/*******************************************************************************
REA - Residual Elimination Algorithm v2
Parameters used to compute generalized coordinate trajectories
that eliminate the need for residuals
*******************************************************************************/

timestep 0.01		/* Output motion time step, if not sepecified, it is set to the input motion time step */
simtimestep 0.01	/* Simulation time step, can set bigger that output time step to speed up optimization search */
tol 0.001;		/* Error toleralance on numerical interator, usually don't set below 0.001 */
kincutofffrequency 6.0	/* This is used to compute appropriate GCVSPL (Woltring) spline smoothing parameters */
grfcutofffrequency 100.0	/* This is used to compute appropriate GCVSPL (Woltring) spline smoothing parameters for the ground reaction forces, torques and cp's */
mrkcutofffrequency 6.0

posfeedbackgain 100.0	/* Option of using some position, velocity feedback when computing desired gen accelerations */
velfeedbackgain 20.0	/* Useful for characterizing distal joint angles which are less related to grf's */
accfeedforwardgain 1.0	

computeMarkerOffset 0	/* Option to compute marker offsets that would account for mismatch between kinematic and forceplate reference frames */


/* Format:  gencoord weight sd_accnoise */
/* Weight is used in computing the overall cost function to be minimized when varying the initial conditions */
/* Use 2.0 for the standard deviation of acceleration noise, per Kuo JBME 1998 */
/* rotational accelerations are in rad/s^2 and translational accelerations are in m/s^2 */
beginreagencoords
pelvis_tilt 	0.0	2.0
pelvis_list 	0.0	2.0
pelvis_rot 	0.0	2.0
pelvis_tx	0.0	2.0
pelvis_ty	0.0	2.0
pelvis_tz	0.0	2.0
lumbar_ext	0.0	2.0
lumbar_latbend 	0.0	2.0
lumbar_rot	0.0	2.0
hip_flex_r	0.0	1.0
hip_add_r	0.0	1.0
hip_rot_r	0.0	1.0
ankle_flex_r	0.0	1.0
hip_flex_l	0.0	1.0
hip_add_l	0.0	1.0
hip_rot_l	0.0	1.0
ankle_flex_l	0.0	1.0
knee_flex_r	0.0	1.0
knee_flex_l	0.0	1.0
endreagencoords


beginprescribedgencoords
arm_add_r
arm_flex_r
arm_rot_r
elbow_flex_r
arm_add_l
arm_flex_l
arm_rot_l
elbow_flex_l
neck_ext
neck_latbend
neck_rot
pro_sup_r
wrist_flex_r
pro_sup_l
wrist_flex_l
subt_angle_r
subt_angle_l
toe_angle_r
toe_angle_l
endprescribedgencoords

/*
hip_flex_r	
hip_add_r		
hip_rot_r		
knee_flex_r	
ankle_flex_r	
subt_angle_r	
hip_flex_l	
hip_add_l		
hip_rot_l		
knee_flex_l	
ankle_flex_l	
subt_angle_l
*/

/*
beginfixedgencoords
neck_ext	0.0
neck_latbend	0.0
neck_rot	0.0
arm_add_r	0.0
arm_flex_r	0.0
arm_rot_r	0.0
elbow_flex_r	0.0
pro_sup_r	60.0
wrist_flex_r	0.0
arm_add_l	0.0
arm_flex_l	0.0
arm_rot_l	0.0
elbow_flex_l	0.0
pro_sup_l	60.0
wrist_flex_l	0.0
toe_angle_r	0.0
toe_angle_l	0.0
endfixedgencoords
*/



/* Format:  force sd_noise [option]*/
/* Estimated standard deviation of the noise in the external force measurements
   A low standard deviation will minimize the difference introduced to the forces 
   option = 1 noise is given as a relative quantity w.r.t. to the vertical force Fy */
beginextforces
fx	0.000001	1
fy	0.000001	1
fz	0.000001	1
mx	0.000001  	1
my	0.000001  	1
mz	0.000001  	1
endextforces
/* cpx	0.01
cpz	0.01 */


