* Update Docs/release_notes.4.0

* Update list of contributors.

* Add some more documentation and comments, and clarify notes in
  output for the recet electric-field/slab-dipole-correction fix.

* Remove Util/pseudo-xml

* Other minor changes in README files


  
		

	

- Thanks to E. Artacho for bug-report.

- Now the dipole correction defaults when using
  an electric field and a slab calculation.

- Thanks to R. Robles for bug-report.

- Added compatibility of the electric field dipole correction

- h2o_dipole and h2o_dipole2 now conforms with the tests
  made in Bengtsson paper.

- Fixed skipped checking for proximity with floating orbitals

- Exposed the chemical_types in chemical.f.
  This enables calling the functions in that code.
  I am guessing it should be made obsolete due to the
  newer types, however, for now it seems appropriate to
  retain this in a broadcasted manner.

- When reparametrization of the pseudos one should not
  reparametrize the Bessel function basis.

- Skipped checking for proximity with floating orbitals

- Added h2_bessel test

- The dipole correction energy should only be counted
  half in the Hartree total energy.
  This may be checked using 2 calculations using water:

  1. Calculate the energy of a dipole corrected slab of
     water with the dipole aligned perpendicular
     to the slab.
  2. Calculate the energy of a doubly water slab with
     oppositely aligned dipoles.

  They should yield similar total energies.

  These tests have been added to the:
  	h2o_dipole
	h2o_dipole2
  tests.

- The dipole correction should be intrinsically used if
  an external electric field is applied to slab calculations.

  Now siesta defaults SlabDipoleCorrection to true for slab systems
  with an external electric field.
  

The Makefile was missing a space between the CFLAGS
and the -c

* The ATOM program is not bundled with Siesta due to licensing
  differences.  Mentions to it throughout the documentation and
  example files have been updated accordingly.

* The file Tests/test.mk has been reverted to the revno 490 version.
  Note that the proper way to run the tests for a given version is
  to descend into the 'Tests' directory directly below the compilation
  directory ('Obj' or other) rather than going to the top-level 'Tests'.

* Syntax changes for compiler complaints reported by Mariella Ippolito
  from CINECA.

* Completion of changes to licensing headers.

modified:
  Docs/siesta.tex
  Examples/README
  Examples/Vps/README
  Src/SiestaXC/vv_vdwxc.F90
  Src/fsiesta_mpi.F90
  Src/write_inp_wannier.F90
  Tests/test.mk
  + Header changes in a number of files
  
		

	

The 'fat' program in Util/COOP computes the projections of specific
band states onto sets of orbitals. Due to an error, the program did
not function correctly when a subset of upper bands was selected with
the '-b' and '-B' flags.

The 'eigfat2plot' utility in Util/Bands now prints an extra field giving
the spin of the state.

modified:
  Util/Bands/eigfat2plot.f90
  Util/COOP/fat.f90
  Util/COOP/main_vars.f90


	

The computation of bands and/or wavefunctions in 'siesta_analysis'
requires an initial setup of the k-point sets involved.  These are
input in ad-hoc fdf blocks with two possible options for the scaling:
'pi/a' and 'ReciprocalLatticeVectors'.

The 'pi/a' option needs a lattice constant, which is determined by
issuing an 'fdf_get' call, whereas the reciprocal lattice vector
option triggers a call to 'redcel' to determine the unit cell.

An immediate problem is the absence of lattice constant or unit-cell
information in the fdf file. This may happen, for example, when the
'use-struct-file' or 'use-save-xv' options are in effect. The program
would either stop when not finding the lattice constant, or, worse,
would implicitly compute a zero unit cell and crash later with
linear-algebra related errors such as faulty Cholesky
decompositions. (The zero-unit-cell case is an unfortunate consequence
of the implicit convention that an absent unit cell means that the
user wants an automatic one.)

A second problem is that, even if the required geometry information is
given in the fdf file, the band/wfn calculation might be happening at
the end of a cell relaxation or MD run, so the actual unit cell is not
that in the fdf file. This should be considered bad practice, but it
might happen.

