Start the standardize the folder. Add org-mode files.

.SimulinkProject/Root.type.EntryPoints/63ca5d6e-cf1c-456e-953b-f40ba1181f39.type.EntryPoint.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info Type="Shutdown" Visible="0" Icon="" File="src/project_shutdown.m" Name="project_shutdown" />

.SimulinkProject/Root.type.EntryPoints/a4ed91fd-d721-41c7-9bd0-c3d905ab3003.type.EntryPoint.xml

@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<Info Type="Shutdown" Visible="0" Icon="" File="project_shutdown.m" Name="project_shutdown" />

.SimulinkProject/Root.type.EntryPoints/bede1981-8866-468d-a7c7-1307e358108e.type.EntryPoint.xml

@@ -1,2 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<Info Type="StartUp" Visible="0" Icon="" File="project_startup.m" Name="project_startup" />

.SimulinkProject/Root.type.EntryPoints/d1613206-2f1a-4f6f-8d33-2e688c9cb3cd.type.EntryPoint.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info Type="StartUp" Visible="0" Icon="" File="src/project_startup.m" Name="project_startup" />

.SimulinkProject/Root.type.Files/src.type.File.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info />

.SimulinkProject/Root.type.Files/src.type.File/1.type.DIR_SIGNIFIER.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info />

.gitignore

@@ -1,3 +1,11 @@
+auto/
+*.tex
+
+**/figs/*.pdf
+**/figs/*.svg
+**/figs/*.tex
+
+
 # Windows default autosave extension
 *.asv
 
@@ -26,9 +34,3 @@ octave-workspace
 
 # Simulink Cache
 *.slxc
-
-# Custom
-Assemblage_grt_rtw/
-Figures/
-data/
-movies/

active_damping/index.org

@@ -0,0 +1,42 @@
+#+TITLE:
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:

analysis/index.org

@@ -0,0 +1,42 @@
+#+TITLE: Some analysis
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:

config.tex

@@ -1,30 +0,0 @@
-% ======================
-% New Commands
-% ======================
-% H Infini
-\newcommand{\hinf}{\mathcal{H}_\infty}
-% H 2
-\newcommand{\htwo}{\mathcal{H}_2}
-% Omega
-\newcommand{\w}{\omega}
-% H-Infinity Norm
-\newcommand{\hnorm}[1]{\|#1\|_\infty}
-% H-2 Norm
-\newcommand{\normtwo}[1]{\|#1\|_2}
-% Norm
-\newcommand{\abs}[1]{\vert #1 \vert}
-% Minimum Subscript
-\newcommand{\smin}{_{\text{min}}}
-% Maximum Subscript
-\newcommand{\smax}{_{\text{max}}}
-% Power Spectral Density
-\newcommand{\psd}[1]{\Phi_{#1}}
-% Amplitude Spectral Density
-\newcommand{\asd}[1]{\phi_{#1}}
-% Cumulative Power Spectrum
-\newcommand{\cps}[1]{\Sigma_{#1}}
-% Cumulative Amplitude Spectrum
-\newcommand{\cas}[1]{\sigma_{#1}}
-% Root Mean Square Value
-\newcommand{\rms}[1]{\sigma_{#1}}
-% ======================

control/index.org

@@ -0,0 +1,42 @@
+#+TITLE:
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:

hac_lac/index.org

@@ -0,0 +1,42 @@
+#+TITLE:
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:

identification/index.org

@@ -0,0 +1,64 @@
+#+TITLE: Identification
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:
+
+* ZIP file containing the data and matlab files                      :ignore:
+#+begin_src bash :exports none :results none
+  if [ matlab/identification_micro_station.m -nt data/identification_micro_station.zip ]; then
+    cp matlab/identification_micro_station.m identification_micro_station.m;
+    zip data/identification_micro_station \
+        mat/data.mat \
+        identification_micro_station.m
+    rm identification_micro_station.m;
+  fi
+#+end_src
+
+#+begin_note
+  All the files (data and Matlab scripts) are accessible [[file:data/identification_micro_station.zip][here]].
+#+end_note
+
+
+* Identification of the micro-station
+
+* Plot the obtained transfer functions
+
+* Compare with the modal measurements

initialize/initializeGround.m

@@ -1,11 +0,0 @@
-function [ground] = initializeGround()
-    %%
-    ground = struct();
-
-    ground.shape = [2, 2, 0.5]; % [m]
-    ground.density = 2800; % [kg/m3]
-    ground.color = [0.5, 0.5, 0.5];
-
-    %% Save
-    save('./mat/stages.mat', 'ground', '-append');
-end

