From 6020b7dc9640200f05353f755c552ce899b0bf2b Mon Sep 17 00:00:00 2001
From: jimmyDunne <dunne.jimmy@gmail.com>
Date: Sun, 11 Nov 2018 12:50:45 -0500
Subject: [PATCH 1/2] minimum set of updates to get current example working

---
 CMakeLists.txt                                 | 18 +++++++++++++-----
 .../gait10dof_Kinematics_Tracking_Tasks.xml    |  0
 .../{ => CMC}/gait10dof_Reserve_Actuators.xml  |  0
 .../CMC/walk_Setup_CMC.xml                     | 10 +++++-----
 .../CMC/walk_Setup_CMC_PathActuator.xml        | 12 ++++++------
 5 files changed, 24 insertions(+), 16 deletions(-)
 rename Tutorials/Design_to_Reduce_Metabolic_Cost/{ => CMC}/gait10dof_Kinematics_Tracking_Tasks.xml (100%)
 rename Tutorials/Design_to_Reduce_Metabolic_Cost/{ => CMC}/gait10dof_Reserve_Actuators.xml (100%)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4b6fe55..68fad6a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,13 +25,21 @@ install(FILES Models/BouncingBlock/run_forward_bouncingBlock.xml
 
 install(FILES Models/Gait10dof18musc/gait10dof18musc.osim
               Models/Gait10dof18musc/subject01.osim
-        DESTINATION Models/Gait10dof18musc)
+							Models/Gait10dof18musc/subject01_metabolics.osim
+							Models/Gait10dof18musc/subject01_metabolics_path_spring.osim
+							Models/Gait10dof18musc/subject01_metabolics_path_actuator.osim
+							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_static.trc
+							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk.trc
+							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.mot
+							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.xml
+							Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
+							Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
+				DESTINATION Models/Gait10dof18musc)
 # TODO subject01_metabolics* files?
-install(DIRECTORY Pipelines/Gait10dof18musc/
+install(DIRECTORY Tutorials/Design_to_Reduce_Metabolic_Cost/
         DESTINATION Models/Gait10dof18musc
-        PATTERN "CMC/ResultsCMC_*" EXCLUDE
-        PATTERN "CMC/controls_43p_r.xml" EXCLUDE
-        PATTERN "CMC/*.osim" EXCLUDE)
+				PATTERN "CMC/walk_Setup_CMC*" EXCLUDE
+				PATTERN "ExperimentalData" EXCLUDE)
 
