A pump apparatus has a downhole pump disposed in a wellbore and has a motor at the surface, and a rod string operatively moved by the motor reciprocates the downhole pump in the wellbore. Downhole data indicative of load and position of the downhole pump is generated using surface measurements and a wave equation model having a damping factor. Actual fluid load lines are determined from the downhole data for upstrokes and downstrokes of the downhole pump, and calculated fluid load lines for from the strokes are determined from the distribution of the load values in the downhole data. The actual fluid load lines are compared to the calculated fluid load lines to determine if the downhole data is over or under-damped. Then, the damping factor of the wave equation model can be adjusted so that new downhole data can be generated with appropriate damping.