kinematics/index.org

@@ -0,0 +1,68 @@
+#+TITLE: Kinematics of the station
+:DRAWER:
+#+STARTUP: overview
+
+#+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="../css/htmlize.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/readtheorg.css"/>
+#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="../css/zenburn.css"/>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/bootstrap.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/jquery.stickytableheaders.min.js"></script>
+#+HTML_HEAD: <script type="text/javascript" src="../js/readtheorg.js"></script>
+
+#+HTML_MATHJAX: align: center tagside: right font: TeX
+
+#+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 matlab/modal_frf_coh.m
+#+PROPERTY: header-args:matlab+ :mkdirp yes
+
+#+PROPERTY: header-args:shell  :eval no-export
+
+#+PROPERTY: header-args:latex  :headers '("\\usepackage{tikz}" "\\usepackage{import}" "\\import{$HOME/MEGA/These/LaTeX/}{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 raw replace :buffer no
+#+PROPERTY: header-args:latex+ :eval no-export
+#+PROPERTY: header-args:latex+ :exports both
+#+PROPERTY: header-args:latex+ :mkdirp yes
+#+PROPERTY: header-args:latex+ :output-dir figs
+:END:
+
+* Introduction                                                       :ignore:
+
+* ZIP file containing the data and matlab files                      :ignore:
+#+begin_src bash :exports none :results none
+  if [ matlab/kinematics.m -nt data/kinematics.zip ]; then
+    cp matlab/kinematics.m kinematics.m;
+    zip data/kinematics \
+        mat/data.mat \
+        kinematics.m
+    rm kinematics.m;
+  fi
+#+end_src
+
+#+begin_note
+  All the files (data and Matlab scripts) are accessible [[file:data/kinematics.zip][here]].
+#+end_note
+
+* 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

kinematics/test2.m

@@ -0,0 +1,71 @@
+%% Compute position angle from R and Q
+thetas_R = zeros(length(pos.Time), 3);
+thetas_Q = zeros(length(pos.Time), 3);
+
+for i = 1:length(pos.Time)
+    [thetax, thetay, thetaz] = RM2angle(R.Data(:, :, i));
+    thetas_R(i, 1) = thetax; thetas_R(i, 2) = thetay; thetas_R(i, 3) = thetaz;
+
+    [thetax, thetay, thetaz] = quaternionToEulerAngles(Q.Data(i, :));
+    thetas_Q(i, 1) = thetax; thetas_Q(i, 2) = thetay; thetas_Q(i, 3) = thetaz;
+end
+
+%% Compute setpoint
+setpoint_c = zeros(length(pos.Time), 6);
+
+for i = 1:length(pos.Time)
+    setpoint_c(i, :) = computeSetpoint(ty.Data(i), ry.Data(i), rz.Data(i));
+end
+
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 1), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 1), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Translation (m)');
+
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 2), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 2), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Translation (m)');
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 3), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 3), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Translation (m)');
+
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 4), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 4), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Rotation (rad)');
+
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 5), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 5), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Rotation (rad)');
+
+%%
+figure;
+hold on;
+plot(pos.Time, pos.Data(:, 6), 'k-', 'DisplayName', 'position');
+plot(pos.Time, setpoint_c(:, 6), '--', 'DisplayName', 'Computed setpoint');
+hold off;
+legend();
+xlabel('Time (s)'); ylabel('Rotation (rad)');

main.m

@@ -1,27 +0,0 @@
-%%
-clear; close all; clc;
-
-%% Open the project
-simulinkproject('./');
-
-%% Initialization
-% Initialize the perturbations
-run init_perturbations.m
-
-% Initialize all the stages parameters
-run init_data.m
-
-%% Demonstration of displacement of all the stages
-run demonstration_main.m
-
-%% Identification
-open id_main.m
-
-%% Active Damping Control
-open act_damp_main.m
-
-%% Control With the Undamped System
-open control_main.m
-
-%% HAC-LAC Control
-open hac_lac_main.m

