Collect all params on same node

[mtwest2718]

This task will require separate file creation writing and closing steps.

• [x] map out the sim-flag logic so a single process file with all variables can be generated
• [x] save each of the variables in its appropriate place
• [x] close each of the sub-components in the proper order

[mtwest2718]

I am thinking that I might combine this with #2. The reason is that the arrays U_m and U_h have distinct names for each of the sub-arrays and presumably the maintainers would like to keep that meta-data info in the files. I will have to check. Also need to check on whether visc and Nexcite need to be broken out into components are not.

[mtwest2718]

Because the .dac functionality still exists, I haven't touched the file_m & file_h name arrays yet. But having "dac" in all the meta info is rather annoying for any post-processing, so I need to learn how to split a string in Fortran.

This seems to be a clear method though I am unsure whether its possible to do this with older compilers...

[mtwest2718]

For each time step & process, all output variables & the grid coordinates are saved to a single HDF5 file

• The conditional logic of when to save different variables remains the same.
• Creating the single HDF5 file is located within the "write variables" section of the output subroutine in IO_rot.f90.
• Each file gets a copy of the grid coordinates, not just the one that contains the initial settings
• All of the old .dac. read/write subroutines remain & are functional with this update.
• One dataspace is generated for the 3D variables as they all have the same rank and dimensions.
• Since each spatial coordinate potentially has a different dimension size, the code generates a distinct dataspace for each.

[mtwest2718]

Stuff not yet done that needs to be

• [x] update compare_output.py to handle consolidated hdf5 data

[mtwest2718]

Since time series generation is dynamic and handled differently than the spatial grid and the output variables, I am not sure how exactly to handle it's porting from dac to hdf5.