[DO NOT MERGE] Iso_io

[matt-chan]

Just starting this PR a bit earlier so I can keep track of API changes.

This PR contains an isolated io module.

There are API changes.

Deprecations:

• LockedH5 and the internal H5 file format have been removed.

Parameters:

• The vasp dump_poscar routine now requires data to contain an attribute cell_frac which contains the return value of the cell.to_frac function.

Return values:

• The obasis attribute no longer contains an instance of obasis. Rather it contains a dict of all elements necessary to instantiate GOBasis. Simply pass it via GObasis(*obasis.values())
• The orb_alpha attribute no longer contains an Orbital instance. It has been replaced by four attributes:
  • orb_alpha: a tuple of (nbasis, nfn). Sufficient to instantiate a Orbital class.
  • orb_alpha_coeffs: formerly Orbitals.coefficients
  • orb_alpha_energies: formerly Orbitals.energies
  • orb_alpha_occs: formerly Orbitals.occs
• The cell attribute is no longer a Cell instance. Rather it contains a numpy array rvecs which is sufficient to instantiate a Cell instance.
• The grid attribute no longer contains an UniformGrid instance. It now contains a dict sufficient to instantiate a UniformGrid instance. It can be used via UniformGrid(*grid.values())
• Vasp IOData instances now require a gvecs attribute to write the coordinates.

Non-API breaking changes:

• The molden coefficient normalization now uses internal code to calculate the overlap integrals. The dependency on gbasis has been removed.

[matt-chan]

Looks like the overlap code will need to be cython'd after all... cp2k unit tests take 2 minutes alone.

It doesn't look too hard though. 60% of the time is spent in a few simple functions that can be replaced.

[tovrstra]

I took a quick look at the overlap code and don't see very obvious opportunities to speed things up at the Python level. add_overlap and its internals seem to be the obvious candidates to move to Cython. The files from CP2K have somewhat weird basis sets but the files are certainly realistic.

[matt-chan]

Okay, so it's Cython'd now! Down to 7s for all the unit tests =). It's still somewhat readable I think? It's ready to review @tovrstra.

PS even if it's okay, please don't merge it back in yet!

[FarnazH]

The isolated io module in this branch is now an independent module with Python 2 & 3 compatibility. Please see: https://github.com/theochem/iodata

[matt-chan]

@tovrstra, I'm going to close the PR soon since @FarnazH moved it to a new repo. It's easier to review in this format though. Is there anything you'd like changed before I do it?

[matt-chan]

Closing since it's been moved to https://github.com/theochem/iodata. The code has diverged too much to make changes here feasible.