nass_simscape.org

@@ -1,85 +0,0 @@
-#+TITLE: Simscape model - Report
-#+LATEX_CLASS: cleanreport
-#+LaTeX_CLASS_OPTIONS: [tocnp, secbreak]
-#+STARTUP: overview
-#+DATE: 11-2018
-#+LaTeX_HEADER: \newcommand{\authorFirstName}{Thomas}
-#+LaTeX_HEADER: \newcommand{\authorLastName}{Dehaeze}
-#+LaTeX_HEADER: \newcommand{\authorEmail}{dehaeze.thomas@gmail.com}
-#+LaTeX_HEADER: \input{config.tex}
-
-* Simscape files for identification
-|------------------------+----+----+----+------+------|
-| Simscape Name          | Ty | Ry | Rz | Hexa | NASS |
-|------------------------+----+----+----+------+------|
-| id micro station       | F  | F  | F  | F    |      |
-| id nano station stages | F  | F  | F  | F    | F    |
-| id nano station config | D  | D  | D  | D    | F    |
-| control nano station   | D  | D  | D  | D    | F    |
-|------------------------+----+----+----+------+------|
-
-* Inputs
-** Perturbations
-|----------+--------------------------------------+------+------|
-| Variable | Meaning                              | Size | Unit |
-|----------+--------------------------------------+------+------|
-| ~Dw~     | Ground motion                        |    3 | [m]  |
-| ~Fg~     | External force applied on granite    |    3 | [N]  |
-| ~Fs~     | External force applied on the Sample |    3 | [N]  |
-|----------+--------------------------------------+------+------|
-
-** Measurement Noise
-|----------+---------+------+------|
-| Variable | Meaning | Size | Unit |
-|----------+---------+------+------|
-|          |         |      |      |
-|----------+---------+------+------|
-
-** Control Inputs
-|----------+-------------------------------------------+------+----------|
-| Variable | Meaning                                   | Size | Unit     |
-|----------+-------------------------------------------+------+----------|
-| ~Fy~     | Actuation force for Ty                    |    1 | [N]      |
-| ~Dy~     | Imposed displacement for Ty               |    1 | [m]      |
-|----------+-------------------------------------------+------+----------|
-| ~My~     | Actuation torque for Ry                   |    1 | [N.m]    |
-| ~Ry~     | Imposed rotation for Ry                   |    1 | [rad]    |
-|----------+-------------------------------------------+------+----------|
-| ~Mz~     | Actuation torque for Rz                   |    1 | [N.m]    |
-| ~Rz~     | Imposed rotation for Rz                   |    1 | [rad]    |
-|----------+-------------------------------------------+------+----------|
-| ~Fh~     | Actuation force/torque for hexapod (cart) |    6 | [N, N.m] |
-| ~Fhl~    | Actuation force/torque for hexapod (legs) |    6 | [N]      |
-| ~Dh~     | Imposed position for hexapod (cart)       |    6 | [m, rad] |
-|----------+-------------------------------------------+------+----------|
-| ~Rm~     | Position of the two masses                |    2 | [rad]    |
-|----------+-------------------------------------------+------+----------|
-| ~Fn~     | Actuation force for the NASS (cart)       |    6 | [N, N.m] |
-| ~Fnl~    | Actuation force for the NASS's legs       |    6 | [N]      |
-| ~Dn~     | Imposed position for the NASS (cart)      |    6 | [m, rad] |
-|----------+-------------------------------------------+------+----------|
-
-* Outputs
-
-|----------+---------------------------------------------+------+--------------|
-| Variable | Meaning                                     | Size | Unit         |
-|----------+---------------------------------------------+------+--------------|
-| ~Dgm~    | Absolute displacement of the granite        |    3 | [m]          |
-| ~Vgm~    | Absolute Velocity of the granite            |    3 | [m/s]        |
-|----------+---------------------------------------------+------+--------------|
-| ~Dym~    | Measured displacement of Ty                 |    1 | [m]          |
-|----------+---------------------------------------------+------+--------------|
-| ~Rym~    | Measured rotation of Ry                     |    1 | [rad]        |
-|----------+---------------------------------------------+------+--------------|
-| ~Rzm~    | Measured rotation of Rz                     |    1 | [rad]        |
-|----------+---------------------------------------------+------+--------------|
-| ~Dhm~    | Measured position of hexapod (cart)         |    6 | [m, rad]     |
-|----------+---------------------------------------------+------+--------------|
-| ~Fnlm~   | Measured force of NASS's legs               |    6 | [N]          |
-| ~Dnlm~   | Measured elongation of NASS's legs          |    6 | [m]          |
-| ~Dnm~    | Measured position of NASS w.r.t NASS's base |    6 | [m, rad]     |
-| ~Vnm~    | Measured absolute velocity of NASS platform |    6 | [m/s, rad/s] |
-| ~Vnlm~   | Measured absolute velocity of NASS's legs   |    6 | [m/s]        |
-|----------+---------------------------------------------+------+--------------|
-| ~Dsm~    | Position of Sample w.r.t. granite frame     |    6 | [m, rad]     |
-|----------+---------------------------------------------+------+--------------|

project_shutdown.m

@@ -1 +0,0 @@
-Simulink.fileGenControl('reset');

