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1084. By Petr Koval on 2019-06-28

small fixes for windows

1083. By Nick Papior on 2019-06-27

Removed transiesta checks for dipole corrections

Essentially I think that dipole corrections are already
correctly handled since they are meant to reverse any
mis-aligned charge-density to not disrupt the cell potential.

For now we have explicitly allow *any* dipole-corrections
to behave JUST as Siesta!

1082. By Nick Papior on 2019-06-27

Streamlined TBtrans output for *.nc files

Now TBT.nc/TBT.SE.nc/TBT.Proj.nc files contain the same meta-data
for the device and electrodes.

This enables easier post-processing since the files may be used
in sisl data-extraction utilities.

Other than output there is no changes.

1081. By Nick Papior on 2019-06-20

Cleaned m_ts_hartree

I now know this is correct since it now deals with a 3D array.
Once in a while (when reading that code) it is easier
to decipher whether it is done correctly by doing explicit
3D arrays.
I have checked against a chain with x/y/z and
plane/elec-plane/elec-box options to assert it yields
the same result in all cases.

1080. By Nick Papior on 2019-06-20

Fixed destruction of pline which should not be done

After changing to fdf_addtoken we should not destroy the
pline since it gets added to the fdf-line list.

Also separated an if-statement which could potentially
lead to incorrect mixing.

1079. By Nick Papior on 2019-06-17

Added checks for -fdf flags on command line

One would think that %include statements works.
However, it will not work since the flags in the file
will be put at the end of the fdf-table.

As such we have made sure that users will not do this
and thus added error messages.

1078. By Nick Papior on 2019-06-12

Fixed phonon output by adding prefactor of 2omega most places

All calculation of DM/COOP/COHP are added 2 omega for PHtrans.
This is empirically done as I think they should still reflect
some kind of population per energy.

Also amended documentation to indicate this.

1077. By Nick Papior on 2019-06-12

Added warnings when V_local is used in atom.F

Patch supplied by A.G. from atom-docs branch.

1076. By Nick Papior on 2019-06-11

Documented real-space self-energy options

And added a reference to the arXiv publication.
Probably it won't be published before b5.

1075. By Nick Papior on 2019-06-11

Documented V-fraction option and added delta-Ef option

Now users can apply manual bias shifts in the electronic
structure between the device region and electrode regions.

Users can also manually shift the electronic structure of the
electrodes when using semi-conducting electrodes. This is
easier than shifting the electronic structure using sisl.