How to Upload Cmc File in the Cmc

This department of the chapter covers how to control CMC execution. The properties governing execution are contained in XML files.  The topics covered in this section include:

CMC Setup File

Execution of the CMC tool is controlled by properties specified in the CMC setup file. Some properties, such as < initial_time > and < final_time >, are specified direct in the CMC setup file. Other backdrop, such as < task_set_file >, refer to additional files that comprise additional settings that affect CMC execution. These are discussed in the sections that follow.

The backdrop for CMC are enclosed inside the opening and closing tags < CMCTool > and </ CMCTool >. The proper name attribute name ="subject01_walk1" specifies the execution proper noun. The names of results files generated will be prefixed with this proper name.

Example 1: XML file for the CMC setup file

<?xml version="one.0" encoding="UTF-8"?>  <OpenSimDocument Version="20302">     <CMCTool name="subject01_walk1">     <!--Proper noun of the .osim file used to construct a model.-->     <model_file> subject01_simbody_adjusted.osim </model_file>      <!--Replace the model's forcefulness set with sets specified in         <force_set_files>? If simulated, the force ready is appended to.-->     <replace_force_set> imitation </replace_force_set>      <!--List of xml files used to construct an force set for the model.-->     <force_set_files> gait2354_CMC_Actuators.xml </force_set_files>      <!--Directory used for writing results.-->     <results_directory> ./subject01_ResultsCMC </results_directory>      <!--Output precision. It is 8 by default.-->     <output_precision> 20 </output_precision>      <!--Initial fourth dimension for the simulation.-->     <initial_time> 0.76000000 </initial_time>      <!--Last fourth dimension for the simulation.-->     <final_time> 1.24000000 </final_time>      <!--Flag indicating whether or not to compute equilibrium values for         states other than the coordinates or speeds. For example, equilibrium         muscle fiber lengths or muscle forces.-->     <solve_for_equilibrium_for_auxiliary_states> true </solve_for_equilibrium_for_auxiliary_states>      <!--Maximum number of integrator steps.-->     <maximum_number_of_integrator_steps> 30000 </maximum_number_of_integrator_steps>      <!--Maximum integration step size.-->     <maximum_integrator_step_size> 1.00000000 </maximum_integrator_step_size>      <!--Minimum integration step size.-->     <minimum_integrator_step_size> 0.00000000 </minimum_integrator_step_size>      <!--Integrator error tolerance. When the error is greater, the integrator         step size is decreased.-->     <integrator_error_tolerance> 0.00000100 </integrator_error_tolerance>      <!--Set of analyses to be run during the investigation.-->     <AnalysisSet name="Analyses">       <objects/>       <groups/>     </AnalysisSet>      <!--Controller objects in the model.-->     <ControllerSet name="Controllers">       <objects/>       <groups/>     </ControllerSet>      <!--XML file (.xml) containing the forces applied to the model as         ExternalLoads.-->     <external_loads_file> subject01_externalForces.xml </external_loads_file>      <!--Motion (.mot) or storage (.sto) file containing the desired point         trajectories.-->     <desired_points_file> </desired_points_file>      <!--Motion (.mot) or storage (.sto) file containing the desired kinematic         trajectories.-->     <desired_kinematics_file> subject01_walk1_RRA_Kinematics_initial_q.sto </desired_kinematics_file>      <!--File containing the tracking tasks. Which coordinates are tracked and         with what weights are specified here.-->     <task_set_file> gait2354_CMC_Tasks.xml </task_set_file>      <!--File containing the constraints on the controls.-->     <constraints_file> gait2354_CMC_ControlConstraints.xml </constraints_file>      <!--File containing the controls output past RRA. These can be used to place         constraints on the residuals during CMC.-->     <rra_controls_file> </rra_controls_file>      <!--Low-laissez passer cut-off frequency for filtering the desired kinematics. A         negative value results in no filtering. The default value is -1.0, then         no filtering.-->     <lowpass_cutoff_frequency> -ten.00000000 </lowpass_cutoff_frequency>      <!--Fourth dimension window over which the desired actuator forces are accomplished.         Muscles forces cannot change instantaneously, so a finite time window         must exist immune. The recommended fourth dimension window for RRA is about 0.001         sec, and for CMC is about 0.010 sec.-->     <cmc_time_window> 0.01000000 </cmc_time_window>      <!--Flag (true or fake) indicating whether or not to use the curvature         filter. Setting this flag to true tin reduce oscillations in the         computed muscle excitations.-->     <use_curvature_filter> false </use_curvature_filter>      <!--Flag (truthful or false) indicating whether to utilise the fast CMC         optimization target. The fast target requires the desired         accelerations to be met. The optimizer fails if the acclerations         constraints cannot be met, so the fast target can exist less robust. The         regular target does not require the acceleration constraints to be         met; it meets them every bit well as information technology can, but information technology is slower and less         accurate.-->     <use_fast_optimization_target> true </use_fast_optimization_target>      <!--Preferred optimizer algorithm (currently back up "ipopt" or "cfsqp",         the latter requiring the osimFSQP library.-->     <optimizer_algorithm> ipopt </optimizer_algorithm>      <!--Perturbation size used past the optimizer to compute numerical         derivatives. A value between 1.0e-iv and 1.0e-8 is usually         approprieate.-->     <optimizer_derivative_dx> one.00000000 </optimizer_derivative_dx>      <!--Convergence criterion for the optimizer. The smaller this value, the         deeper the convergence. Decreasing this number tin can improve a solution,         only will also probable increase ciphering time.-->     <optimizer_convergence_criterion> 0.00010000 </optimizer_convergence_criterion>      <!--Maximum number of iterations for the optimizer.-->     <optimizer_max_iterations> 200 </optimizer_max_iterations>      <!--Print level for the optimizer, 0 - iii. 0=no press, 3=detailed         press, 2=in between-->     <optimizer_print_level> 0 </optimizer_print_level>      <!--Truthful-false flag indicating whether or not to turn on verbose press         for cmc.-->     <use_verbose_printing> simulated </use_verbose_printing>  	<!--Listing of individual Actuators past individual or user-defined group name to exist excluded from CMC's control.-->  	<actuators_to_exclude />   </CMCTool>  </OpenSimDocument>              