run_simulations.m

@@ -1,41 +0,0 @@
-%% Open Loop simulation and save the final state
-steady_time = 10;
-
-initializeSimConf(struct('Tsim', steady_time, 'cl_time', steady_time));
-
-set_param('sim_nano_station_ctrl',...
-          'SaveFinalState','on',...
-          'FinalStateName','myOperPoint',...
-          'SaveCompleteFinalSimState','on'...
-);
-
-sim('sim_nano_station_ctrl');
-
-save('./data/myOperPoint.mat', 'myOperPoint');
-
-set_param('sim_nano_station_ctrl',...
-          'SaveFinalState','off',...
-          'SaveCompleteFinalSimState','off'...
-);
-
-save('./data/exp_open_loop.mat', 'Dmeas');
-
-%% Close the Loop and start from steady state
-sim_time = 10;
-
-initializeSimConf(struct('Tsim', steady_time+sim_time, 'cl_time', steady_time));
-
-load('./data/myOperPoint.mat', 'myOperPoint');
-
-set_param('sim_nano_station_ctrl',...
-          'LoadInitialState','on',...
-          'InitialState','myOperPoint'...
-);
-
-sim('sim_nano_station_ctrl');
-
-set_param('sim_nano_station_ctrl',...
-          'LoadInitialState','off' ...
-);
-
-save('./data/exp_close_loop_xyz.mat', 'Dmeas');

slprj/sl_proj.tmw

@@ -1,2 +0,0 @@
-Simulink Coder project marker file. Please don't change it. 
-slprjVersion: 9.0_037

src/computePsdDispl.m

@@ -1,3 +1,14 @@
+% computePsdDispl
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/computePsdDispl.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:computePsdDispl>>
+
+% This Matlab function is accessible [[file:src/computePsdDispl.m][here]].
+
+
 function [psd_object] = computePsdDispl(sys_data, t_init, n_av)
     i_init = find(sys_data.time > t_init, 1);
 

src/computeSetpoint.m

@@ -0,0 +1,70 @@
+% computeSetpoint
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/computeSetpoint.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:computeSetpoint>>
+
+% This Matlab function is accessible [[file:src/computeSetpoint.m][here]].
+
+
+function setpoint = computeSetpoint(ty, ry, rz)
+%%
+setpoint = zeros(6, 1);
+
+%% Ty
+Ty = [1 0 0 0  ;
+      0 1 0 ty ;
+      0 0 1 0  ;
+      0 0 0 1 ];
+
+% Tyinv = [1 0 0  0  ;
+%          0 1 0 -ty ;
+%          0 0 1  0  ;
+%          0 0 0  1 ];
+
+%% Ry
+Ry = [ cos(ry) 0 sin(ry) 0 ;
+      0       1 0       0 ;
+      -sin(ry) 0 cos(ry) 0 ;
+      0        0 0       1 ];
+
+% TMry = Ty*Ry*Tyinv;
+
+%% Rz
+Rz = [cos(rz) -sin(rz) 0 0 ;
+      sin(rz)  cos(rz) 0 0 ;
+      0        0       1 0 ;
+      0        0       0 1 ];
+
+% TMrz = Ty*TMry*Rz*TMry'*Tyinv;
+
+%% All stages
+% TM = TMrz*TMry*Ty;
+
+TM = Ty*Ry*Rz;
+
+[thetax, thetay, thetaz] = RM2angle(TM(1:3, 1:3));
+
+setpoint(1:3) = TM(1:3, 4);
+setpoint(4:6) = [thetax, thetay, thetaz];
+
+%% Custom Functions
+function [thetax, thetay, thetaz] = RM2angle(R)
+    if abs(abs(R(3, 1)) - 1) > 1e-6 % R31 != 1 and R31 != -1
+        thetay = -asin(R(3, 1));
+        thetax = atan2(R(3, 2)/cos(thetay), R(3, 3)/cos(thetay));
+        thetaz = atan2(R(2, 1)/cos(thetay), R(1, 1)/cos(thetay));
+    else
+        thetaz = 0;
+        if abs(R(3, 1)+1) < 1e-6 % R31 = -1
+            thetay = pi/2;
+            thetax = thetaz + atan2(R(1, 2), R(1, 3));
+        else
+            thetay = -pi/2;
+            thetax = -thetaz + atan2(-R(1, 2), -R(1, 3));
+        end
+    end
+end
+end

