----------------------------------------------------------
Mar 16 2013  Tristana Sondon  trunk-434--atom-filt+qconf-3
Synch to trunk 343

added:
  Docs/CHANGES.minim
  Docs/timing.CHANGES
  Src/die.F
  Src/m_dminim.F90
  Src/m_zminim.F90
  Src/timer_tree.f90
  Tests/OMM_h2o/
  Tests/OMM_h2o/Makefile
  Tests/OMM_h2o/OMM_h2o.fdf
  Tests/OMM_h2o/OMM_h2o.pseudos
  Tests/OMM_si/
  Tests/OMM_si/Makefile
  Tests/OMM_si/OMM_si.fdf
  Tests/OMM_si/OMM_si.pseudos
  Tests/Reference-xml/OMM_h2o.xml
  Tests/Reference-xml/OMM_si.xml
  Tests/Reference/OMM_h2o.out
  Tests/Reference/OMM_si.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.TRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/elec_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100/tbt_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.TRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/elec_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_0.25V/tbt_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.TRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/elec_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition/tbt_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.TRANS
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/elec_au_100.out
  Tests/Reference/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/tbt_au_100.out
  Tests/TranSiesta-TBTrans/ts_au_100/
  Tests/TranSiesta-TBTrans/ts_au_100/Au.psf
  Tests/TranSiesta-TBTrans/ts_au_100/au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100/elec_au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100/makefile
  Tests/TranSiesta-TBTrans/ts_au_100/script.sh
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/Au.psf
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/elec_au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/makefile
  Tests/TranSiesta-TBTrans/ts_au_100_0.25V/script.sh
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/Au.psf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/elec_au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/makefile
  Tests/TranSiesta-TBTrans/ts_au_100_repetition/script.sh
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/Au.psf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/elec_au_100.fdf
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/makefile
  Tests/TranSiesta-TBTrans/ts_au_100_repetition_0.25V/script.sh
  Util/JobList/
  Util/JobList/Examples/
  Util/JobList/Examples/Ice/
  Util/JobList/Examples/Ice/H.psf
  Util/JobList/Examples/Ice/O.psf
  Util/JobList/Examples/Ice/defaults.fdf
  Util/JobList/Examples/Ice/dzp.fdf
  Util/JobList/Examples/Ice/filter100.fdf
  Util/JobList/Examples/Ice/iceChecks.jobs
  Util/JobList/Examples/Ice/iceVIII.fdf
  Util/JobList/Examples/Ice/iceXI.fdf
  Util/JobList/Examples/Ice/meshCutoff.gplot
  Util/JobList/Examples/Ice/meshCutoff.jobs
  Util/JobList/Examples/Ice/pseudoLMKLL.fdf
  Util/JobList/Examples/Ice/pseudoPBE.fdf
  Util/JobList/Examples/Ice/pseudoVV.fdf
  Util/JobList/Examples/Ice/queue.sh
  Util/JobList/Examples/Ice/qzp.fdf
  Util/JobList/Examples/Ice/tzp.fdf
  Util/JobList/README
  Util/JobList/Src/
  Util/JobList/Src/Makefile
  Util/JobList/Src/countJobs.f90
  Util/JobList/Src/getResults.f90
  Util/JobList/Src/horizontal.f90
  Util/JobList/Src/jobList.f90
  Util/JobList/Src/runJobs.f90
modified:
  Docs/CHANGES
  Docs/TS-npa.CHANGES
  Docs/TranSiestaUpdate.pdf
  Docs/siesta.tex
  Src/MPI/mpi.F
  Src/MPI/mpi_siesta.f90
  Src/Makefile
  Src/SiestaXC/makefile
  Src/compute_dm.F
  Src/fdf/fdf.F90
  Src/fdf/fdf.Standard
  Src/fft.F
  Src/iopipes.F90
  Src/local_DOS.F
  Src/m_glob_sparse.F90
  Src/m_hs_matrix.f90
  Src/m_hsx.F
  Src/m_iodm.F
  Src/m_timer.F90
  Src/m_ts_electrode.F90
  Src/m_ts_gf.F90
  Src/m_ts_in_siesta.F
  Src/m_ts_scattering.F
  Src/m_walltime.f90
  Src/matel.f
  Src/mixer.F
  Src/molecularmechanics.F90
  Src/post_scf_work.F
  Src/projected_DOS.F
  Src/reinit.F
  Src/setup_H0.F
  Src/setup_hamiltonian.F
  Src/siesta_analysis.F
  Src/siesta_end.F
  Src/siesta_forces.F
  Src/siesta_init.F
  Src/siesta_options.F90
  Src/timer.F90
  Src/ts_init.F90
  Src/write_subs.F
  Tests/Makefile
  Util/README
  Util/TBTrans_rep/m_tbt_options.F90
  Util/TBTrans_rep/tbtrans.F90

----------------------------------------------------------
Nov 27 2012  Alberto Garcia   trunk-426--atom-filt+qconf-3
Added chargeconf-h2o test and reference outputs

Added Emilio's test. 
Updated the reference output for filteret test.

added:
  Docs/CHANGES.charconf
  Tests/Reference/chargeconf-h2o.out
  Tests/chargeconf-h2o/
  Tests/chargeconf-h2o/chargeconf-h2o.fdf
  Tests/chargeconf-h2o/chargeconf-h2o.pseudos
  Tests/chargeconf-h2o/makefile
modified:
  Tests/Reference/h2o_filteret_basis.out

----------------------------------------------------------
Nov 27 2012  Alberto Garcia   trunk-426--atom-filt+qconf-2
Merged Emilio's charge-confinement code

Pending to investigate the initialization of the
qcoe, qyuk, and qwid variables.

added:
  Docs/CHANGES.charconf
  Tests/chargeconf-h2o/
  Tests/chargeconf-h2o/chargeconf-h2o.fdf
  Tests/chargeconf-h2o/chargeconf-h2o.pseudos
  Tests/chargeconf-h2o/makefile
modified:
  Docs/siesta.tex
  Src/atom.F
  Src/basis_specs.f
  Src/basis_types.f
  Src/initatom.f

----------------------------------------------------------
Nov 26 2012  Alberto Garcia   trunk-426--atom-filt+qconf-1
Merged Julian's filteret basis code

There are some cosmetic changes, but it would be too difficult to
disentangle them from the relevant changes.

added:
  Tests/Reference/h2o_filteret_basis.out
  Tests/h2o_filteret_basis/
  Tests/h2o_filteret_basis/h2o_filteret_basis.fdf
  Tests/h2o_filteret_basis/h2o_filteret_basis.pseudos
  Tests/h2o_filteret_basis/makefile
modified:
  Docs/siesta.tex
  Src/atm_transfer.f
  Src/atm_types.f
  Src/atmparams.f
  Src/atom.F
  Src/basis_specs.f
  Src/basis_types.f
  Src/initatom.f
  Src/m_filter.f90
  Src/old_atmfuncs.f
