org-theme/index.org

#+TITLE: Test File for the Org Mode Theme
#+SUBTITLE: Simple set of CSS and JS files
:DRAWER:
#+STARTUP: overview

#+OPTIONS: num:t toc:t |:t p:t f:t todo:t tasks:t pri:t tags:t <:t *:t

#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas

#+HTML_LINK_HOME: ../index.html
#+HTML_LINK_UP:   ../index.html

#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="dist/style.css"/>
#+HTML_HEAD: <script type="text/javascript" src="dist/script.js"></script>

#+LaTeX_CLASS: scrreprt
#+LaTeX_HEADER_EXTRA: \input{preamble.tex}
#+LaTeX_HEADER_EXTRA: \addbibresource{ref.bib}

#+CSL_STYLE: ieee.csl

#+BIND: org-latex-default-table-environment "tabular"
#+BIND: org-latex-tables-booktabs nil

#+PROPERTY: header-args:matlab  :session *MATLAB*
#+PROPERTY: header-args:matlab+ :comments org
#+PROPERTY: header-args:matlab+ :results none
#+PROPERTY: header-args:matlab+ :exports both
#+PROPERTY: header-args:matlab+ :eval no-export
#+PROPERTY: header-args:matlab+ :output-dir figs
#+PROPERTY: header-args:matlab+ :tangle no
#+PROPERTY: header-args:matlab+ :mkdirp yes

#+PROPERTY: header-args:shell  :eval no-export

#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/Cloud/tikz/org/}{config.tex}")
#+PROPERTY: header-args:latex+ :imagemagick t :fit yes
#+PROPERTY: header-args:latex+ :iminoptions -scale 100% -density 150
#+PROPERTY: header-args:latex+ :imoutoptions -quality 100
#+PROPERTY: header-args:latex+ :results file raw replace
#+PROPERTY: header-args:latex+ :buffer no
#+PROPERTY: header-args:latex+ :eval no-export
#+PROPERTY: header-args:latex+ :exports results
#+PROPERTY: header-args:latex+ :mkdirp yes
#+PROPERTY: header-args:latex+ :output-dir figs
#+PROPERTY: header-args:latex+ :post pdf2svg(file=*this*, ext="png")
:END:

* Basics
** Normal Markup
You can make words *bold*, /italic/, _underlined_, =verbatim= and ~code~, and, if you must, +strike-through+.

Here is some inline code Matlab code: src_matlab[:exports code]{[K,CL,gamma] = mixsyn(G,W1,[],W3);}.

** Links to Footnotes

A link to a footnote[fn:1] and to another footnote[fn:2].

** Lists
*Unordered List*:
- Lorem ipsum dolor sit amet, consectetur adipiscing elit.
- Nam aliquet euismod viverra.
- Phasellus turpis nisi, faucibus a orci et, faucibus fermentum ligula.

*List with Tasks*:
- [ ] Task 1
- [X] Task 2
- [-] Sub-tasks:
  - [ ] Sub-task 1
  - [X] Sub-task 2

*Ordered List*:
1. In libero odio, imperdiet eget ex a, vulputate suscipit tellus.
2. Etiam sed leo ex.
3. Integer eu rutrum turpis.


*Nested Lists*:
- Nulla facilisi.
- Donec vulputate risus ut lectus bibendum, vitae fringilla odio tempus.
  1. In libero odio, imperdiet eget ex a, vulputate suscipit tellus.
  2. Etiam sed leo ex.
     - Nulla facilisi.
     - Donec vulputate risus ut lectus bibendum, vitae fringilla odio tempus.
  3. Integer eu rutrum turpis.
- Ut porta, quam id mattis feugiat, augue mauris bibendum sapien, a pulvinar mi lorem vitae nunc.
  - Integer eu rutrum turpis.
    - Sed pretium mattis nibh, vel lobortis augue semper vel.

*Definition List*:
- Lorem ipsum :: dolor sit amet, consectetur adipiscing elit.  Mauris laoreet
     sollicitudin venenatis.  Duis sed consequat dolor.
- Etiam feugiat :: pharetra sapien et semper.  Nunc ornare lacus sit amet massa
     auctor, vitae aliquam eros interdum.  Mauris arcu ante, imperdiet vel purus
     ac, bibendum faucibus diam.  Ut blandit nec mi at ultricies.  Donec eget
     mattis nisl.  In sed nibh felis.  Cras quis convallis orci.
- Sed aliquam :: odio sed faucibus aliquam, arcu augue elementum justo, ut
     vulputate ligula sem in augue.  Maecenas ante felis, pellentesque auctor
     semper non, eleifend quis ante.  Fusce enim orci, suscipit ac dapibus et,
     fermentum eu tortor.  Duis in facilisis ante, quis faucibus dolor.  Etiam
     maximus lorem quis accumsan vehicula.