The minimal solution adopted (encoded in routine get_kpoints_scale)
consists of attempting to read the lattice constant for the 'pi/a'
case, as before, but to use the unit-cell information in the
'siesta_geom' module for the reciprocal-lattice-vectors case.  This
information is not enough for the 'pi/a' option, since no record is
kept of any centering options for cubic systems, so 'a' cannot be
directly determined from the volume of the unit cell.  Note that the
setup information is handled at the beginning of the run (during the
initialization in 'siesta_init'.

A message is printed to warn the user about possible inconsistencies
if the unit-cell changes by the end of the run. In any case, the
practice of computing bands or wavefunctions at the end of a
geometry-changing run should be discouraged.

added:
  Src/get_kpoints_scale.f90
modified:
  Src/Makefile
  Src/bands.F
  Src/writewave.F
	

- After having build siesta in the Obj directory
  a natural procedure would be to go to Tests
  and run the tests:
      make
  However, the default SIESTA is not pointing to
  the Obj.
  Further the REFERENCE_DIR is not pointing to the
  correct reference directory when in the top Tests
  directory.

  Hence the procedure is:
  1. cd Obj
  2. ../Src/obj_setup.sh
  3. <create arch.make>
  4. make
  5. cd ../Tests/
  6. make
  
modified:
  Tests/test.mk

modified:
  Src/Confs
  

* In Util/Gen-basis/Makefile, the treatment of COMP_LIBS can be
  improved with a form suggested by Pedro Brandimarte, which will
  work even if there are multiple files in COMP_LIBS.

modified:
  Util/Gen-basis/Makefile
  

* In Util/Gen-basis/Makefile, the treatment of COMP_LIBS can be
  improved with a form suggested by Pedro Brandimarte, which will
  work even if there are multiple files in COMP_LIBS.

modified:
  Util/Gen-basis/Makefile
  

* Include proper headers

* Add Docs/Contributors.txt and NOTICE.txt files.

* Update READMEs and LICENSE files in several directories.

* Remove Pseudo/atom, Util/test-xml

* Remove DOM files from Src/xmlparser

* The reference directory's path was incorrect in Tests/test.mk

* In Util/Gen-basis/Makefile, the treatment of COMP_LIBS did not
  properly cover all cases.

modified:
  Tests/test.mk
  Util/Gen-basis/Makefile
  

* Include proper headers

* Add Docs/Contributors.txt and NOTICE.txt files.

* Update READMEs and LICENSE files in several directories.

* Remove Pseudo/atom, Util/test-xml

* Remove DOM files from Src/xmlparser

When alloc-report-level is 1 or 3, a report is printed at every
peak. This hanged in MPI runs. Now only the root node peaks are
printed.

(Thanks to Nick R. Papior)

modified:
  Src/alloc.F90
  Docs/siesta.tex
  

* Interim release and technical notes.

* Some older .CHANGES files have been moved to the 'branch-changes'
  directory.

* Older release notes moved to the 'older-release-notes' directory.