src/converErrorBasis.m

@@ -0,0 +1,136 @@
+% converErrorBasis
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/converErrorBasis.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:converErrorBasis>>
+
+% This Matlab function is accessible [[file:src/converErrorBasis.m][here]].
+
+
+function error_nass = convertErrorBasis(pos, setpoint, ty, ry, rz)
+% convertErrorBasis -
+%
+% Syntax: convertErrorBasis(p_error, ty, ry, rz)
+%
+% Inputs:
+%    - p_error - Position error of the sample w.r.t. the granite [m, rad]
+%    - ty - Measured translation of the Ty stage [m]
+%    - ry - Measured rotation of the Ry stage [rad]
+%    - rz - Measured rotation of the Rz stage [rad]
+%
+% Outputs:
+%    - P_nass - Position error of the sample w.r.t. the NASS base [m]
+%    - R_nass - Rotation error of the sample w.r.t. the NASS base [rad]
+%
+% Example:
+%
+
+%% If line vector => column vector
+if size(pos, 2) == 6
+    pos = pos';
+end
+
+if size(setpoint, 2) == 6
+    setpoint = setpoint';
+end
+
+%% Position of the sample in the frame fixed to the Granite
+P_granite = [pos(1:3); 1]; % Position [m]
+R_granite = [setpoint(1:3); 1]; % Reference [m]
+
+%% Transformation matrices of the stages
+% T-y
+TMty = [1 0 0 0  ;
+        0 1 0 ty ;
+        0 0 1 0  ;
+        0 0 0 1 ];
+
+% R-y
+TMry = [ cos(ry) 0 sin(ry) 0 ;
+        0       1 0       0 ;
+        -sin(ry) 0 cos(ry) 0 ;
+        0        0 0       1 ];
+
+% R-z
+TMrz = [cos(rz) -sin(rz) 0 0 ;
+        sin(rz)  cos(rz) 0 0 ;
+        0        0       1 0 ;
+        0        0       0 1 ];
+
+%% Compute Point coordinates in the new reference fixed to the NASS base
+% P_nass = TMrz*TMry*TMty*P_granite;
+P_nass = TMrz\TMry\TMty\P_granite;
+R_nass = TMrz\TMry\TMty\R_granite;
+
+dx = R_nass(1)-P_nass(1);
+dy = R_nass(2)-P_nass(2);
+dz = R_nass(3)-P_nass(3);
+
+%% Compute new basis vectors linked to the NASS base
+% ux_nass = TMrz*TMry*TMty*[1; 0; 0; 0];
+% ux_nass = ux_nass(1:3);
+% uy_nass = TMrz*TMry*TMty*[0; 1; 0; 0];
+% uy_nass = uy_nass(1:3);
+% uz_nass = TMrz*TMry*TMty*[0; 0; 1; 0];
+% uz_nass = uz_nass(1:3);
+
+ux_nass = TMrz\TMry\TMty\[1; 0; 0; 0];
+ux_nass = ux_nass(1:3);
+uy_nass = TMrz\TMry\TMty\[0; 1; 0; 0];
+uy_nass = uy_nass(1:3);
+uz_nass = TMrz\TMry\TMty\[0; 0; 1; 0];
+uz_nass = uz_nass(1:3);
+
+%% Rotations error w.r.t. granite Frame
+% Rotations error w.r.t. granite Frame
+rx_nass = pos(4);
+ry_nass = pos(5);
+rz_nass = pos(6);
+
+% Rotation matrices of the Sample w.r.t. the Granite
+Mrx_error = [1 0              0 ;
+            0 cos(-rx_nass) -sin(-rx_nass) ;
+            0 sin(-rx_nass)  cos(-rx_nass)];
+
+Mry_error = [ cos(-ry_nass) 0 sin(-ry_nass) ;
+              0             1 0 ;
+            -sin(-ry_nass) 0 cos(-ry_nass)];
+
+Mrz_error = [cos(-rz_nass) -sin(-rz_nass) 0 ;
+            sin(-rz_nass)  cos(-rz_nass) 0 ;
+            0              0             1];
+
+% Rotation matrix of the Sample w.r.t. the Granite
+Mr_error = Mrz_error*Mry_error*Mrx_error;
+
+%% Use matrix to solve
+R = Mr_error/[ux_nass, uy_nass, uz_nass]; % Rotation matrix from NASS base to Sample
+
+[thetax, thetay, thetaz] = RM2angle(R);
+
+error_nass = [dx; dy; dz; thetax; thetay; thetaz];
+
+%% Custom Functions
+function [thetax, thetay, thetaz] = RM2angle(R)
+    if abs(abs(R(3, 1)) - 1) > 1e-6 % R31 != 1 and R31 != -1
+        thetay = -asin(R(3, 1));
+        % thetaybis = pi-thetay;
+        thetax = atan2(R(3, 2)/cos(thetay), R(3, 3)/cos(thetay));
+        % thetaxbis = atan2(R(3, 2)/cos(thetaybis), R(3, 3)/cos(thetaybis));
+        thetaz = atan2(R(2, 1)/cos(thetay), R(1, 1)/cos(thetay));
+        % thetazbis = atan2(R(2, 1)/cos(thetaybis), R(1, 1)/cos(thetaybis));
+    else
+        thetaz = 0;
+        if abs(R(3, 1)+1) < 1e-6 % R31 = -1
+            thetay = pi/2;
+            thetax = thetaz + atan2(R(1, 2), R(1, 3));
+        else
+            thetay = -pi/2;
+            thetax = -thetaz + atan2(-R(1, 2), -R(1, 3));
+        end
+    end
+end
+
+end

