fill}
-\newpage
+
-\thispagestyle{empty}
-\vspace*{\fill}
 The research presented in this manuscript has been possible thanks to the Fonds de la recherche scientifique (FRS-FNRS) through a FRIA grant given to Thomas Dehaeze.
-\vspace*{\fill}
+
+#+begin_export latex
+% \newpage
+% \thispagestyle{empty}
+% \vspace*{\fill}
+% The research presented in this manuscript has been possible thanks to the Fonds de la recherche scientifique (FRS-FNRS) through a FRIA grant given to Thomas Dehaeze.
+% \vspace*{\fill}
 #+end_export
 
 * Table of Contents                                                   :ignore:
@@ -649,7 +654,7 @@ A more comprehensive review of actively controlled end-stations is provided in S
 #+attr_latex: :width 0.95\linewidth
 [[file:figs/introduction_stages_villar.jpg]]
 #+end_subfigure
-#+attr_latex: :caption \subcaption{\label{fig:introduction_stages_nazaretski} NSLS-II HXN - Microscope. 1 and 2 are focusing optics, 3 is the sample location, 4 the sample stage and 5 the interferometers \cite{nazaretski17_desig_perfor_x_ray_scann}}
+#+attr_latex: :caption \subcaption{\label{fig:introduction_stages_nazaretski} NSLS-II HXN. 1 and 2 are focusing optics, 3 is the sample location, 4 the sample stage and 5 the interferometers \cite{nazaretski17_desig_perfor_x_ray_scann}}
 #+attr_latex: :options {0.48\textwidth}
 #+begin_subfigure
 #+attr_latex: :scale 0.9
@@ -1535,7 +1540,7 @@ The cumulative amplitude spectrum of the distance $d$ with all three active damp
 All three active damping methods give similar results.
 
 #+name: fig:uniaxial_cas_active_damping
-#+caption: Comparison of the acrlong:cas of the distance $d$ for all three active damping techniques.
+#+caption: Comparison of the Cumulative Amplitude Spectrum of the distance $d$ for all three active damping techniques.
 #+attr_latex: :options [htbp]
 #+begin_figure
 #+attr_latex: :caption \subcaption{\label{fig:uniaxial_cas_active_damping_soft}$k_n = 0.01\,\text{N}/\upmu\text{m}$}
@@ -2487,7 +2492,7 @@ For small values of $\omega_i$, the added damping is limited by the maximum allo
 For larger values of $\omega_i$, the attainable damping ratio decreases as a function of $\omega_i$ as was predicted from the root locus plot of Figure\nbsp{}ref:fig:rotating_iff_root_locus_hpf_large.
 
 #+name: fig:rotating_iff_modified_effect_wi
-#+caption: Root loci for several high-pass filter cut-off frequency (\subref{fig:rotating_root_locus_iff_modified_effect_wi}). The achievable damping ratio decreases as $\omega_i$ increases (\subref{fig:rotating_iff_hpf_optimal_gain}).
+#+caption: Root loci for several high-pass filter cut-off frequency (\subref{fig:rotating_root_locus_iff_modified_effect_wi}). Achievable damping ratio decreases as $\omega_i$ increases (\subref{fig:rotating_iff_hpf_optimal_gain}).
 #+attr_latex: :options [htbp]
 #+begin_figure
 #+attr_latex: :caption \subcaption{\label{fig:rotating_root_locus_iff_modified_effect_wi}Root locus}
@@ -2727,7 +2732,7 @@ It does not increase the low-frequency coupling as compared to the Integral Forc
 #+attr_latex: :caption \subcaption{\label{fig:rotating_rdc_root_locus}Root locus for Relative Damping Control}
 #+attr_latex: :options {0.49\linewidth}
 #+begin_subfigure
-#+attr_latex: :scale 0.8
+#+attr_latex: :scale 0.9
 [[file:figs/rotating_rdc_root_locus.png]]
 #+end_subfigure
 #+attr_latex: :caption \subcaption{\label{fig:rotating_rdc_damped_plant}Damped plant using Relative Damping Control}
@@ -2949,7 +2954,7 @@ The gain is chosen such that 99% of modal damping is obtained (obtained gains ar
 | $0.01\,\text{N}/\upmu\text{m}$ |  1600 |               0.99 |
 | $1\,\text{N}/\upmu\text{m}$  |  8200 |               0.99 |
 | $100\,\text{N}/\upmu\text{m}$ | 80000 |               0.99 |
-#+latex: \captionof{table}{\label{tab:rotating_rdc_opt_params_nass}Obtained optimal parameters for the acrlong:rdc}
+#+latex: \captionof{table}{\label{tab:rotating_rdc_opt_params_nass}Obtained optimal parameters for the RDC}
 #+end_minipage
 