added:
  Docs/Changelog-from-trunk-462.txt
  Docs/branch-changes/
  Docs/older-release-notes/
  Docs/older-release-notes/release.notes_3.0
  Docs/older-release-notes/release.notes_3.1
  Docs/older-release-notes/release.notes_3.2
  Docs/release_notes.4.0-beta
renamed:
  Docs/BSC.CHANGES => Docs/branch-changes/BSC.CHANGES
  Docs/CHANGES.charconf => Docs/branch-changes/CHANGES.charconf
  Docs/CHANGES.minim => Docs/branch-changes/CHANGES.minim
  Docs/Grid.CHANGES => Docs/branch-changes/Grid.CHANGES
  Docs/KNOWN.ISSUES.BSC-patch => Docs/branch-changes/KNOWN.ISSUES.BSC-patch
  Docs/Mixing.CHANGES => Docs/branch-changes/Mixing.CHANGES
  Docs/TS-npa.CHANGES => Docs/branch-changes/TS-npa.CHANGES
  Docs/TranSiestaUpdate.pdf => Docs/older-release-notes/TranSiestaUpdate.pdf
  Docs/atom-filt+qconf.CHANGES => Docs/branch-changes/atom-filt+qconf.CHANGES
  Docs/fdf.CHANGES => Docs/branch-changes/fdf.CHANGES
  Docs/gga.CHANGES => Docs/branch-changes/gga.CHANGES
  Docs/mixrho.CHANGES => Docs/branch-changes/mixrho.CHANGES
  Docs/radfunc.CHANGES => Docs/branch-changes/radfunc.CHANGES
  Docs/rc-4.0.CHANGES => Docs/branch-changes/rc-4.0.CHANGES
  Docs/release.notes_0.11 => Docs/older-release-notes/release.notes_0.11
  Docs/release.notes_0.9 => Docs/older-release-notes/release.notes_0.9
  Docs/release.notes_1.1 => Docs/older-release-notes/release.notes_1.1
  Docs/release.notes_1.3 => Docs/older-release-notes/release.notes_1.3
  Docs/release.notes_2.0 => Docs/older-release-notes/release.notes_2.0
  Docs/timing.CHANGES => Docs/branch-changes/timing.CHANGES
  Docs/wannier-merge.CHANGES => Docs/branch-changes/wannier-merge.CHANGES
  Docs/wannier.CHANGES => Docs/branch-changes/wannier.CHANGES
modified:
  Docs/siesta.tex

* To enable quick compilation with no external libraries, some
  lapack/blas routines have been added to the Src/Libs directory.

  A minimal example of arch.make: Src/Sys/nolibs.make

  Note that some optional features do depend on the availability of
  external libraries, such as netCDF and fftw.
  
added:
  Src/Libs/svd_omm_lapack.f
modified:
  Src/Libs/blas.f
  Src/Libs/makefile
  Src/Sys/nolibs.make
  Util/Gen-basis/Makefile  

* Updated new.gnubands in Util/Bands to enhance spin processing
  and optional production of labels in tick marks.

  (Nick R. Papior)
  
* A new experimental program g2c_ng in Util/Grid offers extended
  and cleaner functionality over the classic grid2cube.

* A new program cdf_laplacian in Util/Grid computes the laplacian
  of a grid function in netCDF format.

  (A. Garcia)
  
added:
  Util/Grid/cdf_laplacian.F90
  Util/Grid/g2c_ng.f
  Util/Grid/m_gridfunc.F90
  Util/Grid/m_struct.f90
modified:
  Util/Bands/Makefile
  Util/Bands/README
  Util/Bands/new.gnubands.f90
  Util/Grid/README
  Util/Grid/makefile
  Util/build_all.sh
		    
	  

The default value of 100 was inadequate for the needs of
k-point supercells for large multipliers.

modified:
  Src/minvec.f
      
	  

Nick R. Papior authored Nov 26, 2015 and Alberto Garcia committed Nov 26, 2015

(Thanks to Nick Papior)

* The recent re-implementation of the heapsort algorithm in routine
  'ordix' in 'sorting.f' (trunk revno 468)  was buggy.

  This affected:

  - The siesta.BONDS file, which did not have optimal ordering of the
    bond-lengths.

  - Some calculations using k-points, as routine 'minvec', used in the
    definition of the effective k-point supercell, calls 'ordix'.
    (The reference outputs for the 'var_cell' and 'si2x1h' tests have
    been modified.)

  - (probably) The re-use of density-matrix information, as the ordering
    of interactions in 'hsparse' also depended on 'ordix' through calls to
    'ordvec'.

  - (maybe) The operation of the "rho-mixing" routines, which use 'ordix'
    for the sorting of stars.

modified:
  Src/sorting.f
  Tests/Reference/si2x1h.out
  Tests/Reference/var_cell.out
      
	  

- Replace pointers by allocatables in {zm,cell}_broyden_optim.
- Split-off read_options from siesta_options to reduce
  dependencies and clarify hidden symbol associations.
- Remove dependency in sparse_matrices
- Fix dependencies in makefiles in Util
- Remove Reference-xml
- Update Reference-out files
- Provide a simple-minded mechanism to flag differences in the
  test outputs ('make check').