src/generateDiagPidControl.m

@@ -1,3 +1,14 @@
+% generateDiagPidControl
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/generateDiagPidControl.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:generateDiagPidControl>>
+
+% This Matlab function is accessible [[file:src/generateDiagPidControl.m][here]].
+
+
 function [K] = generateDiagPidControl(G, fs)
     %%
     pid_opts = pidtuneOptions(...

src/identifyPlant.m

@@ -1,3 +1,14 @@
+% identifyPlant
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/identifyPlant.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:identifyPlant>>
+
+% This Matlab function is accessible [[file:src/identifyPlant.m][here]].
+
+
 function [sys] = identifyPlant(opts_param)
     %% Default values for opts
     opts = struct();

src/init_simulation.m

@@ -0,0 +1,19 @@
+% Simulation Initialization
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/init_simulation.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:init_simulation>>
+
+% This Matlab script is accessible [[file:src/init_simulation.m][here]].
+
+% This script runs just before the simulation is started.
+% It is used to load the simulation configuration and the controllers used for the simulation.
+
+
+%% Load all the data used for the simulation
+load('./mat/sim_conf.mat');
+
+%% Load Controller
+load('./mat/controllers.mat');

src/initializeAxisc.m

@@ -1,3 +1,14 @@
+% Center of gravity compensation
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeAxisc.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeAxisc>>
+
+% This Matlab function is accessible [[file:src/initializeAxisc.m][here]].
+
+
 function [axisc] = initializeAxisc()
     %%
     axisc = struct();

src/initializeExperiment.m

@@ -1,3 +1,14 @@
+% Experiment
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeExperiment.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeExperiment>>
+
+% This Matlab function is accessible [[file:src/initializeExperiment.m][here]].
+
+
 function [] = initializeExperiment(exp_name, sys_mass)
     if strcmp(exp_name, 'tomography')
         opts_sim = struct(...

src/initializeGranite.m

@@ -1,3 +1,14 @@
+% Granite
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeGranite.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeGranite>>
+
+% This Matlab function is accessible [[file:src/initializeGranite.m][here]].
+
+
 function [granite] = initializeGranite()
     %%
     granite = struct();

src/initializeGround.m

@@ -0,0 +1,22 @@
+% Ground
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeGround.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeGround>>
+
+% This Matlab function is accessible [[file:src/initializeGround.m][here]].
+
+
+function [ground] = initializeGround()
+    %%
+    ground = struct();
+
+    ground.shape = [2, 2, 0.5]; % [m]
+    ground.density = 2800; % [kg/m3]
+    ground.color = [0.5, 0.5, 0.5];
+
+    %% Save
+    save('./mat/stages.mat', 'ground', '-append');
+end

src/initializeInputs.m

@@ -1,3 +1,14 @@
+% Inputs
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeInputs.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeInputs>>
+
+% This Matlab function is accessible [[file:src/initializeInputs.m][here]].
+
+
 function [inputs] = initializeInputs(opts_param)
     %% Default values for opts
     opts = struct(   ...
@@ -136,7 +147,7 @@ function [inputs] = initializeInputs(opts_param)
 
     %% Ry
     TMRy = [ cos(ry) 0 sin(ry) 0 ;
-           0       1 0       0 ;
+          0       1 0       0 ;
           -sin(ry) 0 cos(ry) 0 ;
           0        0 0       1 ];
 

src/initializeMicroHexapod.m

@@ -1,3 +1,14 @@
+% Micro Hexapod
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeMicroHexapod.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeMicroHexapod>>
+
+% This Matlab function is accessible [[file:src/initializeMicroHexapod.m][here]].
+
+
 function [micro_hexapod] = initializeMicroHexapod(opts_param)
     %% Default values for opts
     opts = struct();
@@ -107,7 +118,7 @@ function [micro_hexapod] = initializeMicroHexapod(opts_param)
         stewart.pos_base = zeros(6, 3);
         stewart.pos_top = zeros(6, 3);
 
