IO revamp

Registered by Nick Papior

All IO routines of data that should/could be read in again should be revamped. This should be performed using a "version" ID for the files.

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Nick Papior
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Nick Papior
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This blue-print should emphasize the need for new IO files.

Importantly the current IO files are somewhat limited by their "strict" order.
I suggest that all files contain a header ID which denotes the file-version.

This will have several advantages:

- If one later decides that the default file-format is poorly constructed creating a compatibility layer between different version is _extremely_ easy, in all its simplicity.
- This will also accommodate the possibility of reverting between two IO possibilities for exa-scale computing where single IO is extremely inefficient.

An explicit suggestion for a fortran record based IO file can be this:
1. <specifier>, <content>, <file-version>
 - <specifier> 1 == Sparse matrix (<sparse>, <extra-dim>), 2 == Sparse matrix (<extra-dim>, <sparse>), 3 == dense matrix, 4 == grid, etc.
 - <content> 1 == Hamiltonian, 2 == Overlap, 3 == DM, 4 == Rho, 5 == dRho, etc.
   Of course <specifier> and <content> are highly linked.
   From <content> and <specifier> the data is "fixed" and uniquely defined.
 - <file-version> is the storage format of the data.
 - This _has_ to be an integer. Using an integer is easier to compare and it allows 2^31 different versions which I think is more than enough.
 - The other option is using strings which I think is sub-optimal. Then the length of the string is also an issue and for different codes writing a string has to be performed equivalently (UPPER/lower case). For consistency and ease I think using an integer is the best way. Generally writing characters is bad practice
2. <n-dimensions>
  <n-dimensions> specify number of dimensions of each element
3. <1-dim-size>, <2-dim-size>, ... <<n-dimension>-size>
4. Actual data is stored here.
  In general the way the data stored is dependent on the <file-version>
5. Additional data dependent on <file-version>

Having this basic infrastructure of IO routines also enables us to more easily extract them to a consistent library.

===== (7 Aug, 2016, NRP)
Come to think about this, I think our first approach should be to get NetCDF4 up and running in full parallel. Tools may easily be created to convert to binary DM, ... formats.


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