/*******************************************************************************
CMC Tracking parameters used in generating muscle actuated simulations of movement
*******************************************************************************/

stepsize 0.01		/* Time interval at which CMC recomputes the muscle excitations */
initstepsize 0.01		/* Time interval at which CMC recomputes the muscle excitations within the initialization period */
numinitsteps 10		/* Number of steps in which to initialize the CMC tracking controller, prior to starting the forward simulation */
numsubsteps 10		/* Number of output steps in motion file for one stepSize, allows output motion file to be written at higher rate */
kincutofffrequency 10.0	/* Low pass filter cutoff frequency for pre-processing kinematic data, set high if REA was used so as not to smooth dynamically consistent solution */
grfcutofffrequency 10.0	/* Low pass filter cutoff frequency for pre-processing ground reaction force and cp data, set high if REA was used so as not to smooth dynamically consistent solution */

mfdObjFun 2		/* Muscle Force Distribution Objective Function: note - all muscle quantities are weighted by muscle volume
			   0-sum of muscle volume-weighted activations squared, 
			   1-sum of muscle volume-weighted normalized (by fl*Fo) tendon forces squared,
			   2-sum of muscle volume-weighted normalized (by fl*Fo) CE forces squared */


/*******************************************************************************
TrackGenCoords are the gen coords in the model that CMC will compute muscle 
excitations to track
	at any time step the desired generalized acceleration
		qddot_des = ka*qddot_exp + kv*(qdot_exp-qdot) + kp*(q_exp-q)
	where
		_exp represents experimental data
		qddot_exp - is the experimental acceration stepSize in the future
		q, qdot - current generalized coordinates and generalized speeds
*******************************************************************************/
begintrackgencoords
/* Form: gencoord ka kv kp */
knee_flex_r	    	1. 20. 100.
endtrackgencoords        

/*******************************************************************************
The CMC parameters file can be used to specify the range of acceptable muscle
excitations and the number of spline points to use in the CMC algorithm when
predicting the achievable forces stepSize in the future.  
Default is used to set the same values for all muscles
The minimum and maximum excitations for individual muscles can then be specified
over specified time ranges
*******************************************************************************/
beginmuscles
/* Form: default minExc maxExc numSplinePts */
default 0.01 1.0 11
/* Following form is used to restrict muscle excitations over specified periods of the simulation */
/* Form: muscle minExc maxExc minTime maxTime                                                     */
/* For example:                                                                                   */
/*      bifemlh_r 0.01 0.011 0.4 0.6                                                              */
/*      bifemlh_r 0.01 0.2 0.62 0.65                                                              */
/* Limits bifemlh_r exc u as follows:  0.1<u<0.011 when 0.4<t<0.6;  0.1<u<0.02 when 0.62<t<0.65   */
endmuscles


/*******************************************************************************
Unconstrained gencoords are driven by the muscle and external forces in the 
forward simulation.  Note that gencoords can be unconstrained and not tracked
or vice-versa.  Generally you would want all tracking gencoords to be listed below
plus the base segment (e.g. pelvis) gencoords if you are simulating walking 
*******************************************************************************/
beginunconstrainedgencoords
knee_flex_r
endunconstrainedgencoords        

/*******************************************************************************
Prescribed gencoords are motion driven by the kinematic data described in the
input motion file.  Generally this list includes gencoords which you have motion
for but do not have sufficient musculoskeletal geometry to drive within a forward 
simulation, e.g. the toe joint in a gait model.
*******************************************************************************/
beginprescribedgencoords
knee_flex_l
endprescribedgencoords       


/*******************************************************************************
Fixed gencoords are set to a constant specified value throughout the simulation.
format: gencoord	fixed_value

*******************************************************************************/
beginfixedgencoords
pelvis_tilt	90.
hip_flex_r	15.
ankle_flex_r	-45.
hip_flex_l	0.
ankle_flex_l	-15.0
hip_add_r	0.
hip_rot_r	0.
subt_angle_r	0.
toe_angle_r	0.
hip_add_l	0.
hip_rot_l	0.
subt_angle_l	0.
toe_angle_l	0.
endfixedgencoords


         
/*******************************************************************************
Options of which data to write to the output motion file (0-no, 1-yes)

reactionsInOutboardBody  This option is used to specify whether joint reactions will be 
                         expressed in the outboard (=1) or inboard (=0) reference frames

The segment option allows you to choose which segment to get joint reaction forces for
beginsegments
segment option (=1 to output, =0 to not ouput (default))
endsegments

*******************************************************************************/
beginoutputoptions
generalizedSpeeds 1
generalizedAccelerations 0
markerKinematics 0
BFMarkerKinematics 0
centerOfMassPosition 0
centerOfMassVelocity 0
massCenterPositions 0
massCenterVelocities 0
extForces 1
extTorques 0
muscleActivations 1
muscleExcitations 1
muscleLengths 0
muscleForces 1
normMuscleForces 0
fiberLengths 0
normFiberLengths 0
tendonLengths 0
fiberVelocities 0
muscleTendonVelocities 1
muscleMomentArms 0
muscleJointTorques 0
jointPowers 0
jointTorques 0
jointReactionForces 1
jointReactionTorques 0
jointReactionPowers 1
jointReactionTorques 1
totalMuscleJointTorques 0
contactForces 0
indQddot 0
indSegmentAcc 0
reactionsInOutboardBody 0
beginsegments
femur_r 1
tibia_r 1
endsegments
constrainedgencoords 0
endoutputoptions