-        alpha_b = stewart.BP.leg.ang*pi/180; % angle de décalage par rapport à 120 deg (pour positionner les supports bases)
+        alpha_b = stewart.BP.leg.ang*pi/180; % angle de décalage par rapport à 120 deg (pour positionner les supports bases)
         alpha_t = stewart.TP.leg.ang*pi/180; % +- offset angle from 120 degree spacing on top
 
         height = (stewart.h-stewart.BP.thickness-stewart.TP.thickness-stewart.Leg.sphere.bottom-stewart.Leg.sphere.top-stewart.SP.thickness.bottom-stewart.SP.thickness.top)*0.001; % TODO
@@ -145,11 +156,11 @@ function [micro_hexapod] = initializeMicroHexapod(opts_param)
 
         stewart.Leg.lenght = 1000*leg_length(1)/1.5;
         stewart.Leg.shape.bot = [0 0; ...
-                                 stewart.Leg.rad.bottom 0; ...
+                                stewart.Leg.rad.bottom 0; ...
-                                 stewart.Leg.rad.bottom stewart.Leg.lenght; ...
+                                stewart.Leg.rad.bottom stewart.Leg.lenght; ...
-                                 stewart.Leg.rad.top stewart.Leg.lenght; ...
+                                stewart.Leg.rad.top stewart.Leg.lenght; ...
-                                 stewart.Leg.rad.top 0.2*stewart.Leg.lenght; ...
+                                stewart.Leg.rad.top 0.2*stewart.Leg.lenght; ...
-                                 0 0.2*stewart.Leg.lenght];
+                                0 0.2*stewart.Leg.lenght];
 
         %% Calculate revolute and cylindrical axes
         rev1 = zeros(6, 3);

src/initializeMirror.m

@@ -1,3 +1,14 @@
+% Mirror
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeMirror.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeMirror>>
+
+% This Matlab function is accessible [[file:src/initializeMirror.m][here]].
+
+
 function [] = initializeMirror(opts_param)
     %% Default values for opts
     opts = struct(...

src/initializeNanoHexapod.m

@@ -1,3 +1,14 @@
+% Nano Hexapod
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeNanoHexapod.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeNanoHexapod>>
+
+% This Matlab function is accessible [[file:src/initializeNanoHexapod.m][here]].
+
+
 function [nano_hexapod] = initializeNanoHexapod(opts_param)
     %% Default values for opts
     opts = struct('actuator', 'piezo');
@@ -114,7 +125,7 @@ function [nano_hexapod] = initializeNanoHexapod(opts_param)
         stewart.pos_base = zeros(6, 3);
         stewart.pos_top = zeros(6, 3);
 
-        alpha_b = stewart.BP.leg.ang*pi/180; % angle de décalage par rapport à 120 deg (pour positionner les supports bases)
+        alpha_b = stewart.BP.leg.ang*pi/180; % angle de décalage par rapport à 120 deg (pour positionner les supports bases)
         alpha_t = stewart.TP.leg.ang*pi/180; % +- offset angle from 120 degree spacing on top
 
         height = (stewart.h-stewart.BP.thickness-stewart.TP.thickness-stewart.Leg.sphere.bottom-stewart.Leg.sphere.top-stewart.SP.thickness.bottom-stewart.SP.thickness.top)*0.001; % TODO
@@ -152,11 +163,11 @@ function [nano_hexapod] = initializeNanoHexapod(opts_param)
 
         stewart.Leg.lenght = 1000*leg_length(1)/1.5;
         stewart.Leg.shape.bot = [0 0; ...
-                                 stewart.Leg.rad.bottom 0; ...
+                                stewart.Leg.rad.bottom 0; ...
-                                 stewart.Leg.rad.bottom stewart.Leg.lenght; ...
+                                stewart.Leg.rad.bottom stewart.Leg.lenght; ...
-                                 stewart.Leg.rad.top stewart.Leg.lenght; ...
+                                stewart.Leg.rad.top stewart.Leg.lenght; ...
-                                 stewart.Leg.rad.top 0.2*stewart.Leg.lenght; ...
+                                stewart.Leg.rad.top 0.2*stewart.Leg.lenght; ...
-                                 0 0.2*stewart.Leg.lenght];
+                                0 0.2*stewart.Leg.lenght];
 