 ***** Comparison of the Obtained Damped Plants
@@ -8055,7 +8060,7 @@ The sensor dynamics estimate $\hat{G}_i(s)$ may be a simple gain or a more compl
 #+caption: Sensor models with and without normalization.
 #+attr_latex: :options [htbp]
 #+begin_figure
-#+attr_latex: :caption \subcaption{\label{fig:detail_control_sensor_model}Model with noise $n_i$ and acrshort:lti transfer function $G_i(s)$}
+#+attr_latex: :caption \subcaption{\label{fig:detail_control_sensor_model}Model with noise $n_i$ and LTI transfer function $G_i(s)$}
 #+attr_latex: :options {0.48\textwidth}
 #+begin_subfigure
 #+attr_latex: :scale 1

phd-thesis.tex

@@ -1,6 +1,6 @@
-% Created 2025-07-09 Wed 19:41
+% Created 2025-07-15 Tue 13:58
 % Intended LaTeX compiler: pdflatex
-\documentclass[a4paper, 10pt, DIV=12, parskip=full, bibliography=totoc]{scrreprt}
+\documentclass[a4paper, twoside, headings=openright, 10pt, DIV=13, BCOR=1cm, parskip=full, bibliography=totoc]{scrreprt}
 
 \input{config.tex}
 \newacronym{adc}{ADC}{Analog to Digital Converter}
@@ -55,7 +55,7 @@
 \addbibresource{ref.bib}
 \addbibresource{phd-thesis.bib}
 \author{Dehaeze Thomas}
-\date{2025-07-09}
+\date{2025-07-15}
 \title{Nano Active Stabilization of samples for tomography experiments: A mechatronic design approach}
 \subtitle{PhD Thesis}
 \hypersetup{
@@ -193,11 +193,15 @@ The organization of the code mirrors that of the manuscript, with corresponding
 All materials have been made available under the MIT License, permitting free reuse.
 
