Simulation of the Micro-kinetic generator
In their Figure 6, they are not modeling the rectification.  They are showing the armature current as being equal to (armature EMF - bus voltage)/(overall resistance) -- but this is not correct.  Under rectification, the current would only flow when the armature EMF exceeds the bus voltage.

So in between the summation block with the bus voltage, and the "1/R" block, you need a block that implements rectification: $$e_{out} = \begin{cases}
0 &amp; e_{in} &lt; 0 \\
e_{in} &amp; e_{in} \ge 0
\end{cases}$$

Either that, or you want to move the \$|x|\$ block into that spot, rather than just feeding an oscilloscope with it (and you want to remove it from the oscilloscope feed).