diff --git a/mat/K_fb.mat b/mat/K_fb.mat
index d08aaed..d8f0750 100644
Binary files a/mat/K_fb.mat and b/mat/K_fb.mat differ
diff --git a/mat/config.mat b/mat/config.mat
index fb46783..b7c98d8 100644
Binary files a/mat/config.mat and b/mat/config.mat differ
diff --git a/mat/controllers.mat b/mat/controllers.mat
index 28d2766..53615cb 100644
Binary files a/mat/controllers.mat and b/mat/controllers.mat differ
diff --git a/mat/inputs.mat b/mat/inputs.mat
index dcef1fd..8e74795 100644
Binary files a/mat/inputs.mat and b/mat/inputs.mat differ
diff --git a/mat/perturbations.mat b/mat/perturbations.mat
index 6606250..bdc319c 100644
Binary files a/mat/perturbations.mat and b/mat/perturbations.mat differ
diff --git a/mat/stages.mat b/mat/stages.mat
index 561cf2c..7503010 100644
Binary files a/mat/stages.mat and b/mat/stages.mat differ
diff --git a/src/computePsdDispl.m b/src/computePsdDispl.m
index aa97514..786f96e 100644
--- a/src/computePsdDispl.m
+++ b/src/computePsdDispl.m
@@ -1,12 +1,12 @@
 % computePsdDispl
 %   :PROPERTIES:
-%   :header-args:matlab+: :tangle src/computePsdDispl.m
+%   :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]].
+% This Matlab function is accessible [[file:../src/computePsdDispl.m][here]].
 
 
 function [psd_object] = computePsdDispl(sys_data, t_init, n_av)
diff --git a/src/computeSetpoint.m b/src/computeSetpoint.m
index df69a3d..5c0f92e 100644
--- a/src/computeSetpoint.m
+++ b/src/computeSetpoint.m
@@ -1,12 +1,12 @@
 % computeSetpoint
 %   :PROPERTIES:
-%   :header-args:matlab+: :tangle src/computeSetpoint.m
+%   :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]].
+% This Matlab function is accessible [[file:../src/computeSetpoint.m][here]].
 
 
 function setpoint = computeSetpoint(ty, ry, rz)
diff --git a/src/converErrorBasis.m b/src/converErrorBasis.m
index 3a33109..b8b6321 100644
--- a/src/converErrorBasis.m
+++ b/src/converErrorBasis.m
@@ -1,12 +1,12 @@
 % converErrorBasis
 %   :PROPERTIES:
-%   :header-args:matlab+: :tangle src/converErrorBasis.m
+%   :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]].
+% This Matlab function is accessible [[file:../src/converErrorBasis.m][here]].
 
 
 function error_nass = convertErrorBasis(pos, setpoint, ty, ry, rz)
diff --git a/src/generateDiagPidControl.m b/src/generateDiagPidControl.m
index 406eea8..f2a71fe 100644
--- a/src/generateDiagPidControl.m
+++ b/src/generateDiagPidControl.m
@@ -1,12 +1,12 @@
 % generateDiagPidControl
 %   :PROPERTIES:
-%   :header-args:matlab+: :tangle src/generateDiagPidControl.m
+%   :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]].
+% This Matlab function is accessible [[file:../src/generateDiagPidControl.m][here]].
 
 
 function [K] = generateDiagPidControl(G, fs)
diff --git a/src/init_simulation.m b/src/init_simulation.m
deleted file mode 100644
index f271b41..0000000
--- a/src/init_simulation.m
+++ /dev/null
@@ -1,19 +0,0 @@
-% 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('sim_conf.mat');
-
-%% Load Controller
-load('controllers.mat');
diff --git a/src/initializeAxisc.m b/src/initializeAxisc.m
index e5e0bd8..8e1d4b1 100644
--- a/src/initializeAxisc.m
+++ b/src/initializeAxisc.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeCedratPiezo.m b/src/initializeCedratPiezo.m
index 60d4285..6441f1a 100644
--- a/src/initializeCedratPiezo.m
+++ b/src/initializeCedratPiezo.m
@@ -1,10 +1,10 @@
 % Cedrat Actuator
-%   :PROPERTIES:
-%   :header-args:matlab+: :tangle ../src/initializeCedratPiezo.m
-%   :header-args:matlab+: :comments org :mkdirp yes
-%   :header-args:matlab+: :eval no :results none
-%   :END:
-%   <<sec:initializeCedratPiezo>>
+% :PROPERTIES:
+% :header-args:matlab+: :tangle ../src/initializeCedratPiezo.m
+% :header-args:matlab+: :comments org :mkdirp yes
+% :header-args:matlab+: :eval no :results none
+% :END:
+% <<sec:initializeCedratPiezo>>
 
 % This Matlab function is accessible [[file:../src/initializeCedratPiezo.m][here]].
 
