Started to rework the experiment file

org/experiments.org

@@ -1,4 +1,4 @@
-#+TITLE: Tomography Experiment
+#+TITLE: Simulation of Scientific Experiments
 :DRAWER:
 #+STARTUP: overview
 
@@ -42,12 +42,13 @@
 :END:
 
 * Introduction                                                       :ignore:
-The goal here is to simulate some scientific experiments with the tuned Simscape model when no control is applied to the nano-hexapod.
+The goal here is to simulate some scientific experiments with the Simscape model when no control is applied to the nano-hexapod.
 
 This has several goals:
 - Validate the model
 - Estimate the expected error motion for the experiments
 - Estimate the stroke that we may need for the nano-hexapod
+- Compare with experiments when control is applied
 
 The document in organized as follow:
 - In section [[sec:simscape_model]] the Simscape model is initialized
@@ -69,20 +70,21 @@ The document in organized as follow:
   simulinkproject('../');
 #+end_src
 
-* Simscape Model
-<<sec:simscape_model>>
-
 #+begin_src matlab
   open('nass_model.slx');
 #+end_src
 
+* Simscape Model
+<<sec:simscape_model>>
+
 We load the shared simulink configuration and we set the =StopTime=.
 #+begin_src matlab
   load('mat/conf_simulink.mat');
-  set_param(conf_simulink, 'StopTime', '5');
+  set_param(conf_simulink, 'StopTime', '2');
 #+end_src
 
 We first initialize all the stages.
+The nano-hexapod is considered to be a rigid body.
 #+begin_src matlab
   initializeGround();
   initializeGranite();
@@ -92,7 +94,7 @@ We first initialize all the stages.
   initializeMicroHexapod();
   initializeAxisc();
   initializeMirror();
-  initializeNanoHexapod('actuator', 'piezo');
+  initializeNanoHexapod('type', 'rigid');
   initializeSample('mass', 1);
 #+end_src
 
@@ -102,9 +104,26 @@ All stage is set to its zero position except the Spindle which is rotating at 60
   initializeReferences('Rz_type', 'rotating', 'Rz_period', 1);
 #+end_src
 
+No controller is used (Open Loop).
+#+begin_src matlab
+  initializeController('type', 'open-loop');
+#+end_src
+
+And we put some gravity.
+#+begin_src matlab
+  initializeSimscapeConfiguration('gravity', true);
+#+end_src
+
+We log the signals for further analysis.
+#+begin_src matlab
+  initializeLoggingConfiguration('log', 'all');
+#+end_src
+
 * Tomography Experiment with no disturbances
 <<sec:tomo_no_dist>>
 ** Introduction                                                     :ignore:
+In this section, a tomography experiment is performed with the sample aligned with the rotation axis.
+No disturbance is included.
 
 ** Simulation Setup
 And we initialize the disturbances to be equal to zero.
@@ -126,7 +145,7 @@ We simulate the model.
 
 And we save the obtained data.
 #+begin_src matlab
-  tomo_align_no_dist = struct('t', t, 'MTr', MTr);
+  tomo_align_no_dist = simout;
   save('./mat/experiment_tomography.mat', 'tomo_align_no_dist', '-append');
 #+end_src
 
@@ -214,6 +233,8 @@ And we save the obtained data.
 * Tomography Experiment with included perturbations
 <<sec:tomo_dist>>
 ** Introduction                                                     :ignore:
+In this section, we also perform a tomography experiment with the sample's center of mass aligned with the rotation axis.
+However this time, we include perturbations such as ground motion and stage vibrations.
 
 ** Simulation Setup
 We now activate the disturbances.
@@ -323,6 +344,10 @@ And we save the obtained data.
 * Tomography when the micro-hexapod is not centered
 <<sec:tomo_hexa_trans>>
 ** Introduction                                                     :ignore:
+In this section, the sample's center of mass is not aligned with the rotation axis anymore.
+This is due to the fact that the micro-hexapod has performed some displacement.
+
+No disturbances are included.
 
 ** Simulation Setup
 We first set the wanted translation of the Micro Hexapod.
@@ -447,6 +472,7 @@ And we save the obtained data.
 * Raster Scans with the translation stage
 <<sec:ty_scans>>
 ** Introduction                                                     :ignore:
+In this section, scans with the translation stage are performed.
 
 ** Simulation Setup
 We set the reference path.