** Links
Here is a list of links to:
- Figure [[fig:general_control_names]]
- Table [[tab:table_with_equations]]
- Listing [[lst:matlab_figure]]
- Specific [[(test)][line of code]]
- Equation eqref:eq:numbered
- Section [[sec:headlines]]
- Bibliographic Reference cite:stanisic14_effec, and cite:schulte11_activ_docum_with_org_mode,dominik10_org_mode_refer_manual_organ_gnu_emacs,stanisic14_effec

** Maths
Here is some inline mathematics: $z = 2$.

Unumbered equation:
\[ F(x) = \int_0^x f(t) dt \]

Using the =equation= environment in Eq. eqref:eq:numbered.
\begin{equation}
  F(s) = \int_0^\infty f(t) e^{-st} dt \label{eq:numbered}
\end{equation}

Using the =align= environment Equations eqref:eq:align_1 and eqref:eq:align_2.
\begin{align}
  \mathcal{F}(a) &= \frac{1}{2\pi i}\oint_\gamma \frac{f(z)}{z - a}\,dz \label{eq:align_1} \\
  \int_D (\nabla\cdot \mathcal{F})\,dV &=\int_{\partial D}\mathcal{F}\cdot n\, dS \label{eq:align_2}
\end{align}

** Verse, Quote

Below is a verse.

#+begin_verse
 Great clouds overhead
 Tiny black birds rise and fall
 Snow covers Emacs

    ---AlexSchroeder
#+end_verse

Below is a quote.

#+begin_quote
Nobody ever figures out what life is all about, and it doesn't matter.
Explore the world.
Nearly everything is really interesting if you go into it deeply enough.

    ---Richard P. Feynman
#+end_quote

** Aside
An aside block can be used as shown below.

#+begin_aside
This is a note about the text using the =aside= environment.
This can be as long as wanted
#+end_aside

Cras elementum ex vel orci congue porttitor. Vestibulum scelerisque gravida mattis. Suspendisse sit amet volutpat felis. Cras luctus porta lectus eget scelerisque. Cras blandit purus vel odio malesuada pellentesque. Interdum et malesuada fames ac ante ipsum primis in faucibus. Morbi eget aliquet sapien. Nunc eu elit in ligula aliquam congue dapibus eu massa. Sed accumsan hendrerit viverra. Quisque purus enim, tristique vitae porttitor eu, feugiat non ligula. Duis vitae ipsum vel quam ultricies ornare quis vitae quam. Vivamus commodo mauris non ex rutrum, sagittis facilisis metus tincidunt. Etiam vel nibh sit amet lorem auctor volutpat vel quis nulla. Quisque nec pharetra justo.

** Inline Task

Some text.

*************** TODO [#C] This is an inline task
SCHEDULED: <2020-11-26 jeu.>
*************** END

Some text.

* Headlines
<<sec:headlines>>

** Second level Headline with tags                              :@home:@work:
*** Third level Headline
**** Fourth level Headline
Aliquam aliquet sagittis lorem in rutrum. Cras pharetra viverra nisi, at placerat felis malesuada elementum. Donec tincidunt pharetra tincidunt. Praesent id lectus eget erat porttitor placerat non a magna. Cras non mauris ex. Morbi ut eros eu tellus egestas dapibus et et est. Aenean sollicitudin nibh enim, sed pulvinar massa iaculis sit amet. Vivamus egestas laoreet varius. Sed finibus libero nec quam tempor, eget viverra sapien fermentum. Donec dictum eleifend velit, vel elementum ex ultrices non. Vivamus mauris ex, ultrices quis sem vel, dapibus lacinia est. Praesent a sapien id diam venenatis finibus non vel justo. Cras sagittis tortor ac rutrum elementum. Maecenas luctus tempor enim, vitae suscipit quam consequat a. Phasellus feugiat congue sapien commodo cursus. Interdum et malesuada fames ac ante ipsum primis in faucibus.