removed:
  Tests/Reference-xml/
  Tests/Reference/partial.out
added:
  Src/read_options.F90
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.AVTRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.TEIG
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.AVTRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.TEIG
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.AVTRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.TEIG
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.AVTRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.TEIG
  Tests/TranSiesta-TBTrans/copy_to_reference.sh
  Tests/TranSiesta-TBTrans/run_tests.sh
modified:
  Docs/siesta.tex
  Src/Makefile
  Src/cell_broyden_optim.F
  Src/diagon.F
  Src/final_H_f_stress.F
  Src/obj_setup.sh
  Src/projected_DOS.F
  Src/proximity_check.F
  Src/siesta_analysis.F
  Src/siesta_forces.F
  Src/siesta_init.F
  Src/siesta_move.F
  Src/siesta_options.F90
  Src/sparse_matrices.F
  Src/state_analysis.F
  Src/state_init.F
  Src/struct_init.F
  Src/write_md_record.F
  Src/write_subs.F
  Src/zm_broyden_optim.F
  Tests/Makefile
  Tests/README
  Tests/Reference/*
  Tests/cmp_digest.sh
  Tests/partial/README
  Tests/test.mk
  Util/Denchar/Src/Makefile
  Util/Gen-basis/Makefile
  Util/STM/ol-stm/Src/Makefile
  Util/SiestaSubroutine/README
  Util/TBTrans/Makefile
  Util/TBTrans_rep/Makefile
  Util/VCA/Makefile
  Util/build_all.sh
      


	  

* The OCCS file, containing the occupation at each k-point,
  is now created only during the scf cycle, in 'diagon'. This
  fixes problems that appeared when 'diagk' was called from
  other routines.
  
* Some arrays in pdoskp were not dimensioned correctly on
  input in pdoskp.

* Added a sanity check for the user-entered ProcessorY.

(Thanks to Nick P. Andersen)

modified:
  Src/diagk.F
  Src/diagk_file.F
  Src/diagon.F
  Src/initparallel.F
  Src/pdoskp.F
	  

* Fix handling of n<3 cases in interpolation.f90 
* Made global variable 'saved' in matel_registry
  (J. Soler, with thanks to Nick P. Andersen)

* Fix uninitialized variable in interpolation.f90.
* Proper check on number of atoms in zmatrix.F.
* Avoid underflow in sorting.f.

  (Thanks to P. Brandimarte)

* In bands.F, only check for LatticeConstant input
  in the "pi/a" case.

modified:
  Src/bands.F
  Src/interpolation.f90
  Src/matel_registry.F90
  Src/sorting.f
  Src/zmatrix.F

-*-*-*-*-* 
IMPORTANT NOTE: This patch will slightly change the output
of most calculations and the detailed results of any
post-processing. Keep this in mind if you need to maintain coherency
within a project. See the rest of the text for ways to restore
backward compatibility.  The reference output files in Tests/Reference
have *not* been updated yet.
-*-*-*-*-*
  
This is the initial patch in a long-overdue clarification work related
to the "outer geometry loop" in Siesta and its interaction with the
analysis of the electronic structure.

The most important changes, following the actual refactoring logic, are:

* Superfluous calls to 'superx' to propagate the new coordinates to
  the auxiliary supercell in 'siesta_move' have been removed, as they
  are already done by 'state_init'.

* The above change has the side effect of leaving inconsistent sets of
  unit cell and supercell coordinates in 'siesta_analysis' if the unit
  cell coordinates used in the latter are those 'moved' by the
  geometry-update routines. To avoid this, and to do the analysis
  using the actual coordinates used in the computation of the
  electronic structure, the coordinates are reset to those values
  (using the *_last arrays) in 'siesta_analysis'.  The old behavior
  can be recovered by using by setting the backward compatibility
  switch 'compat-pre-v4-dynamics' to 'true'.


* To guarantee that the DM and H used in the analysis correspond to
  the latest electronic structure computed, there should be no mixing
  at the end of the scf loop. This behavior, which was optional until
  now (controlled by the value of scf-mix-after-convergence) is now
  the default. The use of DM_out instead of DM_mixed provides also a
  truly variational total-energy and more consistent forces. If the
  scf cycle is carried out mixing H, H(DM_in) is recovered by
  re-setting H to Hold in siesta_forces at the end of the cycle.