@@ -25,8 +25,8 @@ function [cedrat] = initializeCedratPiezo(opts_param)
   cedrat.k = 10e7; % Linear Stiffness of each "blade" [N/m]
   cedrat.ka = 10e7; % Linear Stiffness of the stack [N/m]
 
-  cedrat.c = 0.1*sqrt(50*cedrat.k); % [N/(m/s)]
-  cedrat.ca = 0.1*sqrt(50*cedrat.ka); % [N/(m/s)]
+  cedrat.c = 0.1*sqrt(1*cedrat.k); % [N/(m/s)]
+  cedrat.ca = 0.1*sqrt(1*cedrat.ka); % [N/(m/s)]
 
   cedrat.L = 80; % Total Width of the Actuator[mm]
   cedrat.H = 45; % Total Height of the Actuator [mm]
diff --git a/src/initializeExperiment.m b/src/initializeExperiment.m
index 3f2f01f..1857f4a 100644
--- a/src/initializeExperiment.m
+++ b/src/initializeExperiment.m
@@ -1,22 +1,16 @@
 % 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>>
+% :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(...
-            'Tsim',    5, ...
-            'cl_time', 5  ...
-        );
-        initializeSimConf(opts_sim);
-
         if strcmp(sys_mass, 'light')
             opts_inputs = struct(...
                 'Dw', true,  ...
diff --git a/src/initializeGranite.m b/src/initializeGranite.m
index 657a701..0eae77f 100644
--- a/src/initializeGranite.m
+++ b/src/initializeGranite.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeGround.m b/src/initializeGround.m
index a4d17f1..a10aac2 100644
--- a/src/initializeGround.m
+++ b/src/initializeGround.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeInputs.m b/src/initializeInputs.m
index 3417fce..3b7b31e 100644
--- a/src/initializeInputs.m
+++ b/src/initializeInputs.m
@@ -1,10 +1,12 @@
-% 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>>
+% TODO 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 function should not be used anymore*. Now there are two functions to initialize disturbances and references.
 
 % This Matlab function is accessible [[file:../src/initializeInputs.m][here]].
 
diff --git a/src/initializeMicroHexapod.m b/src/initializeMicroHexapod.m
index f78609d..47c3c9d 100644
--- a/src/initializeMicroHexapod.m
+++ b/src/initializeMicroHexapod.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeMirror.m b/src/initializeMirror.m
index 8e7b7f4..4f280ee 100644
--- a/src/initializeMirror.m
+++ b/src/initializeMirror.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeNanoHexapod.m b/src/initializeNanoHexapod.m
index 0c8682e..846289e 100644
--- a/src/initializeNanoHexapod.m
+++ b/src/initializeNanoHexapod.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeRy.m b/src/initializeRy.m
index 821cd5b..eb88acd 100644
--- a/src/initializeRy.m
+++ b/src/initializeRy.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeRz.m b/src/initializeRz.m
index c2c456b..c33dd8b 100644
--- a/src/initializeRz.m
+++ b/src/initializeRz.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeSample.m b/src/initializeSample.m
index 9b7676b..f950007 100644
--- a/src/initializeSample.m
+++ b/src/initializeSample.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/initializeSimConf.m b/src/initializeSimConf.m
deleted file mode 100644
index 234e641..0000000
--- a/src/initializeSimConf.m
+++ /dev/null
@@ -1,44 +0,0 @@
-% 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]
-                  'Tsim',    10,    ... % Simulation time [s]
-                  'cl_time', 0,     ... % Close Loop time [s]
-                  'gravity', false  ... % Gravity along the z axis
-    );
-
-    %% Populate opts with input parameters
-    if exist('opts_param','var')
-        for opt = fieldnames(opts_param)'
-            opts.(opt{1}) = opts_param.(opt{1});
-        end
-    end
-
-    %%
-    sim_conf = struct();
-
-    %%
-    sim_conf.Ts = opts.Ts;
-    sim_conf.Tsim = opts.Tsim;
-    sim_conf.cl_time = opts.cl_time;
-
-    %% Gravity
-    if opts.gravity
-        sim_conf.g = -9.8; %#ok
-    else
-        sim_conf.g = 0; %#ok
-    end
-
-    %% Save
-    save('./mat/sim_conf.mat', 'sim_conf');
-end
diff --git a/src/initializeTy.m b/src/initializeTy.m
index ccbce0f..f710994 100644
--- a/src/initializeTy.m
+++ b/src/initializeTy.m
@@ -1,10 +1,10 @@
 % 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>>
+% :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]].
 