*** Third level Headline
**** Fourth level Headline
Aliquam aliquet sagittis lorem in rutrum. Cras pharetra viverra nisi, at placerat felis malesuada elementum. Donec tincidunt pharetra tincidunt. Praesent id lectus eget erat porttitor placerat non a magna. Cras non mauris ex. Morbi ut eros eu tellus egestas dapibus et et est. Aenean sollicitudin nibh enim, sed pulvinar massa iaculis sit amet. Vivamus egestas laoreet varius. Sed finibus libero nec quam tempor, eget viverra sapien fermentum. Donec dictum eleifend velit, vel elementum ex ultrices non. Vivamus mauris ex, ultrices quis sem vel, dapibus lacinia est. Praesent a sapien id diam venenatis finibus non vel justo. Cras sagittis tortor ac rutrum elementum. Maecenas luctus tempor enim, vitae suscipit quam consequat a. Phasellus feugiat congue sapien commodo cursus. Interdum et malesuada fames ac ante ipsum primis in faucibus.

** TODO Second level Headline with Schedule
SCHEDULED: <2020-11-26 jeu.>

Aliquam aliquet sagittis lorem in rutrum. Cras pharetra viverra nisi, at placerat felis malesuada elementum. Donec tincidunt pharetra tincidunt. Praesent id lectus eget erat porttitor placerat non a magna. Cras non mauris ex. Morbi ut eros eu tellus egestas dapibus et et est. Aenean sollicitudin nibh enim, sed pulvinar massa iaculis sit amet. Vivamus egestas laoreet varius. Sed finibus libero nec quam tempor, eget viverra sapien fermentum. Donec dictum eleifend velit, vel elementum ex ultrices non. Vivamus mauris ex, ultrices quis sem vel, dapibus lacinia est. Praesent a sapien id diam venenatis finibus non vel justo. Cras sagittis tortor ac rutrum elementum. Maecenas luctus tempor enim, vitae suscipit quam consequat a. Phasellus feugiat congue sapien commodo cursus. Interdum et malesuada fames ac ante ipsum primis in faucibus.

** [#B] Second level Headline with a priority
Aliquam aliquet sagittis lorem in rutrum. Cras pharetra viverra nisi, at placerat felis malesuada elementum. Donec tincidunt pharetra tincidunt. Praesent id lectus eget erat porttitor placerat non a magna.

** TODO [#C] Second level Headline with TODO State
Vivamus egestas laoreet varius. Sed finibus libero nec quam tempor, eget viverra sapien fermentum. Donec dictum eleifend velit, vel elementum ex ultrices non. Vivamus mauris ex, ultrices quis sem vel, dapibus lacinia est. Praesent a sapien id diam venenatis finibus non vel justo.

** DONE [#A] Second level Headline with DONE State
CLOSED: [2020-11-26 jeu. 18:53]
Cras sagittis tortor ac rutrum elementum. Maecenas luctus tempor enim, vitae suscipit quam consequat a. Phasellus feugiat congue sapien commodo cursus. Interdum et malesuada fames ac ante ipsum primis in faucibus.

*** WAIT Third level Headline with DONE State
CLOSED: [2020-11-26 jeu. 18:53]
Cras non mauris ex. Morbi ut eros eu tellus egestas dapibus et et est. Aenean sollicitudin nibh enim, sed pulvinar massa iaculis sit amet.

* Blocks

#+begin_seealso
 =seealso= block.
#+end_seealso

#+begin_hint
 =hint= block.
#+end_hint

#+begin_definition
 =definition= block.
#+end_definition

#+begin_important
 =important= block.
#+end_important

#+begin_exampl
 =exampl= block.
#+end_exampl

#+begin_exercice
 =exercice= block.
#+end_exercice

#+begin_question
 =question= block.
#+end_question

#+begin_answer
 =answer= block.
#+end_answer

#+begin_summary
 =summary= block.
#+end_summary

#+begin_note
 =note= block.
#+end_note

#+begin_caution
 =caution= block.
#+end_caution

#+begin_warning
 =warning= block.
#+end_warning

* Source Blocks
** Matlab Init                                             :noexport:ignore:
#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
  <<matlab-dir>>
#+end_src

#+begin_src matlab :exports none :results silent :noweb yes
  <<matlab-init>>
#+end_src

** Figures
#+begin_src matlab
  t = 0:0.01:5; % Time [s]
  x = sin(2*pi*t); % Output Voltage [V]
#+end_src

#+begin_src matlab
  figure;
  plot(t, x);
  xlabel('Time [s]'); ylabel('Voltage [V]');
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
  exportFig('figs/matlab_fig_example.pdf', 'width', 'wide', 'height', 'normal');
#+end_src

#+name: fig:matlab_fig_example
#+caption: Matlab Figure
#+RESULTS:
[[file:figs/matlab_fig_example.png]]

** Table Result

#+begin_src matlab
  x = 1:10;
  y = x.^2;
#+end_src

#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
  data2orgtable([x', y'], {}, {'$x$', '$y = x^2$'}, ' %.0f ');
#+end_src

#+name: tab:table_name
#+caption: Table caption
#+RESULTS:
| $x$ | $y = x^2$ |
|-----+-----------|
|   1 |         1 |
|   2 |         4 |
|   3 |         9 |
|   4 |        16 |
|   5 |        25 |
|   6 |        36 |
|   7 |        49 |
|   8 |        64 |
|   9 |        81 |
|  10 |       100 |

** Inline Results

Results can be automatically outputed as shown below.

