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488. By Nick Papior on 2016-02-26

Add generic citation helper

- It was previously difficult to figure
  out which papers where of significance when
  using SIESTA.
  This addition adds the capability of on-the-fly
  creation of .bib files for users to easier find
  the papers that are being used in their corresponding
  run.

added:
  Src/m_cite.F90
modified:
  Src/Makefile
  Src/m_efield.F
  Src/siesta_init.F
  Src/ts_init.F90

487. By Nick Papior on 2016-02-21

empty merge for rel-4.0

486. By Nick Papior on 2016-02-17

[merge] Fixed auxiliary array usage for ksv and optical (tests not updated)

- ksv:
  This routine used Hkin as a work-array for calculating
  certain quantities for polarization calculations.

  This may lead to inadvertently destroying reliance
  across calculations which are not intended.

  This bug has been fixed by introducing the allocation
  of the work-array in the ksv routine, directly.

  Furthermore, we have explicitly added the => null()
  when initializing several of the pointers.

- optical:
  This routine used Eold, Dold and Hkin as
  work-arrays for calculating optical properties.

  We have fixed these issues and moved allocation into
  the routine.

  Furthermore there were several "saved" variables
  which were not needed to be saved.

  All variables were re-calculated on each entry-point.
  This has also been fixed.

  Streamlined the algorithm for calculating transition-rates.

- phirphi_opt:
  Reduced memory by ENDLESS.
  It allocated an enourmous amount of memory of which only 1 element
  was used at a time.
  If the full matrix is going to be needed, then re-instantiate the
  comments !N.
  The si-optical test yields the same result and I see no problem
  in the current algorithm.

modified:
  Src/born_charge.F
  Src/ksv.f
  Src/optical.F
  Src/phirphi_opt.f
  Src/siesta_analysis.F

485. By Alberto Garcia on 2016-02-17

Add GPL notices and headers

* 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
* Replace old copyright notice in Src/Confs

This revision touches a large number of files due to the
change in licensing and copyright.

The other major change is the removal of the Pseudo/atom subtree,
which is now distributed independently.

484. By Alberto Garcia on 2016-02-05

Merge fixes from rel-4.0 branch

* Fix Tests/test.mk and Genbasis makefile

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

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.

* Fix peak alloc report in MPI

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

(Thanks to Nick R. Papior)

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

modified:
  Tests/test.mk
  Util/Gen-basis/Makefile
  Src/alloc.F90
  Docs/siesta.tex
added:
  Docs/branch-changes/
  Docs/older-release-notes/

483. By Alberto Garcia on 2015-12-18

Add lapack and blas code in Libs to support OMM and SVD

* 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

482. By Alberto Garcia on 2015-12-17

New versions of grid2cube and gnubands. Laplacian of grid functions

* 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

481. By Alberto Garcia on 2015-11-26

Increase the number of allowed iterations in minvec

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

modified:
  Src/minvec.f

480. By Nick Papior on 2015-11-26

Fix bug in heapsort routine

(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

479. By Alberto Garcia on 2015-10-04

Assorted fixes and cleanup. Update reference outputs

- 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