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714. By Nick Papior on 2018-07-04

Finished the implementation of the supercell changes

Now the DM_history and reading of a DM enables reading from different
nsc patterns.

713. By Nick Papior on 2018-07-04

Bugfix in the copy_supercell routine

Also added a new subroutine to correct a supercell_sp_d2 in-place.
This 2nd routine will change the column values to the new supercell places
and if the new supercell does not exist the value will be deleted.
A further reduction of the sparse pattern must happen in another
routine.

712. By Nick Papior on 2018-07-04

Added nsc to DM output

Now the first record in DM files contain:

   no_u, nspin, nsc(1), nsc(2), nsc(3)

which tells off the supercell information. This is necessary
to transfer any matrix from one supercell pattern to another
supercell pattern.

I have checked that older codes will still read the files.
This is not surprising since fortran's read statements tries
to read the variables specified. If the requested input is too
short, then the rest is simply discarded. I.e. the files are forward
and backward compatible!

711. By Nick Papior on 2018-07-04

First commit for the sp-copy

A first attempt on implementing a SC1-sp -> SC2-sp
routine has been created.

The routine is agnostic on orbital ordering so it should
also handle cases were orbitals swap places (e.g. due to MD
simulations).

710. By Nick Papior on 2018-06-28

Merged r936, fixed electrode options for tbtrans and electrode expansion

709. By Nick Papior on 2018-06-28

Merged new DOS flags

Now LDOS and PDOS may use a single DOS.kgrid specification
which enables simpler input options and more streamlined ways of
handling this.

Enabled an LDOS kgrid instead of the SCF one

This enables one to fine-tune the LDOS calculation
although it should be less sensitive to k-points it may be useful.

1) All kpoints_* are renamed to kpoint_* for clarity.

2) The LDOS and PDOS k-points are defaulted to the DOS k-points
   and thus have a common reference. This means that one can specify:
      DOS.kgrid.Cutoff
   which will act as k-grid for LDOS and PDOS calculations.

3) reset_kpoint* routines have been added which cleans the memory
   upon siesta exit.

4) Changed local_DOS.F to local_DOS.F90

Also enabled LDOS and PDOS energy specification with respect to EF. I.e. now
users may select the energy-range with respect to the Fermi-level.

708. By Nick Papior on 2018-06-26

Merged r935, Bulk-init expansion

707. By Alberto Garcia on 2018-06-26

Merged 4.1 r933-934: EDM setting; diag*g and pdos*g with auxcell. NaiveAuxCell

706. By Nick Papior on 2018-06-18

Merged r927-932, ion table precision, transiesta fixes and FA/FC precision

705. By Nick Papior on 2018-06-18

Enabled kgrid.MonkhorstPack as list input (only if block is not present)

When the MonkhorstPack block is not present the kgrid can be read
from the kgrid.MonkhorstPack list, i.e.

kgrid.MonkhorstPack [10 10 10]

which will create a 10 x 10 x 10 MP grid.