diff --git a/src/project_startup.m b/src/project_startup.m
index 92f186a..f7204f9 100644
--- a/src/project_startup.m
+++ b/src/project_startup.m
@@ -3,12 +3,6 @@
 % 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;
-save('./mat/config.mat', 'freqs', 'save_fig');
-
-%%
 project = simulinkproject;
 projectRoot = project.RootFolder;
 
diff --git a/src/runSimulation.m b/src/runSimulation.m
index 9a151ef..24737e1 100644
--- a/src/runSimulation.m
+++ b/src/runSimulation.m
@@ -1,56 +1,56 @@
 % runSimulation
 %   :PROPERTIES:
-%   :header-args:matlab+: :tangle src/runSimulation.m
+%   :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]].
+% 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')
-        K_obj = load('./mat/K_fb.mat');
-        K = K_obj.(sprintf('K_%s_%s', sys_mass, sys_name)); %#ok
-        save('./mat/controllers.mat', 'K');
+      K_obj = load('./mat/K_fb.mat');
+      K = K_obj.(sprintf('K_%s_%s', sys_mass, sys_name)); %#ok
+      save('./mat/controllers.mat', 'K');
     elseif strcmp(ctrl_type, 'cl') && strcmp(act_damp, 'iff')
-        K_obj = load('./mat/K_fb_iff.mat');
-        K = K_obj.(sprintf('K_%s_%s_iff', sys_mass, sys_name)); %#ok
-        save('./mat/controllers.mat', 'K');
+      K_obj = load('./mat/K_fb_iff.mat');
+      K = K_obj.(sprintf('K_%s_%s_iff', sys_mass, sys_name)); %#ok
+      save('./mat/controllers.mat', 'K');
     elseif strcmp(ctrl_type, 'ol')
-        K = tf(zeros(6)); %#ok
-        save('./mat/controllers.mat', 'K');
+      K = tf(zeros(6)); %#ok
+      save('./mat/controllers.mat', 'K');
     else
-        error('ctrl_type should be cl or ol');
+      error('ctrl_type should be cl or ol');
     end
 
     %% Active Damping
     if strcmp(act_damp, 'iff')
-        K_iff_crit = load('./mat/K_iff_crit.mat');
-        K_iff = K_iff_crit.(sprintf('K_iff_%s_%s', sys_mass, sys_name)); %#ok
-        save('./mat/controllers.mat', 'K_iff', '-append');
+      K_iff_crit = load('./mat/K_iff_crit.mat');
+      K_iff = K_iff_crit.(sprintf('K_iff_%s_%s', sys_mass, sys_name)); %#ok
+      save('./mat/controllers.mat', 'K_iff', '-append');
     elseif strcmp(act_damp, 'none')
-        K_iff = tf(zeros(6)); %#ok
-        save('./mat/controllers.mat', 'K_iff', '-append');
+      K_iff = tf(zeros(6)); %#ok
+      save('./mat/controllers.mat', 'K_iff', '-append');
     end
 
     %%
     if strcmp(sys_name, 'pz')
       initializeNanoHexapod(struct('actuator', 'piezo'));
     elseif strcmp(sys_name, 'vc')
-        initializeNanoHexapod(struct('actuator', 'lorentz'));
+      initializeNanoHexapod(struct('actuator', 'lorentz'));
     else
-        error('sys_name should be pz or vc');
+      error('sys_name should be pz or vc');
     end
 
     if strcmp(sys_mass, 'light')
       initializeSample(struct('mass', 1));
     elseif strcmp(sys_mass, 'heavy')
-        initializeSample(struct('mass', 50));
+      initializeSample(struct('mass', 50));
     else
-        error('sys_mass should be light or heavy');
+      error('sys_mass should be light or heavy');
     end
 
     %% Run the simulation