  Also, to preserve the right H for analysis it is necessary to
  avoid overwriting it in post_scf_work. This is now done by default,
  except if the option 'scf-recompute-h-after-scf' is 'true'.

  There is another switch for pre-v4.0 compatibility in this context:
  If 'compat-pre-v4-dm-h' is 'true', the 'scf-mix-after-convergence'
  and 'scf-recompute-h-after-scf' options are activated too.

  Some comments have been added to siesta_forces to document possible
  further clarifications.

* For clarity, each MD or geometry-optimization flavor has now its own
  self-contained logic block in 'siesta_move'. This has uncovered a
  few issues that have been corrected:

  - The quenched forms of the Verlet and Parrinello-Rahman (PR)
    schemes, which are actually relaxations, did not check for
    convergence before moving the atoms (PR did not check at any
    point).  Now the 'constrained' forces and stress are checked
    before invoking the routines. In the case of PR, a 'target stress'
    can optionally be subtracted from the constrained stress (a
    further form of constraint that was previously only available
    (internally) in the standard relaxation routines). A future update
    might put all these constraint conditions in 'fixed', but care
    should be taken to study their interaction with the MD
    variable-cell routines. A future revision might look into the
    effectiveness of the variable-cell routines.
    There is a new example in Tests for quenched MD relaxation.

  - The geometry output in 'siesta_move' is now exclusively done for
    checkpointing purposes, and typically involves the 'moved'
    geometries.  The current geometry output is done in 'state_init',
    and any final output in 'siesta_analysis'.

  - Some output calls have been removed where they did not make much
    sense (as in the FC or server blocks).

  - The deprecated 'phonon' support has been removed.

* Siesta_analysis outputs the 'current' final geometry, and not the
  'moved' one. The old behavior can be recovered by using the
  'compat-pre-v4-dynamics' switch.

* The default 'dynamics' option has been changed from 'verlet' to 'CG'.
  There should really be a new 'single-point' default which completely
  avoids 'siesta_move'. The old behavior can be recovered by using the
  'compat-pre-v4-dynamics' switch.

* Single-point calculations do not write .STRUCT_NEXT_ITER files, and
  the coordinates in the XV file are the current ones, unmoved.
  Extra output in siesta_options is avoided for this case.

* The headings for the beginning of the dynamics blocks are now
  more concrete.

Other minor changes:

* Fix the IO field widths in the bonds routine to support more atoms.

* Add a few more deallocations in several routines, and change the
  'routine' field in some deallocations to match the allocations
  (notably for arrays in the 'sparse_matrices' module)

* Cosmetic changes in the output format for dynamics headings

* Atomic displacements for force-constant runs are output in Ang.

removed:
  Src/phonon.F
added:
  Src/m_target_stress.F
  Tests/si2x1h-quench/
  Tests/si2x1h-quench/makefile
  Tests/si2x1h-quench/si2x1h-quench.fdf
  Tests/si2x1h-quench/si2x1h-quench.pseudos
modified:
  Docs/siesta.tex
  Src/Makefile
  Src/atomlist.f
  Src/bonds.f
  Src/dhscf.F
  Src/diag2g.F
  Src/diag2k.F
  Src/final_H_f_stress.F
  Src/fixed.F
  Src/ioxv.F
  Src/m_check_supercell.f
  Src/m_pulay.F90
  Src/new_dm.F
  Src/post_scf_work.F
  Src/save_density_matrix.F
  Src/siesta_analysis.F
  Src/siesta_forces.F
  Src/siesta_init.F
  Src/siesta_move.F
  Src/siesta_options.F90
  Src/sparse_matrices.F
  Src/state_analysis.F
  Src/state_init.F
  Src/write_subs.F

* Associate auxiliary array auxloc in slave nodes even if
  not used in mpi_reduce call (Nick P. Andersen).

* Add missing files in Test/wannier.

