1. 08 Aug, 2016 1 commit
    • Nick R. Papior's avatar
      Updated documentation of the diag part. · c23d7c51
      Nick R. Papior authored
      More flags are converted into the new fdfentry method.
      
      Fixed references for the transiesta electrode setup
      and the mixing variables.
      One should use the fdfindex* variant for sub-options in
      blocks.
      c23d7c51
  2. 06 Aug, 2016 1 commit
    • Nick R. Papior's avatar
      Fixed a few remaining things of the documentation · eee1540f
      Nick R. Papior authored
      Added documentation at the top of the siesta.tex
      file. There a short explanation of the simple
      mechanisms for writing new documentation is created.
      
      Added nag package which will complain about certain
      use of ancient commands.
      eee1540f
  3. 05 Aug, 2016 5 commits
  4. 04 Aug, 2016 7 commits
    • Nick R. Papior's avatar
      Added Docs/release.sh script for easy creation of tar.gz · 40648c90
      Nick R. Papior authored
      This script enables easier release tar.gz files with a consistent
      format.
      The main functionality is that it will create a folder:
         siesta-releases
      in the main folder where it will create a branch at the specified
      tag. It will subsequently build the documentation and create
      any necessary changes to the code that is necessary before
      making the code available publicly.
      
      This script is provided by Nick R. Papior
      40648c90
    • Nick R. Papior's avatar
      Moved many of the CHANGES files to the branch-changes · 5d094062
      Nick R. Papior authored
      Their use will probably be discouraged to be used.
      
      The one main use for future CHANGES would provide a complete (single)
      detailed description of the branch changes.
      5d094062
    • Nick R. Papior's avatar
      Updated documentation for change of list in fdf · 66a3de1f
      Nick R. Papior authored
      Added documentation of PEXSI
      
      Added documentation of Accuracy control and principal
      cell connections.
      66a3de1f
    • Nick R. Papior's avatar
      Merged transiesta · 6d014704
      Nick R. Papior authored
      Added die routine for non-complete principal connections
      and precision control of the SE convergence.
      
      Changed the { to [ for list construction in FDF.
      
      Added fdf_bphysical to read 'VN' (value name)
      6d014704
    • Nick R. Papior's avatar
      Added fdf_bphysical and change { to [ in list creations · 477be823
      Nick R. Papior authored
      The sample.f90 has been checked and works correctly and
      thus all lists may now be used as [. This is to accommodate
      future { for dictionaries etc.
      
      Added a fdf_bphysical routine for reading physical quantities
      in blocks.
      
      Added a copy statement to the dictionary.
      477be823
    • Alberto Garcia's avatar
      Merged PEXSI-solver interface code · fd38db27
      Alberto Garcia authored
      Please see the manual for the new options related to the PEXSI
      solver. Keep in mind that this solver is competitive only for very
      large calculations.
      
      Alberto Garcia thanks Lin Lin, Chao Yang, Georg Huhs, and Nick Papior
      for their help with the design and coding of the interface.
      
      Developer note: Please see the "Notes for PEXSI operation" in
      Src/siesta.F for a brief overview of the basic coding changes
      that need to be kept into account for further development work.
      
      
      fd38db27
    • Alberto Garcia's avatar
      Use SIESTA__PEXSI as symbol, and .LDOS. instead of .localdos. · da222183
      Alberto Garcia authored
      Updated "ifdefs" to use SIESTA__PEXSI as flag. 
      
      PEXSI local DOS routines now use  .LDOS. fdf flags. Updated test files.
      
      (+ make previous 2D-array MPI "gather" interface changes in .lit files)
      
      
      
      da222183
  5. 03 Aug, 2016 1 commit
    • Alberto Garcia's avatar
      Cleaner fix for init_spin behavior · 9e8f530c
      Alberto Garcia authored
      The nspin, spinor_dim, et al integer pointers in 'm_init' have now
      been initialized to 'null()', and the 'init_spin' routine is now
      called by all processes in 'siesta_init'.  This is the cleanest way to
      fix the problem described in the previous commit.
      
      Note that the PEXSI routines still use the 'nspin' variable internally
      to refer to both 'spinor_dim' and 'h_spin_dim'. This will be changed when
      mixed-spin solving is implemented.
      
      modified:
        Src/m_spin.F90
        Src/siesta_init.F
      
      
      
      9e8f530c
  6. 01 Aug, 2016 1 commit
  7. 31 Jul, 2016 2 commits
    • Nick R. Papior's avatar
      Added accuracy control to transiesta on a per-electrode case · 7170066d
      Nick R. Papior authored
      Through fdf-flags one may control the accuracy required for the
      convergence of the self-energies. This enables finer control of
      the self-energy calculations and in some cases it may be useful.
      7170066d
    • Alberto Garcia's avatar
      Fix bug related to init_spin behavior · 11a4dbbe
      Alberto Garcia authored
      The PEXSI-only processes do not call 'init_spin', and rely on a
      broadcast from the Siesta_worker nodes to get certain information. As
      nspin, spinor_dim, et al were integer pointers in 'm_init', they were
      undefined on entry to the PEXSI interface routines, causing segfaults.
      They have been converted to plain integers for now, pending a review
      of other possible ways to fix the problem. 
      
      Some pointers in sparse_matrices have been initialized to null().
      
