GitLab

Due to an oversight, the "j" values were not inserted correctly in
the data structures after reading the .ion.nc netcdf files.

Also, "j" values were unconditionally written to netcdf files, even
when "lj" projectors were not in use.

Some more changes brought over from the material for the 4.1.5 release.

* Add python script for GitLab releases.
* mnt: minor fixes for the release.sh
* mnt: typos in atom.F
* Clarifications for SO and PEXSI in the manual
* (doc): Update README in Util/pdosxml
* Refactor Util/Scripting

While the updates pertain to the rel-4.1 branch, the new files are
more updated than most in the master branch, and they include features
that have been previously merged.

test: reduced test requirements for SOC
mnt: prepared release.sh and fixed links in *.tex files
bug: fixed writing Ef to .nc file in corner cases
Rename ChangeLog.md to ReleaseNotes.md and remove old-style file
bug: allowed slabdipolecorrection to accept empty values
mnt: added new simd construct for Bloch
doc: added debug options for gfortran and intel

Add python script for GitLab releases.

See merge request !46

This will help understanding what it does.

The main purpose of the script is to create a SIESTA release on GitLab.

The script may also be used to delete a release from GitLab or to replace the
description (text) of an existing release.  These two additional features will
work for any GitLab release (not only for SIESTA releases).

And amended ReleaseNotes with exact version and tagging date

Fixed version.info for 4.1.5

Provide links to current scripting options, and put the old scripts in
a separate subdirectory.

All tests have been updated.

This also updates TS script that copies the test output back to the
reference directory.
Signed-off-by: Nick Papior <nickpapior@gmail.com>

Now
1. they are not required to converge
2. k-points reduced substantially
3. mesh-cutoff reduced substantially

It should mean that the tests are actually runable in a couple
of minutes (rather than hours!). The original test values
are there for reference for users.

This adds a link to the latest article describing siesta
developments and allows users to see this.

I also note that users should clearly state which version
of siesta they are using to clarify this for readers.

Added MODULOP which makes mod operations on negative indices
much easier.

Now links in manual are updated and we have consistency.

Sometimes the Ef variable was not written because of option clashes.
Now we always write Ef with either DM or H writes.

The old RELEASE_NOTES file has been phased out in favor of the
ReleaseNotes.md file (renamed from ChangeLog.md).

In this way we can have a single file, with a more appropriate name,
to record changes in the context of different releases.

In this way we can have a single file, with a more
appropriate name, to record changes in the context
of different releases.

Now empty values respect equivalence with true for slabdipolecorrection.
Also amended some documentation stuff.

This is mainly meant for benchmarking and feature testing

This enables users to find information in the documentation.

Now we store the H(-R) for positive directions
adn H(R) for negative directions and use the reverse
phases.

This means we get faster indexing when creating the
matrices for SE calculations. I have checked that
the results are the same.

This brings a much needed clean-up of comments and
array indices in the TS approach.
Basically many of the comments were wrong based on
a transposed view of the matrix + phases.

Additionally we had the dm_update routine doing
the transposing of the matrix calculations.
This was very awkward. This is only for the EQ
with

 DM_eq \propto (Gf - Gf^\dagger)

Now we do it a little easier and do it in the
respective add_DM routines, this makes
dm_update much easier to comprehend and it
should also be faster since searching the sparse
elements should be slower than indexing the transpose
array element in add_DM.
This means we have a problem for ts_dq in the MUMPS@k
solver. The difference in minor but may result in
slower dEf convergence.

Cleaned up all phase calculations, now they are
all based on dot_product(k, sc_off) which is easier
to comprehend.

Cleaned up MUMPS scattering matrix calculation. It is
easier to understand now.

For the self-energy calculations we now rely on Siesta
to provide a Hermitian matrix. I.e. we do not calculate
H = (H + H^A) / 2. Generally Siesta behaves very well and
we should trust this. This may introduce slight noises
in the calculations. We could, if large noises occur make
this feature optional. Secondly, the transfer matrix
is not symmetrized, so one could argue that this needs to
be done in any case.
SPEEDUP.

For Hk we also remove this symmetrization and shift the
Fermi-level in one go. This removes a complete loop of
the sparse matrix elements in Hk.
SPEEDUP.

ts_dq calculations now have more is_nan checks and also
prints out the charge accummulated at Ef.
The interpolation from the file also tries to decide
whether the change in Ef co-incides with the sign of dq.
If not the file interpolation will be turned off for
that iteration. Generally a tight dq tolerance requires
a smaller TS.dQ.Factor.

All phase changes have been applied to the tbtrans code.
This also encouraged a small clean-up in the orb_current
calculation, merged some if-statements.

I ran all BTD, LAPACK and MUMPS calculations
for gamma and k-points. All give the same results.

This could only have affected certain corner case
calculations of tbtrans, but those should have
resulted in seg-faults.

None that I have found, seen or heard of.

Added interfaces to make them easier to extend.