 This approach represents a modest contribution towards a more open, reliable, and collaborative scientific ecosystem.
-\newpage
-\thispagestyle{empty}
 \vspace*{\fill}
+
 The research presented in this manuscript has been possible thanks to the Fonds de la recherche scientifique (FRS-FNRS) through a FRIA grant given to Thomas Dehaeze.
-\vspace*{\fill}
+
+% \newpage
+% \thispagestyle{empty}
+% \vspace*{\fill}
+% The research presented in this manuscript has been possible thanks to the Fonds de la recherche scientifique (FRS-FNRS) through a FRIA grant given to Thomas Dehaeze.
+% \vspace*{\fill}
 \clearpage
 \dominitoc
 \tableofcontents
@@ -523,7 +527,7 @@ A more comprehensive review of actively controlled end-stations is provided in S
 \begin{center}
 \includegraphics[scale=1,scale=0.9]{figs/introduction_stages_nazaretski.png}
 \end{center}
-\subcaption{\label{fig:introduction_stages_nazaretski} NSLS-II HXN - Microscope. 1 and 2 are focusing optics, 3 is the sample location, 4 the sample stage and 5 the interferometers \cite{nazaretski17_desig_perfor_x_ray_scann}}
+\subcaption{\label{fig:introduction_stages_nazaretski} NSLS-II HXN. 1 and 2 are focusing optics, 3 is the sample location, 4 the sample stage and 5 the interferometers \cite{nazaretski17_desig_perfor_x_ray_scann}}
 \end{subfigure}
 \caption{\label{fig:introduction_active_stations}Example of two end-stations with real-time position feedback based on an online metrology.}
 \end{figure}
@@ -1346,7 +1350,7 @@ All three active damping methods give similar results.
 \end{center}
 \subcaption{\label{fig:uniaxial_cas_active_damping_stiff}$k_n = 100\,\text{N}/\upmu\text{m}$}
 \end{subfigure}
-\caption{\label{fig:uniaxial_cas_active_damping}Comparison of the \acrlong{cas} of the distance \(d\) for all three active damping techniques.}
+\caption{\label{fig:uniaxial_cas_active_damping}Comparison of the Cumulative Amplitude Spectrum of the distance \(d\) for all three active damping techniques.}
 \end{figure}
 \paragraph{Conclusion}
 Three active damping strategies have been studied for the \acrfull{nass}.
@@ -2233,7 +2237,7 @@ For larger values of \(\omega_i\), the attainable damping ratio decreases as a f
 \end{center}
 \subcaption{\label{fig:rotating_iff_hpf_optimal_gain}Attainable damping ratio as a function of $\omega_i/\omega_0$. Maximum and optical control gains are also shown}
 \end{subfigure}
-\caption{\label{fig:rotating_iff_modified_effect_wi}Root loci for several high-pass filter cut-off frequency (\subref{fig:rotating_root_locus_iff_modified_effect_wi}). The achievable damping ratio decreases as \(\omega_i\) increases (\subref{fig:rotating_iff_hpf_optimal_gain}).}
+\caption{\label{fig:rotating_iff_modified_effect_wi}Root loci for several high-pass filter cut-off frequency (\subref{fig:rotating_root_locus_iff_modified_effect_wi}). Achievable damping ratio decreases as \(\omega_i\) increases (\subref{fig:rotating_iff_hpf_optimal_gain}).}
 \end{figure}
 \paragraph{Obtained Damped Plant}
 To study how the parameter \(\omega_i\) affects the damped plant, the obtained damped plants for several \(\omega_i\) are compared in Figure~\ref{fig:rotating_iff_hpf_damped_plant_effect_wi_plant}.
@@ -2438,7 +2442,7 @@ It does not increase the low-frequency coupling as compared to the Integral Forc
 \begin{figure}[htbp]
 \begin{subfigure}{0.49\linewidth}
 \begin{center}
-\includegraphics[scale=1,scale=0.8]{figs/rotating_rdc_root_locus.png}
+\includegraphics[scale=1,scale=0.9]{figs/rotating_rdc_root_locus.png}
 \end{center}
 \subcaption{\label{fig:rotating_rdc_root_locus}Root locus for Relative Damping Control}
 \end{subfigure}
@@ -2651,7 +2655,7 @@ The gain is chosen such that 99\% of modal damping is obtained (obtained gains a
 \(100\,\text{N}/\upmu\text{m}\) & 80000 & 0.99\\
 \bottomrule
 \end{tabularx}}
-\captionof{table}{\label{tab:rotating_rdc_opt_params_nass}Obtained optimal parameters for the acrlong:rdc}
+\captionof{table}{\label{tab:rotating_rdc_opt_params_nass}Obtained optimal parameters for the RDC}
 \end{minipage}
 \paragraph{Comparison of the Obtained Damped Plants}
 Now that the optimal parameters for the three considered active damping techniques have been determined, the obtained damped plants are computed and compared in Figure~\ref{fig:rotating_nass_damped_plant_comp}.
@@ -7451,7 +7455,7 @@ The sensor dynamics estimate \(\hat{G}_i(s)\) may be a simple gain or a more com
 \begin{center}
 \includegraphics[scale=1,scale=1]{figs/detail_control_sensor_model.png}
 \end{center}
-\subcaption{\label{fig:detail_control_sensor_model}Model with noise $n_i$ and acrshort:lti transfer function $G_i(s)$}
+\subcaption{\label{fig:detail_control_sensor_model}Model with noise $n_i$ and LTI transfer function $G_i(s)$}
 \end{subfigure}
 \begin{subfigure}{0.48\textwidth}
 \begin{center}

setup.org

@@ -125,6 +125,9 @@ I reduce the size of tables so that longer tables can still fit into an A4 (redu
 ** Geometry
 
 # \usepackage[paperheight=24.41cm,paperwidth=17.21cm,bottom=3cm,left=1.4cm,right=2cm,heightrounded]{geometry}
+#+begin_src latex
+ % \usepackage[bottom=2.5cm]{geometry}
+#+end_src
 
 ** Penalties
 #+begin_src latex