/* REAMARKERS allows a specific marker on a body segment 
   to be included in the overall cost function that is minimized
   via variation of the initial gencoords and genspeeds.  
Format:
beginreamarkers
mrk_name weight
mrk_name weight
...
...
endreamarkers
*/

beginreamarkers
RASI	5.0
LASI	5.0
RPSI	5.0
LPSI	5.0
RLK	5.0
LLK	5.0
LLA 	10.0
RLA	10.0
RLF	1.0
RMF	1.0
LLF	1.0
LMF	1.0
RMW	1.0
LMW	1.0
RLW	1.0
LLW	1.0
RB5	1.0
LB5	1.0
RHE	1.0
LHE	1.0
RALH	1.0
RAMH	1.0
RPLH	1.0
RPMH	1.0
RC7	1.0
RPPT	1.0
RAPT	1.0
RADT	1.0
RPDT	1.0
LPPT	1.0
LAPT	1.0
LADT	1.0
LPDT	1.0
RPPS	1.0
RADS	1.0
RPDS	1.0
RAPS	1.0
LPPS	1.0
LADS	1.0
LPDS	1.0
LAPS	1.0
RLP	1.0
RMP	1.0
RPDA	1.0
RPPA	1.0
RAPA	1.0
RADA	1.0
LPDA	1.0
LPPA	1.0
LAPA	1.0
LADA	1.0
LPUN	1.0
LDUN	1.0
LPMF	1.0
LPLF	1.0
RPUN	1.0
RDUN	1.0
RPMF	1.0
RPLF	1.0
RLSX	1.0
RMSX	1.0
RLIX	1.0
LPLW	1.0
RPLW	1.0
LDLW	1.0
RDLW	1.0
RFT4	1.0
RFT5	1.0
LFT4	1.0
LFT5	1.0
endreamarkers

/*
R.Heel	    100.0 
R.MT5	    100.0 
L.Heel	    100.0 
L.MT5	    100.0 
*/

/* Prescribedmarker allows a specific marker on a body segment 
   to precisely track x, y, and/or z translational motions descibe
   via a data trajectory in the motion file
   This is done while dynamic equilibrium
   is solved within the residual elimination algorithm.  
Format:
beginprescribedmarker marker_name
pos_data_x  xdata_column_name
pos_data_y  ydata_column_name
pos_data_z  zdata_column_name
pos_feedback_gain	...feedback gain on position used to correct the acceleration
vel_feedback_gain	...feedback gain on velocity used to correct the acceleration
scale_w_erf min max	...includes the marker error weighting when the normalized external reaction forces acting on the marker segement are between the min and max values, useful for tracking foot motion during stance but not swing
	e.g. scale_w_erf 0.05 1.0 would turn on a foot marker scaling during stance
*/

/*
beginprescribedmarker R.Ankle
pos_data_x R.Ankle_px 100.0
pos_data_y R.Ankle_py 100.0
pos_data_z R.Ankle_pz 100.0
endprescribedmarker

*/




/*******************************************************************************
Options on which data to write to the output motion file (0-no, 1-yes)
*******************************************************************************/
beginoutputoptions
generalizedSpeeds 0
generalizedAccelerations 0
markerKinematics 1
BFMarkerKinematics 0
centerOfMassPosition 0
centerOfMassVelocity 0
massCenterPositions 0
massCenterVelocities 0
extForces 1
extTorques 1
muscleActivations 0
muscleExcitations 0
muscleLengths 0
muscleForces 0
normMuscleForces 0
fiberLengths 0
normFiberLengths 0
tendonLengths 0
fiberVelocities 0
muscleTendonVelocities 0
muscleMomentArms 0
muscleJointTorques 0
jointPowers 0
jointTorques 0
jointReactionForces 0
jointReactionTorques 0
totalMuscleJointTorques 0
contactForces 0
indQddot 0
indSegmentAcc 0
endoutputoptions