Specifying the Model

The <model_file> specifies the name of the .osim file used to construct and initialize the model. The <force_set_files> are a list of actuators set file names, each of which may be included as actuators of the model. These actuators are in add-on to whatever actuators specified in the model file that are already office of the model. <replace_force_set>, if set to true, indicates that the actuator sets listed in <force_set_files> should supplant whatsoever actuators that are already role of the model otherwise actuators are appended.

Specifying Initial and Terminal Times

The properties < initial_time > and < final_time > specify the time interval over which CMC is to be run. Be enlightened that CMC uses 0.030 seconds starting from the specified initial time to initialize whatever muscle states. In addition, to avoid undesirable effects having to do with the processing of the desired kinematics and external loads, it is prudent not to start CMC at the very kickoff of the desired kinematics but to allow a buffer. One or two pct of a gait wheel, for example, is usually sufficient.

Specifying Integrator Settings

The < maximum_number_of_integrator_steps > belongings indicates the maximum number of steps CMC can take during a run of the tool before terminating. Making the < integrator_accuracy > finer (smaller) will decrease the integrator footstep size.

Specifying Analyses and Results

Whatever number of bachelor analyses can be added to a CMC run. To get a list of available analyses, open the CMC tool in the GUI and become the the Analyses pane and click on Add or meet the Analyses affiliate.

There are several properties associated with the analyses results. < results_directory > specifies the directory where results should be written. < output_precision > specifies how many decimal places should be used when writing results. A value of 20 is sufficient to avoid round-off error when reading results back in during other steps in the workflow. < step_interval > specifies how oftentimes to record results during numerical integration. A value of 10 means tape results every ten integration steps.

Specifying Desired Kinematics

The file containing the desired kinematics is specified using the property < desired_kinematics_file >. A low-pass cutoff frequency for filtering the kinematics can exist specified using the holding < lowpass_cutoff_frequency >. An order 50 Finite Impulse Response Filter (FIR) is currently used. If the desired kinematics have already been filtered, equally is commonly the example by the time the CMC tool is used, specify a negative cutoff frequency to foreclose any filtering at all.

Specifying External Loads

There can be multiple sets of footing reaction forces for different locations on the body. These are specified in the file identified by the < external_loads_file > tags. The external loads .xml file specifies the source file for input forces and to which location and body the forces are to be applied. See Inverse Dynamics for additional details for applying whatsoever number of external loads equally bespeak forces and/or trunk torques.

Note: Across all steps in the OpenSim workflow, information technology is important to apply the aforementioned settings for specifying the external loads.

Controlling the Optimizer

A number of properties are available for controlling the optimizer. < use_fast_ optimization_target > specifies whether the fast or wearisome optimization target should exist used (How RRA Works). < optimizer_derivative_dx > specifies the perturbation size in the controls for calculating numerical derivatives. < optimizer_convergence_criterion > specifies a convergence criterion; the smaller this value, the deeper the convergence. < optimizer_max_iterations > specifies an iteration limit for each time footstep. < optimizer_print_level > allows diagnostic information to be printed. The larger the number (up to a maximum of 3), the more information that is printed.