 install(FILES Models/Gait2354_Simbody/gait2354_simbody.osim
         DESTINATION Models/Gait2354_Simbody)
diff --git a/Tutorials/Design_to_Reduce_Metabolic_Cost/gait10dof_Kinematics_Tracking_Tasks.xml b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/gait10dof_Kinematics_Tracking_Tasks.xml
similarity index 100%
rename from Tutorials/Design_to_Reduce_Metabolic_Cost/gait10dof_Kinematics_Tracking_Tasks.xml
rename to Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/gait10dof_Kinematics_Tracking_Tasks.xml
diff --git a/Tutorials/Design_to_Reduce_Metabolic_Cost/gait10dof_Reserve_Actuators.xml b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/gait10dof_Reserve_Actuators.xml
similarity index 100%
rename from Tutorials/Design_to_Reduce_Metabolic_Cost/gait10dof_Reserve_Actuators.xml
rename to Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/gait10dof_Reserve_Actuators.xml
diff --git a/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
index a129932..d073565 100644
--- a/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
+++ b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
@@ -6,9 +6,9 @@
 		<!--Replace the model's force set with sets specified in <force_set_files>? If false, the force set is appended to.-->
 		<replace_force_set>false</replace_force_set>
 		<!--List of xml files used to construct an force set for the model.-->
-		<force_set_files>../gait10dof_Reserve_Actuators.xml</force_set_files>
+		<force_set_files>CMC/gait10dof_Reserve_Actuators.xml</force_set_files>
 		<!--Directory used for writing results.-->
-		<results_directory>ResultsCMC</results_directory>
+		<results_directory>CMC/ResultsCMC</results_directory>
 		<!--Output precision.  It is 8 by default.-->
 		<output_precision>8</output_precision>
 		<!--Initial time for the simulation.-->
@@ -40,13 +40,13 @@
 			<groups />
 		</ControllerSet>
 		<!--XML file (.xml) containing the forces applied to the model as ExternalLoads.-->
-		<external_loads_file>../ExperimentalData/subject01_walk_grf.xml</external_loads_file>
+		<external_loads_file>subject01_walk_grf.xml</external_loads_file>
 		<!--Motion (.mot) or storage (.sto) file containing the desired point trajectories.-->
 		<desired_points_file />
 		<!--Motion (.mot) or storage (.sto) file containing the desired kinematic trajectories.-->
-		<desired_kinematics_file>../RRA/ResultsRRA/subject_adjusted_Kinematics_q.sto</desired_kinematics_file>
+		<desired_kinematics_file>RRA/ResultsRRA/subject_adjusted_Kinematics_q.sto</desired_kinematics_file>
 		<!--File containing the tracking tasks. Which coordinates are tracked and with what weights are specified here.-->
-		<task_set_file>../gait10dof_Kinematics_Tracking_Tasks.xml</task_set_file>
+		<task_set_file>CMC/gait10dof_Kinematics_Tracking_Tasks.xml</task_set_file>
 		<!--File containing the constraints on the controls.-->
 		<constraints_file />
 		<!--File containing the controls output by RRA. These can be used to place constraints on the residuals during CMC.-->
diff --git a/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
index 1de2313..2df4a6b 100644
--- a/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
+++ b/Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
@@ -6,9 +6,9 @@
 		<!--Replace the model's force set with sets specified in <force_set_files>? If false, the force set is appended to.-->
 		<replace_force_set>false</replace_force_set>
 		<!--List of xml files used to construct an force set for the model.-->
-		<force_set_files>../gait10dof_Reserve_Actuators.xml</force_set_files>
+		<force_set_files>CMC/gait10dof_Reserve_Actuators.xml</force_set_files>
 		<!--Directory used for writing results.-->
-		<results_directory>ResultsCMC</results_directory>
+		<results_directory>CMC/ResultsCMC</results_directory>
 		<!--Output precision.  It is 8 by default.-->
 		<output_precision>8</output_precision>
 		<!--Initial time for the simulation.-->
@@ -40,15 +40,15 @@
 			<groups />
 		</ControllerSet>
 		<!--XML file (.xml) containing the forces applied to the model as ExternalLoads.-->
-		<external_loads_file>../ExperimentalData/subject01_walk_grf.xml</external_loads_file>
+		<external_loads_file>subject01_walk_grf.xml</external_loads_file>
 		<!--Motion (.mot) or storage (.sto) file containing the desired point trajectories.-->
 		<desired_points_file />
 		<!--Motion (.mot) or storage (.sto) file containing the desired kinematic trajectories.-->
-		<desired_kinematics_file>../RRA/ResultsRRA/subject_adjusted_Kinematics_q.sto</desired_kinematics_file>
+		<desired_kinematics_file>RRA/ResultsRRA/subject_adjusted_Kinematics_q.sto</desired_kinematics_file>
 		<!--File containing the tracking tasks. Which coordinates are tracked and with what weights are specified here.-->
-		<task_set_file>../gait10dof_Kinematics_Tracking_Tasks.xml</task_set_file>
+		<task_set_file>CMC/gait10dof_Kinematics_Tracking_Tasks.xml</task_set_file>
 		<!--File containing the constraints on the controls.-->
-		<constraints_file>controls_43p_r.xml</constraints_file>
+		<constraints_file>CMC/controls_43p_r.xml</constraints_file>
 		<!--File containing the controls output by RRA. These can be used to place constraints on the residuals during CMC.-->
 		<rra_controls_file />
 		<!--Low-pass cut-off frequency for filtering the desired kinematics. A negative value results in no filtering. The default value is -1.0, so no filtering.-->

From 4da639cbd1ff970c6088f42a7551a00ae90576d8 Mon Sep 17 00:00:00 2001
From: Christopher Dembia <cld72@cornell.edu>
Date: Sun, 11 Nov 2018 10:58:46 -0800
Subject: [PATCH 2/2] Fix indentation.

---
 CMakeLists.txt | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 68fad6a..cd84429 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,16 +25,16 @@ install(FILES Models/BouncingBlock/run_forward_bouncingBlock.xml
 
 install(FILES Models/Gait10dof18musc/gait10dof18musc.osim
               Models/Gait10dof18musc/subject01.osim
-							Models/Gait10dof18musc/subject01_metabolics.osim
-							Models/Gait10dof18musc/subject01_metabolics_path_spring.osim
-							Models/Gait10dof18musc/subject01_metabolics_path_actuator.osim
-							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_static.trc
-							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk.trc
-							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.mot
-							Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.xml
-							Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
-							Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
-				DESTINATION Models/Gait10dof18musc)
+              Models/Gait10dof18musc/subject01_metabolics.osim
+              Models/Gait10dof18musc/subject01_metabolics_path_spring.osim
+              Models/Gait10dof18musc/subject01_metabolics_path_actuator.osim
+              Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_static.trc
+              Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk.trc
+              Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.mot
+              Tutorials/Design_to_Reduce_Metabolic_Cost/ExperimentalData/subject01_walk_grf.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC.xml
+              Tutorials/Design_to_Reduce_Metabolic_Cost/CMC/walk_Setup_CMC_PathActuator.xml
+        DESTINATION Models/Gait10dof18musc)
 # TODO subject01_metabolics* files?
 install(DIRECTORY Tutorials/Design_to_Reduce_Metabolic_Cost/
         DESTINATION Models/Gait10dof18musc