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 4 commits
  4. 04 Aug, 2016 5 commits
  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 5 commits
    • Alberto Garcia's avatar
      Remove old pexsi code · a074e723
      Alberto Garcia authored
      removed:
        Src/OldPEXSI/
        Src/dummy_pexsi/
        Src/m_pexsi_solver.F90_old
      
      a074e723
    • Nick R. Papior's avatar
      Fixed utility build and exact library names · 3b4dcdf9
      Nick R. Papior authored
      Changing the libvardict is now complete. There
      where several problems in utilities.
      
      Fixed all references for fdf_global_get.
      3b4dcdf9
    • Nick R. Papior's avatar
      Removed fdf_global module · fec346c6
      Nick R. Papior authored
      - The fdf library inherently handles parallel access.
        Thus the fdf_global module was unnecessary.
        It has been removed and all calls changed.
      fec346c6
    • Nick R. Papior's avatar
      Fixes compilation of Nick libraries · 5a50364a
      Nick R. Papior authored
      - libvardict.a has changed name to libfdict.a
        to make it easier to grasp.
      
      - In both NCDF and fdict libs the PP processor
        command has changed name to CPP (PP is non-standard).
      
        Further the default CPP command is now $(FC) -E -P -x c
        which may be overwritten using CPP in arch.make
      5a50364a
    • Nick R. Papior's avatar
      Added documentation of external libraries · 9fc41419
      Nick R. Papior authored
      Documented BLAS/LAPACK/ScaLAPACK/MPI/OpenMP/NetCDF4
      in the manual.
      
      Also added documentation of how to compile and run
      siesta using OpenMP.
      
      The NetCDF4 documentation is now also in place.
      9fc41419
  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 2 commits
    • 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 1 commit
  15. 21 Jul, 2016 4 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
    • Nick R. Papior's avatar
      Added tbtrans documentation · c5d44d75
      Nick R. Papior authored
      - The tbtrans documentation is nearly complete.
        Currently I think I only need to document the projection
        stuff.
      
      - The tbtrans manual is a separate document. This is because
        I hope it will encourage the use of tbtrans as a separate
        program.
      
      - Added preliminary placeholder for transiesta article.
      
      - Updated keywords for electrodes to be more generic.
        Now TSHS == HS and Rep.A1 is not used anymore.
        TSDE == DE
      
      - Cleaned the molecular mechanics module.
      c5d44d75
    • Alberto Garcia's avatar
      Updated manual · 14541464
      Alberto Garcia authored
      Note that ELPA code is embedded in the Siesta distribution for now.
      Eventually, Siesta should link to an external pre-compiled ELPA library.
      
      
      
      14541464
  16. 19 Jul, 2016 3 commits
  17. 18 Jul, 2016 1 commit
    • Nick R. Papior's avatar
      Added more TS documentation · 738bb601
      Nick R. Papior authored
      - Added equilibrium contour documentation
      
      - Added non-equilibrium contour documentation
      
      - Added how to put in atoms in the input block
      
      - Reduced the Fermi function cutoff energy (2.5 kT)
        is now the new minimum.
      738bb601
  18. 15 Jul, 2016 1 commit
  19. 13 Jul, 2016 2 commits
    • Nick R. Papior's avatar
      Added documentation of transiesta · 5148a7d4
      Nick R. Papior authored
      - Updated the documentation to contain information regarding
        the regular transiesta options.
      
      - There are still quite a bit of flags that needs to be added.
      5148a7d4
    • Nick R. Papior's avatar
      Removed all references to "contiguous" attribute · 41f4c265
      Nick R. Papior authored
      - Further the atom_graph and m_supercell now have
        restricted their module use to be privatized.
      
      - All source files have their contiguous attribute
        removed.
      
        We should add this as a preprocessor flag in case
        the compiler supports it.
      
        Several older compilers does not support this :(
      41f4c265
  20. 08 Jul, 2016 1 commit