         %% Calculate revolute and cylindrical axes
         rev1 = zeros(6, 3);

src/initializeRy.m

@@ -1,3 +1,14 @@
+% Tilt Stage
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeRy.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeRy>>
+
+% This Matlab function is accessible [[file:src/initializeRy.m][here]].
+
+
 function [ry] = initializeRy(opts_param)
     %% Default values for opts
     opts = struct('rigid', false);
@@ -47,7 +58,7 @@ function [ry] = initializeRy(opts_param)
     ry.c.rad  = 10*(1/5)*sqrt(ry.k.rad/ry.m);
     ry.c.rrad = 10*(1/5)*sqrt(ry.k.rrad/ry.m);
     ry.c.tilt = 10*(1/1)*sqrt(ry.k.tilt/ry.m);
-    
+
     %% Positioning parameters
     ry.z_offset = 0.58178; % Z-Offset so that the center of rotation matches the sample center [m]
 

src/initializeRz.m

@@ -1,3 +1,14 @@
+% Spindle
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeRz.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeRz>>
+
+% This Matlab function is accessible [[file:src/initializeRz.m][here]].
+
+
 function [rz] = initializeRz(opts_param)
     %% Default values for opts
     opts = struct('rigid', false);

src/initializeSample.m

@@ -1,3 +1,14 @@
+% Sample
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeSample.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeSample>>
+
+% This Matlab function is accessible [[file:src/initializeSample.m][here]].
+
+
 function [sample] = initializeSample(opts_param)
     %% Default values for opts
     sample = struct('radius', 100, ...
@@ -13,7 +24,7 @@ function [sample] = initializeSample(opts_param)
             sample.(opt{1}) = opts_param.(opt{1});
         end
     end
-    
+
     %%
     sample.k.x = 1e8;
     sample.c.x = sqrt(sample.k.x*sample.mass)/10;

src/initializeSimConf.m

@@ -1,3 +1,14 @@
+% Simulation Configuration
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeSimConf.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeSimConf>>
+
+% This Matlab function is accessible [[file:src/initializeSimConf.m][here]].
+
+
 function [] = initializeSimConf(opts_param)
     %% Default values for opts
     opts = struct('Ts',      1e-4,  ... % Sampling time [s]

src/initializeTy.m

@@ -1,3 +1,14 @@
+% Translation Stage
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/initializeTy.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:initializeTy>>
+
+% This Matlab function is accessible [[file:src/initializeTy.m][here]].
+
+
 function [ty] = initializeTy(opts_param)
     %% Default values for opts
     opts = struct('rigid', false);
@@ -8,7 +19,7 @@ function [ty] = initializeTy(opts_param)
             opts.(opt{1}) = opts_param.(opt{1});
         end
     end
-    
+
     %%
     ty = struct();
 

src/project_shutdown.m

@@ -0,0 +1,5 @@
+
+
+% When the project closes, it runs the =project_shutdown.m= script defined below.
+
+Simulink.fileGenControl('reset');

src/project_startup.m

@@ -1,3 +1,8 @@
+
+
+% When the project opens, a startup script is ran.
+% The startup script is defined below and is exported to the =project_startup.m= script.
+
 %%
 freqs = logspace(-1, 3, 1000);
 save_fig = false;

src/runSimulation.m

@@ -1,3 +1,14 @@
+% runSimulation
+%   :PROPERTIES:
+%   :header-args:matlab+: :tangle src/runSimulation.m
+%   :header-args:matlab+: :comments org :mkdirp yes
+%   :header-args:matlab+: :eval no :results none
+%   :END:
+%   <<sec:runSimulation>>
+
+% This Matlab function is accessible [[file:src/runSimulation.m][here]].
+
+
 function [] = runSimulation(sys_name, sys_mass, ctrl_type, act_damp)
     %% Load the controller and save it for the simulation
     if strcmp(ctrl_type, 'cl') && strcmp(act_damp, 'none')
@@ -27,7 +38,7 @@ function [] = runSimulation(sys_name, sys_mass, ctrl_type, act_damp)
 
     %%
     if strcmp(sys_name, 'pz')
-    	initializeNanoHexapod(struct('actuator', 'piezo'));
+      initializeNanoHexapod(struct('actuator', 'piezo'));
     elseif strcmp(sys_name, 'vc')
         initializeNanoHexapod(struct('actuator', 'lorentz'));
     else
@@ -35,7 +46,7 @@ function [] = runSimulation(sys_name, sys_mass, ctrl_type, act_damp)
     end
 
     if strcmp(sys_mass, 'light')
-    	initializeSample(struct('mass', 1));
+      initializeSample(struct('mass', 1));
     elseif strcmp(sys_mass, 'heavy')
         initializeSample(struct('mass', 50));
     else