Settings for the CMC algorithm

A number of backdrop are available for controlling the CMC algorithm proper. < cmc_time_window > specifies the time allowed for fourth dimension-dependent actuators like muscles to change force. If the window is too small, actuator forces will not have enough freedom to generate the desired accelerations. If the window is besides large, the control volition be too coarse to let for good tracking (How RRA Works). < use_curvature_filter > specifies whether or not to apply a curvature filter to computed excitations. If control values are oscillating, the curvature filter can used to attenuate these oscillations. To apply the curvature filter, set up < use_curvature_filter > to true . < adjust_com_to_reduce_residuals > is a belongings used for remainder reduction (Affiliate three). During CMC, this property should be fix to simulated .

Specifying Tracking Tasks and Control Constraints

Which coordinates should exist tracked and how those coordinates should be tracked are specified in a split XML file specified past the property < task_set_file >. Constraints on the controls (e.g., muscle excitations) are also specified in a separate XML file using the belongings < constraints_file >. These files are covered below.

Specifying Actuators to Exclude

In version iii.1 and later, you can tell CMC to ignore specific actuators by calculation them to the list of actuators using the property <actuators_to_exclude>. This is useful if you have, for instance, a model component with its own controller.

Task Set File

A task set is used to specify which coordinates (e.g., articulation angles) in a model should follow a desired kinematic trajectory. Information technology also specifies the relative weighting between coordinates.

Job Sets

Tasks, the class objects used to specify a tracking goal, are kept in sets. Sets are lists of objects. The individual tasks are found between opening and endmost xml tags < objects > and </ objects >.

Job Types

Although at that place will be additional task types in the future, such equally orientation and bespeak tracking, currently only tracking of generalized coordinates (or joints) is supported. The properties for each joint task are enclosed between opening and closing XML tags < CMC_Joint > and </ CMC_Joint >.

Instance 2: XML file for the CMC job set file

<?xml version="1.0" encoding="UTF-eight"?>   <CMC_TaskSet name="gait2354_CMC">     <objects>       <CMC_Joint name="pelvis_tz">        <on> true </on>        <agile> true false false </agile>        <weight> 1.0e0 </weight>        <kp> 100.0 </kp>        <kv> xx.0 </kv>        <coordinate> pelvis_tz </coordinate>      </CMC_Joint>       <CMC_Joint name="hip_flexion_r">        <on> true </on>        <active> true false fake </active>        <weight> 1.0e2 </weight>        <kp> 100.0 </kp>        <kv> xx.0 </kv>        <coordinate> hip_flexion_r </coordinate>      </CMC_Joint>     </objects>   </CMC_TaskSet>

Task Properties

The belongings < on > is used to plow a task on or off. The < active > property specifies which component of task is active. While other job types might accept three components, articulation tasks only accept one, so the typical setting is true faux false . Backdrop < kp > and < kv > specify the position and velocity error gains, respectively. See How RRA Works for an caption of error gains. The < coordinate > property specifies to which model coordinate a chore applies. The value of the belongings must agree with the name of the model coordinate exactly. Joints can be translational (due east.g., pelvis_tz) or rotational (e.thou., hip_flexion_r).

Control Constraints File

Control Sets

The properties governing the controls in a simulation are contained in a < ControlSet >. Controls are functions that vary as a function of time. Currently, two types of controls are supported: < ControlConstant > and < ControlLinear >. < ControlConstant > objects are constant for any value of time. < ControlLinear > objects consist of an assortment of paired time and control values or nodes (i.e., [t1,x1], [t2,x2], … [tn,xn]). These values are linearly interpolated to determine the value of the command at a detail fourth dimension. < ControlLinear > is the class most usually used during CMC and is reviewed further beneath.

Default Objects

Many control objects within a file may have the same values for a number of properties. At the beginning of a command set, there is a defaults department, demarcated by the opening and closing tags < defaults > and </ defaults >, that can exist used to specify default property values. If a command has the aforementioned value as the default control, that belongings need not be repeated.

Properties of <ControlLinear> Command Type

A number of properties are used to describe the <ControlLinear> command type.