      A test to catch non-collinear or spin-orbit cases has been added
      before the call to the PEXSI solver.
      
      Note that the PEXSI routines still use the 'nspin' variable internally
      to refer to both 'spinor_dim' and 'h_spin_dim'. This will be changed when
      mixed-spin solving is implemented.
      
      Added Tests/sih-pexsi-spin.
      
      modified:
        Src/compute_dm.F
        Src/m_spin.F90
        Src/siesta_analysis.F
        Src/sparse_matrices.F
      added:
        Tests/sih-pexsi-spin
      
      
      
      11a4dbbe
  8. 30 Jul, 2016 2 commits
    • Alberto Garcia's avatar
      Put back the MPI interfaces · 3632a252
      Alberto Garcia authored
      The custom MPI interfaces in Src/MPI are now compiled
      by default, except if the preprocessor option
      
       -DNO_MPI_INTERFACES
      
      is specified.
      
      + 2D arrays have to be passed as a(1,1) in the
        mpi_(all)gather calls in the pexsi modules...
      
      + Update pexsi arch.makes in Src/Sys
      
      
      
      3632a252
    • Alberto Garcia's avatar
      Wrap PEXSI code within preprocessor blocks · af3efe33
      Alberto Garcia authored
      The mechanism is similar to that used for TranSiesta.
      
      (Also wrapped ELPA code within MPI preprocessor blocks)
      
      
      af3efe33
  9. 29 Jul, 2016 8 commits
  10. 28 Jul, 2016 1 commit
  11. 27 Jul, 2016 1 commit
  12. 26 Jul, 2016 1 commit
    • Alberto Garcia's avatar
      Clarify the options and filenames to output H and DM · e2206a1a
      Alberto Garcia authored
      For backwards compatibility, a single SystemLabel.DM file
      is produced by default. If the blocked-format option
      
          Write.Blocked.Matrix T
      
      is used, a variety of files with the '.blocked' suffix might be
      produced. See the manual for a full explanation.
      
      Note that the above performance-enhancing option is NOT enabled
      by default.
      
      modified:
        Docs/siesta.tex
        Src/m_iodm_old.F
        Src/save_density_matrix.F
      
      
      
      
      
      
      
      e2206a1a
  13. 25 Jul, 2016 4 commits
    • Nick R. Papior's avatar
      Merged elpa+MRRR · e47fdf9d
      Nick R. Papior authored
      - The ELPA library is now enabled through:
          Diag.ELPA T
        it relies on intrinicly added ELPA library.
      
        Later it may be externally linked.
      
        In addition to the elpa+MRR branch we have:
        defaulted the kernels.
        This is necessary in case the user does not pre-define
        the kernels.
      
      - The MRRR library is now enabled through:
          Diag.MRRR T
        it requires the ScaLAPACK library to have the MRRR routines.
      
        Currently there is no handling if the ScaLAPACK library does
        not have these routines.
      e47fdf9d
    • Alberto Garcia's avatar
      Sync to trunk-531 · 889a1e54
      Alberto Garcia authored
      889a1e54
    • Nick R. Papior's avatar
      Added documentation of charge/hartree gate · 72a6d8a7
      Nick R. Papior authored
      - The Charge/Hartree gate is now documented.
      
      - Added an \ifdeprecated which may be used to
        keep old flags in the manual.
      
      - The old mixing options are now deprecated and
        partially removed (may be re-instantiated by
        setting \deprecatedtrue in the heading)
        However, the options are not used.
      72a6d8a7
    • Nick R. Papior's avatar
      Added -o to gnubands, made new.gnubands -> gnubands · 0324b86c
      Nick R. Papior authored
      - Updated gnubands utility
      
      - Added -o option for gnubands.
      
        It now allows direct writing to a file without
        piping.
      
      - Re-formatted eigfat2plot (no code change)
      0324b86c
  14. 22 Jul, 2016 2 commits
  15. 21 Jul, 2016 3 commits
    • Nick R. Papior's avatar
      Enabled size compilation of manual, as well as screen · 51e5af32
      Nick R. Papior authored
      - Updated the makefile for the documentation.
        Now it can build the manual in different formats:
      
          make SIZE=10|11|12
          
        will control the font-size of the manual.
      
      - One can also compile the manual in a screen, two-column format
        which may be easier to read on a big screen.
      
          make all
      
        will create all different documentations:
           siesta.pdf, siesta-screen.pdf
           tbtrans.pdf, tbtrans-screen.pdf
      51e5af32
    • Nick R. Papior's avatar
      Fixed geometry constrainst and wrap-arounds fixes lp:1605304 · 4c347da6
      Nick R. Papior authored
      - Allow negative ranges of atoms without specifying the step
        number
      4c347da6
    • Alberto Garcia's avatar
      Sync to trunk-525 (after TS merge + few revs) · f1ee1164
      Alberto Garcia authored
      NOTES: Work in progress.
      Tests run. Some differences still to be explored
      
      write_dm interface: For now, files of the form SystemLabel.DM_MIXED
      and SystemLabel.DM_OUT are produced by Nick's new routine.
      
      Files such as DM_OUT and DM_MIXED (as well as H_DMGEN and H_MIXED) are
      produced by AG's write_spmatrix.
      
      
      
      
      f1ee1164