* Streamline the wannier interface output.

added:
  Tests/wannier/makefile
  Tests/wannier/wannier.pseudos
modified:
  Src/compute_pw_matrix.F90
  Src/m_digest_nnkp.F90
  Src/write_inp_wannier.F90

* Added backward compatibility logic to the previous changes,
  plus some more comments.

This is a summary of the changes in this branch, useful for a merge
log message.

Clarify the geometry and DM and H logic in siesta_move and siesta_analysis
  
This is the initial patch in a long-overdue clarification work related
to the "outer geometry loop" in Siesta and its interaction with the
analysis of the electronic structure.

The most important changes, following the actual refactoring logic, are:

* Superfluous calls to 'superx' to propagate the new coordinates to
  the auxiliary supercell in 'siesta_move' have been removed, as they
  are already done by 'state_init'.

* The above change has the side effect of leaving inconsistent sets of
  unit cell and supercell coordinates in 'siesta_analysis' if the unit
  cell coordinates used in the latter are those 'moved' by the
  geometry-update routines. To avoid this, and to do the analysis
  using the actual coordinates used in the computation of the
  electronic structure, the coordinates are reset to those values
  (using the *_last arrays) in 'siesta_analysis'.

* To guarantee that the DM and H used in the analysis correspond to
  the latest electronic structure computed, there should be no mixing
  at the end of the scf loop. This behavior, which was optional until
  now (controlled by the value of scf-mix-after-convergence) is now
  the default. The use of DM_out instead of DM_mixed provides also a
  truly variational total-energy and more consistent forces. If the
  scf cycle is carried out mixing H, H(DM_in) is recovered by
  re-setting H to Hold in siesta_forces at the end of the cycle.

  Also, to preserve the right H for analysis it is necessary to
  avoid overwriting it in post_scf_work. This is now done by default,
  except if the option 'scf-recompute-h-after-scf' is 'true'.

  There is a new general switch for pre-v4.0 compatibility in this
  context: If 'compat-pre4-dm-h' is 'true', the
  'scf-mix-after-convergence' and 'scf-recompute-h-after-scf' options
  are activated too.

  Some comments have been added to siesta_forces to document possible
  further clarifications.

* For clarity, each MD or geometry-optimization flavor has now its own
  self-contained logic block in 'siesta_move'. This has uncovered a
  few issues that have been corrected:

  - The quenched forms of the Verlet and Parrinello-Rahman (PR)
    schemes, which are actually relaxations, did not check for
    convergence before moving the atoms (PR did not check at any
    point).  Now the 'constrained' forces and stress are checked
    before invoking the routines. In the case of PR, a 'target stress'
    can optionally be subtracted from the constrained stress (a
    further form of constraint that was previously only available
    (internally) in the standard relaxation routines). A future update
    might put all these constraint conditions in 'fixed', but care
    should be taken to study their interaction with the MD
    variable-cell routines. A future revision might look into the
    effectiveness of the variable-cell routines.
    There is a new example in Tests for quenched MD relaxation.

  - The geometry output in 'siesta_move' is now exclusively done for
    checkpointing purposes, and typically involves the 'moved'
    geometries.  The current geometry output is done in 'state_init',
    and any final output in 'siesta_analysis'.

  - Some output calls have been removed where they did not make much
    sense (as in the FC or server blocks).

  - The deprecated 'phonon' support has been removed.

* Siesta_analysis outputs the 'current' final geometry, and not the
  'moved' one.

* The default 'dynamics' option has been changed from 'verlet' to 'CG'.
  There should really be a new 'single-point' default which completely
  avoids 'siesta_move'.

* Single-point calculations do not write .STRUCT_NEXT_ITER files, and
  the coordinates in the XV file are the current ones, unmoved.
  Extra output in siesta_options is avoided for this case.

* The headings for the beginning of the dynamics blocks are now
  more concrete.

(Javier Junquera, after work by Richard Korytar, and Alberto Garcia)

Siesta can now read the .nnkp file produced by Wannier90 and output
the *.amn, *.mmn, *.eig (see below), and UNK* files needed by
post-processing with that program, which generates maximally-localized
Wannier functions.

