Better handling of DFT+U calculations

[ezpzbz]

context:

When we start of a workchain with a structure that has magnetic ordering, we have species with different kinds in StructureData to reflect this. For example:

Li Fe1 Fe2 P S
2 1 1 2 8

which would require LDAUU of:

0 5.3 5.3 0 0

Currently, if use requests DFT+U calculation, the LDAU section of INCAR is constructed in setup_protocols for all stages. This results in an issue that will cause wokchain to fail. Once a stage is finished with structure as output, and considering that we do not attach converged spins to the structure, the resulting structure will have species as:

Li Fe P S
2 2 2 8

which would require LDAUU of:

0 5.3 0 0

which is not given as it is made before this. This will result in parsing errors.

Solution:

• [x] Move construction of LDAU section from setup_protocol to get_stage_incar. This way we ensure that we always construct the section for current structure.
• [x] Attach information about converged spin to the relaxed structure when parsin it:
• This needs to be done in parser.
• We need to use site-projected magnetization for this purpose. However, these can have negligible but non-zero values that StructureData would treat them differently. Therefore, we consider a threshold (0.1) and will change the magnetization to zero if the absolute value of them is below threshold. So: converged_magmoms will be modified:

  magmoms = [0 if abs(mag)<0.1 else mag for mag in magmoms]

  resulting in:

  [0, 0, -3.682, 3.682, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

  Then,

  vrun = Vasptun('vasprun.xml')
  structure = vrun.final_structure
  structure.add_spin_by_site(magmoms)