• < is_model_control > indicates whether or not a control belongs to the model. Musculus excitations and actuator controls in general are examples of such controls. For specifying control constraints for CMC, this belongings should always be truthful .
• < extrapolate > specifies that the value of the control should be extrapolated when the time value is outside the valid time range of a command (due east.thou., earlier t1 or later on tn).
• < default_min > and < default_max > specify the default minimum and default maximum values, respectively, of a control. For muscles, these are frequently 0.02 and 1.00 every bit in Example 3, below
• < use_steps > specifies whether or not the value of a control should be linearly interpolated between nodes. If set to true , a control is treated as a step function in which the value of a step is adamant past the value of the nearest node to the right or, equivalently, after in time. For CMC, it generally works amend for muscle excitations to use steps.

Instance 3: XML file for the CMC control constraints file

<?xml version="1.0" encoding="UTF-8"?>     <ControlSet name="gait2354_CMC">       <defaults>         <ControlLinear name="default">          <is_model_control> truthful </is_model_control>          <extrapolate> true </extrapolate>          <default_min> 0.02 </default_min>          <default_max> 1.00 </default_max>          <use_steps> true </use_steps>        </ControlLinear>        </defaults>       <objects>         <!--Residual actuators -->        <ControlLinear name="FX.excitation">          <default_min> -i.0 </default_min>          <default_max> 1.0 </default_max>          <use_steps> imitation </use_steps>        </ControlLinear>         <!-- Reserve actuators -->        <ControlLinear name="hip_flexion_r_reserve.excitation">          <default_min> -thou </default_min>          <default_max> grand </default_max>        </ControlLinear>         <!-- Muscles -->        <ControlLinear name="glut_med1_r.excitation" />        <ControlLinear proper noun="glut_med2_r.excitation" />        <ControlLinear name="glut_med3_r.excitation" />        <ControlLinear name="bifemlh_r.excitation" />        <ControlLinear proper name="bifemsh_r.excitation" />     </objects>   </ControlSet>

Case 4: Using control constraints file to constrain CMC excitations to match EMG information

When using CMC, sometimes the optimizer will cull to activate a muscle during a function of the movement when it should not be activated. For example, based on EMG recordings during running, we know that soleus should not have much action during swing. But sometimes CMC will cull to activate the musculus since it is non informed nearly the EMG data. To get a improve match with experimental EMG, we can constrain the activation CMC chooses for soleus during a specific time period of the movement.

Below is an instance of a constraint, where the right soleus is specified to exist off betwixt 0.7272 and 0.9945s.

The control constraints are displayed in the Excitation Editor GUI. Lines take been added to illustrate how the nodes are connected. The value associated with a node is applied before the specified time. In other words, when interpreting a control or its constraint (min or max value) it is the value from the future node at t(i+1) to the nowadays node at t(i) that is practical.

<ControlLinear name="soleus_r.excitation">      <min_nodes>           <ControlLinearNode>                <t>0.7272</t>                <value>0.02</value>           </ControlLinearNode>           <ControlLinearNode>                <t>0.9945</t>                <value>0.02</value>           </ControlLinearNode>           <ControlLinearNode>                <t>1.143</t>                <value>0.02</value>           </ControlLinearNode>      </min_nodes>      <max_nodes>           <ControlLinearNode>                <t>0.7272</t>                <value>1</value>           </ControlLinearNode>           <ControlLinearNode>                <t>0.9945</t>                <value>0.02</value>           </ControlLinearNode>           <ControlLinearNode>                <t>1.143</t>                <value>1</value>           </ControlLinearNode>      </max_nodes> </ControlLinear>

Residual Actuators

Rest actuators are actuators that act directly between the model and the ground. These are used to control the global position and orientation of a model. If the residuals for a simulation have been reduced (see Balance Reduction Algorithm), the loads applied by these actuators should be relatively pocket-size. However, dissimilar muscles, the remainder actuators can employ negative likewise every bit positive forces. The minimum and maximum control values hither, therefore, differ from the default values set at the top of the example file (0.02 and i.0) and must be specified explicitly (-1.0 and 1.0).

Reserve Actuators

Reserve actuators are actuators that can make upwards for bereft muscle strength during a simulation. Even so, they should merely apply pregnant loads (east.k., forces above 1 N or 1 Nm) when necessary. To penalize the use of reserve actuators, the minimum and maximum control values are allowed to be very large (-1000 and m in Example three above). Forces are specified in newtons and torques in newton-meters.

Muscles

When a control has the same property values as that specified in the defaults section at the top of the command constraints file (Case iii), it is only necessary to have a one-line entry that specifies the proper noun of the control.

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Source: https://simtk-confluence.stanford.edu:8443/display/OpenSim/CMC+Settings+Files+and+XML+Tag+Definitions

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