The most relevant changes in the code needed to support this
functionality are detailed below. For practical guidance, see the
manual, the simple test in Tests/wannier, and the suite of Wannier90
examples adapted for Siesta in

   http://personales.unican.es/junqueraj/Wannier-examples.tar.gz


* To implement support for "projection functions", which might not be
  pure radial functions, but hybrids with mixed angular momentum and
  varying spatial orientation, as well as to provide support of
  arbitrary kinds of radial functions for future developments, the
  'matel' framework has been extended:

  Matel (actually renamed to 'new_matel') now accepts two generalized
  indexes instead of the two pairs of indexes previously used. The
  generalized indexes can represent either a normal "radial function",
  as in previous Siesta usage, or a "projection function". The indexes
  are obtained via a "check-in" into a registry of functions, which
  keeps track of the nature of the functions and provides the needed
  evaluators and accessors for 'new_matel'.

  The relevant code is in 'matel_registry', 'new_matel', and
  'register_rfs'. The latter shows how to "register" the usual radial
  functions for PAOs, KB projectors, etc. 

* Bloch states are computed and saved, instead of being recomputed as
  needed, to avoid problems with irreproducible random phases and
  linear combinations within degenerate subspaces.

* At this point the parallelization of the new code is only "over
  orbitals". It is not yet possible to parallelize the operations over
  the k-points on the grid. The production of the UNK* files can be
  slow if there are many k-points and bands.

* There is not yet support for "spinor wavefunctions". In the case of
  spin-polarized calculations, separate spin-up and spin-down
  processings are needed.

* There is not yet support for interaction with Wannier90 in "library
  mode", due to licensing issues.

* The "eigenvalue file" for Wannier90 has extension .eigW to avoid
  clashes with the standard Siesta eigenvalue file in case-insensitive
  filesystems.

removed:
  Src/matel.f
added:
  Docs/radfunc.CHANGES
  Docs/wannier-merge.CHANGES
  Docs/wannier.CHANGES
  Src/amn.F90
  Src/broadcast_projections.F
  Src/compute_pw_matrix.F90
  Src/delk.F
  Src/diagonalizeHk.F90
  Src/m_digest_nnkp.F90
  Src/m_noccbands.f
  Src/m_orderbands.F
  Src/m_overkkneig.F90
  Src/m_planewavematrix.F90
  Src/m_planewavematrixvar.F90
  Src/m_trialorbitalclass.f90
  Src/m_writedelk.F
  Src/matel_registry.F90
  Src/mmn.F90
  Src/new_matel.f
  Src/register_rfs.F90
  Src/reordpsi.F
  Src/siesta2wannier90.F90
  Src/write_inp_wannier.F90
  Tests/wannier/		-- New test
  Tests/wannier/wannier.fdf
  Tests/wannier/wannier.nnkp
modified:
  Docs/siesta.tex
  Src/Makefile
  Src/alloc.F90		-- New z3 and z4 generics
  Src/m_mpi_utils.F
  Src/atm_types.f       -- Fields for global index storage
  Src/atmfuncs.f        -- Global index management
  Src/dhscf.F           -- New routine to compute PW matrix elements
  Src/mneighb.f         -- Added 'x0' module variable
  Src/parallelsubs.F	-- Catch special blocksize case
  Src/mesh.F		-- Extra bookeeping
  Src/meshdscf.F
  Src/meshsubs.F
  Src/kinefsm.f		-- New matel
  Src/naefs.f
  Src/nlefsm.f
  Src/overfsm.f
  Src/overlap.f
  Src/phirphi.f
  Src/phirphi_opt.f
  Src/siesta_analysis.F		-- Actual w90 processing
  Src/siesta_init.F
  Src/siesta_options.F90
  Src/spher_harm.f		-- Two implementations of YLMEXP.

    

* The headings for the beginning of the dynamics blocks are now
  more concrete.

* New example for quenched MD relaxation.

added:
  Tests/si2x1h-quench/
  Tests/si2x1h-quench/makefile
  Tests/si2x1h-quench/si2x1h-quench.fdf
  Tests/si2x1h-quench/si2x1h-quench.pseudos
modified:
  Src/siesta_move.F
  Src/state_init.F