Move base issue motor direction

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Update: When move base sends a cmd_vel that is translated to say -1,-1 on the wheels the gazebo model moves backwards, but in rviz it moves forward. If I negate the values then the model moves forward but backwards in rviz. What would cause this?

Here are my setting also.

rrbot:
  # Publish all joint states -----------------------------------
  joint_state_controller:
    type: joint_state_controller/JointStateController
    publish_rate: 50

  # Position Controllers ---------------------------------------
  joint1_position_controller:
    type: effort_controllers/JointVelocityController
    joint: joint1
    pid: {p: 30, i: 1, d: 1, i_clamp: 100}
  joint2_position_controller:
    type: effort_controllers/JointVelocityController
    joint: joint2
    pid: {p: 30, i: 1, d: 1, i_clamp: 100}

TrajectoryPlannerROS:
  # for details see: <a href="http://www.ros.org/wiki/base_local_planner">http://www.ros.org/wiki/base_local_planner</a>
  max_vel_x: .005
  max_trans_vel: .05
  min_vel_x: .05
  min_trans_vel: .05
  max_rotational_vel: .025   # 0.1 rad/sec = 5.7 degree/sec
  min_in_place_rotational_vel: .025

  acc_lim_th: .005
  acc_lim_x:  .005
  acc_lim_y:  0

More data on inversion:

[ INFO] [1381338035.462489594, 4.700000000]: pv1=[-0.913283] pv2=[-0.913356]
[ INFO] [1381338035.462557027, 4.700000000]: er1=[-0.086717] er2=[-0.086644] 
[ INFO] [1381338035.462593604, 4.700000000]: sp1=[-1.000000] sp2=[-1.000000] 


[ INFO] [1381338036.459313255, 4.800000000]: pv1=[-0.908281] pv2=[-0.912306]
[ INFO] [1381338036.459382353, 4.800000000]: er1=[1.408281] er2=[1.412306] 
[ INFO] [1381338036.459414965, 4.800000000]: sp1=[0.500000] sp2=[0.500000]

Update: I have been seeing this now for a while. Move base will send a positive velocity on a wheel and in the very next sequence send a negative one or vice verse. Is there any configuration that will stop navigation from doing this. Not all motors can change direction like this. Would this be a new feature? Does anyone else see this behavior in move base?

I am running move base navigation and got the following which is causing a problem for the motor controls. I am not sure why this is happening could be initial odometry but in either case. I am using the gazebo ros velocity controller.

The navigation starts sending cmd velocities of -5 -5 then it switches to 1 1. Which cause the system to react violently. I would like a smooth transition so that the wheels do get thrown into reverse. notice the error continues to build even though the set point stays steady after the initial values.

The numbers I get are as follows from the joint state controller msg.

pv=process_value

er=error

sp=set_point

pv1=[-0.057762] pv2=[-0.045411]
er1=[0.057762] er2=[0.045411] 
sp1=[0.000000] sp2=[0.000000] 

pv1=[-0.339482] pv2=[-0.292756]
er1=[-0.160518] er2=[-0.207244] 
sp1=[-0.500000] sp2=[-0.500000] 

pv1=[-0.406273] pv2=[-0.389512]
er1=[-0.093727] er2=[-0.110488] 
sp1=[-0.500000] sp2=[-0.500000] 

pv1=[-0.111645] pv2=[-0.368285]
er1=[1.111645] er2=[1.368285] 
sp1=[1.000000] sp2=[1.000000] 

pv1=[-0.115296] pv2=[-0.294882]
er1=[1.115296] er2=[1.294882] 
sp1=[1.000000] sp2=[1.000000] 

pv1=[-0.209185] pv2=[-0.315181]
er1=[1.209185] er2=[1.315181] 
sp1=[1.000000] sp2=[1.000000 ...