Make documentation consistent

[menon-karthik]

The documentation for the governing equations is inconsistent in terms of nomenclature and is also slightly different from the implemented equations in some places. This makes the documentation a little hard to use.

Just as an example, in the RCR boundary condition documentation page, we use $P_{ref}$ for the distal pressure, but it is Pd in the code; there are $Q^e$ and $P^e$ in the equations, but not in the schematic and the label $P_C$ is in the wrong place; the order of equations in the code is actually reversed. I'm assuming this is the case in many other places (for example, I haven't even bothered putting in the equations for ClosedLoopHeartPulmonary).

We should go through and make sure things are consistent. Also, they might not be consistent with the ROM simulation guide.

Should we continue having the documentation in two places or can we get rid of the ROM simulation guide and just provide a link to this documentation since it's much more comprehensive and is also connected to code updates?

[mrp089]

Yes! With #53 we should have all the documentation from simvascular.github.io in Doxygen. I'll delete the simvascular.github.io content and link to Doxygen.

Additionally, I'll go over the blocks and make sure the Doxygen matches with the code.

[menon-karthik]

Just so we don't forget to fix this as part of this issue: the documentation in ROM simulation guide has drifted further since the recent gen-α commit. The governing equations themselves (for example, the handling of non-linear terms) are different in the two places.

[mrp089]

@menon-karthik, ok to close?

[menon-karthik]

There is still some block-specific documentation that is not consistent between the equations/figures in Doxygen and the actual equations implemented. I will look at that and clean up in the next couple of days.

I am already fixing some of it while implementing the chamber block (#81), so this might not have its own pull request.