#+begin_src matlab :results value replace
  sqrt(2)
#+end_src

#+RESULTS:
: 1.4142


#+begin_src matlab :results output replace
  y
#+end_src

#+RESULTS:
: y =
:      1     4     9    16    25    36    49    64    81   100

** Caption and Reference

Captions can be added to code blocks.
Moreover, we can link to specific bode blocks (Listing [[lst:matlab_figure]] or [[lst:matlab_svd]]).

#+name: lst:matlab_figure
#+caption: Code to produce a nice contour plot
#+begin_src matlab
  figure;
  [X,Y,Z] = peaks;
  contour(X,Y,Z,20)
#+end_src

#+begin_src matlab :tangle no :exports results :results file replace
  exportFig('figs/matlab_logo.pdf', 'width', 'small', 'height', 'normal');
#+end_src

#+name: fig:matlab_logo
#+caption: Obtained Contour Plot
#+RESULTS:
[[file:figs/matlab_logo.png]]

#+name: lst:matlab_svd
#+caption: Code to compute the Singular Value Decomposition
#+begin_src matlab :results output replace
  A = [1 2; 3 4; 5 6; 7 8]
  [U,S,V] = svd(A)
#+end_src

#+RESULTS:
#+begin_example
A = [1 2; 3 4; 5 6; 7 8]
A =
     1     2
     3     4
     5     6
     7     8
[U,S,V] = svd(A)
U =
        -0.152483233310201         -0.82264747222566        -0.394501022283829        -0.379959133877596
        -0.349918371807964         -0.42137528768458         0.242796545704357         0.800655879510063
        -0.547353510305727       -0.0201031031435029         0.697909975442776        -0.461434357387336
         -0.74478864880349         0.381169081397575        -0.546205498863303        0.0407376117548695
S =
          14.2690954992615                         0
                         0         0.626828232417541
                         0                         0
                         0                         0
V =
        -0.641423027995072         0.767187395072177
        -0.767187395072177        -0.641423027995072
#+end_example

** Source Blocks with Line Numbers

The Listing [[lst:matlab_line_numbers]] has line numbers as the =-n= option was used.

Specific lines of codes can be referenced.
For instance, the code used to specify the wanted the vertical label is on line [[(test)]].

#+name: lst:matlab_line_numbers
#+caption: Specify Labels
#+begin_src matlab +n -r
  figure;
  plot(t, x)
  xlabel('Time [s]');
  ylabel('Output [V]'); (ref:test)
#+end_src

Numbering can be continued by using =+n= option as shown below.
#+begin_src matlab +n
  figure;
  plot(t, u)
  xlabel('Time [s]');
  ylabel('Input [V]');
#+end_src

* Images

Figure [[fig:general_control_names]] shows the results of the Tikz code of listing [[lst:tikz_test]].

#+name: lst:tikz_test
#+caption: Tikz code that is used to generate Figure [[fig:general_control_names]]
#+begin_src latex :file general_control_names.pdf :exports both
  \begin{tikzpicture}

    % Blocs
    \node[block={2.0cm}{2.0cm}] (P) {$P$};
    \node[block={1.5cm}{1.5cm}, below=0.7 of P] (K) {$K$};

    % Input and outputs coordinates
    \coordinate[] (inputw)  at ($(P.south west)!0.75!(P.north west)$);
    \coordinate[] (inputu)  at ($(P.south west)!0.25!(P.north west)$);
    \coordinate[] (outputz) at ($(P.south east)!0.75!(P.north east)$);
    \coordinate[] (outputv) at ($(P.south east)!0.25!(P.north east)$);

    % Connections and labels
    \draw[<-] (inputw) node[above left, align=right]{(weighted)\\exogenous inputs\\$w$} -- ++(-1.5, 0);
    \draw[<-] (inputu) -- ++(-0.8, 0) |- node[left, near start, align=right]{control signals\\$u$} (K.west);

    \draw[->] (outputz) node[above right, align=left]{(weighted)\\exogenous outputs\\$z$} -- ++(1.5, 0);
    \draw[->] (outputv) -- ++(0.8, 0) |- node[right, near start, align=left]{sensed output\\$v$} (K.east);
  \end{tikzpicture}
#+end_src

#+name: fig:general_control_names
#+caption: General Control Configuration
#+RESULTS:
[[file:figs/general_control_names.png]]

* Tables

Table [[tab:table_with_equations]] shows a table with some mathematics inside.

