Hotfixes for issues

[jpmorgan98]

Opening this PR for easier contribution, do not approve until all changes have been responded. I have responded to most of reviewers comments and made some edits

Changes:

• Adding doc strings to public functions in input_.py
• Adding a runtime error for when a continuous energy xsec library is uninitiated
• Fixing plotting and other functions
• Adding some extra notes to the MPI users guide and links to the reference solution Missing/incomplete Documentation #174

Still need to be responded to:

• @spasmann, can you edit the iqmc docstring?
• eigenvalue/smrg7 fails with ERROR: Particle census bank is full Broken examples #173
• c5g7/3d/TDX the default particle number does not resolve to the reference solution.
• eigenvalue/2d_c5g7 fails to plot with the following error. I think this is due to the "C" argument to pcolormesh only having 1 dimension