1. 04 Aug, 2016 2 commits
    • 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
  2. 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
  3. 31 Jul, 2016 1 commit
    • 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
  4. 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
  5. 29 Jul, 2016 6 commits
  6. 28 Jul, 2016 1 commit
  7. 27 Jul, 2016 1 commit
  8. 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
  9. 25 Jul, 2016 3 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 -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
  10. 22 Jul, 2016 1 commit
  11. 21 Jul, 2016 5 commits
  12. 13 Jul, 2016 1 commit
    • 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
  13. 11 Jul, 2016 1 commit
  14. 10 Jul, 2016 2 commits
  15. 09 Jul, 2016 2 commits
  16. 05 Jul, 2016 2 commits
    • Nick R. Papior's avatar
      Added si111-spinpol reference test · c89d2f88
      Nick R. Papior authored
      - The spin polarized Si111 test had never been 
        added to the reference.
      c89d2f88
    • Nick R. Papior's avatar
      Merged spin type · 4e4b376b
      Nick R. Papior authored
      - The spin data-type has been added.
        This encompass a simple derived data type
        to contain all relevant information regarding
        the dimensionality of different parts of the
        physical quantities.
      
        I.e. it knows how big the Hamiltonian, Density matrix,
        Energy density matrix, Grids, etc. are dependent on the
        system setup.
      
        All future use of the spin variables should pass the
          type(tSpin) :: spin
        and use its components.
      
      - To see an example (correct use), see vmat.F90
      4e4b376b
  17. 28 Jun, 2016 2 commits
    • Nick R. Papior's avatar
      Fixes dH read in tbtrans · de8d2342
      Nick R. Papior authored
      - The dH read is now consistent with sisl.
      
        In a future commit we will delete the Util/TS/TB
        folder as that has been fully superseeded with sisl.
      
      - Updated option print-out of dH options
      
      - Fixed reading the netcdf data with not all levels
        existing
      
      - Fixed reading from dH with multiple spin indices
      de8d2342
    • Nick R. Papior's avatar
      Fixes LDA+U implementation by also allowing non-GGA-PBE XC · 0d5cb765
      Nick R. Papior authored
      - Also explicitly adds several broadcast calls of the
        LDA+U internals. Some are redundant, but for clarity
        they are added
      0d5cb765
  18. 23 Jun, 2016 2 commits
    • Alberto Garcia's avatar
      Merged 4.0-500 · 0db35441
      Alberto Garcia authored
      * Update list of contributors.
      * Electric-field/slab-dipole-correction fix.
      * Fix to avoid ps reparametrization in bessel case
      * Remove Util/pseudo-xml
      * Other minor changes in README files
      
      0db35441
    • Alberto Garcia's avatar
      Release of siesta-4.0 · 7440a27d
      Alberto Garcia authored
      * 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
      
      
        
      		
      
      	
      7440a27d
  19. 22 Jun, 2016 4 commits