#+name: tab:table_with_equations
#+caption: A Simple table with included math
| $N$ | $N^2$ | $N^3$ | $N^4$ | $\sqrt n$ | $\sqrt[4]N$ |
|-----+-------+-------+-------+-----------+-------------|
|   1 |     1 |     1 |     1 |         1 |           1 |
|   2 |     4 |     8 |    16 | 1.4142136 |   1.1892071 |
|   3 |     9 |    27 |    81 | 1.7320508 |   1.3160740 |
#+TBLFM: $2=$1^2::$3=$1^3::$4=$1^4::$5=sqrt($1)::$6=sqrt(sqrt(($1)))

#+name: tab:table_without_head
#+caption: Table without Head
|     | *1* | *2* | *3* | *4* | *5* |
| *1* |   1 |   2 |   3 |   4 |   5 |
| *2* |   2 |   4 |   6 |   8 |  10 |
| *3* |   3 |   6 |   9 |  12 |  15 |
| *4* |   4 |   8 |  12 |  16 |  20 |
| *5* |   5 |  10 |  15 |  20 |  25 |

#+name: tab:table_multiple_heads
#+caption: Table with multiples groups
|                         |        *Classical Control*         |           *Modern Control*           |                            *Robust Control*                             |
| <l>                     |                <c>                 |                 <c>                  |                                   <c>                                   |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Date*                  |               1930-                |                1960-                 |                                  1980-                                  |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Tools*                 |         Transfer Functions         |       State Space formulation        |                               Disk margin                               |
|                         |           Nyquist Plots            |          Riccati Equations           | Systems and Signals Norms ($\mathcal{H}_\infty$, $\mathcal{H}_2$ Norms) |
|                         |             Bode Plots             |                                      |                     Closed Loop Transfer Functions                      |
|                         |       Phase and Gain margins       |                                      |                           Weighting Functions                           |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Control Architectures* | Proportional, Integral, Derivative |         Full State Feedback          |                      General Control Configuration                      |
|                         |            Leads, Lags             |               LQR, LQG               |                                                                         |
|                         |                                    |            Kalman Filters            |                                                                         |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Advantages*            |          Study Stability           |         Automatic Synthesis          |                           Automatic Synthesis                           |
|                         |               Simple               |                 MIMO                 |                                  MIMO                                   |
|                         |              Natural               |         Optimization Problem         |                          Optimization Problem                           |
|                         |                                    |                                      |                          Guaranteed Robustness                          |
|                         |                                    |                                      |                   Easy specification of performances                    |
|-------------------------+------------------------------------+--------------------------------------+-------------------------------------------------------------------------|
| *Disadvantages*         |           Manual Method            |       No Guaranteed Robustness       |                  Required knowledge of specific tools                   |
|                         |             Only SISO              | Difficult Rejection of Perturbations |               Need a reasonably good model of the system                |

* Details

Below is some content hidden until you click the bar.

#+HTML: <details><summary>Hiden Part</summary>
Almost anything can be put here for instance this table below.

#+name: tab:table_with_equations_bis
#+caption: A Simple table with included math
| $N$ | $N^2$ | $N^3$ | $N^4$ | $\sqrt n$ | $\sqrt[4]N$ |
|-----+-------+-------+-------+-----------+-------------|
|   1 |     1 |     1 |     1 |         1 |           1 |
|   2 |     4 |     8 |    16 | 1.4142136 |   1.1892071 |
|   3 |     9 |    27 |    81 | 1.7320508 |   1.3160740 |
#+TBLFM: $2=$1^2::$3=$1^3::$4=$1^4::$5=sqrt($1)::$6=sqrt(sqrt(($1)))

#+HTML: </details>

This =details= blocks can even be put in other blocks are shown below.

#+HTML: <details><summary>Answer</summary>
It is approximately *12,742 km*
#+HTML: </details>

#+begin_question
What is the approximate diameter of the earth?

#+HTML: <details><summary>Answer</summary>
It is approximately *12,742 km*
#+HTML: </details>
#+end_question

* Videos

yt:SzA2YODtgK4

* Bibliography                                                        :ignore:
#+latex: \printbibliography

* Footnotes                                                           :ignore:

[fn:1] A long foot note. Lorem ipsum dolor sit amet, consectetur adipiscing elit. With a reference to Figure [[fig:general_control_names]].
[fn:2] An other footnote.