1. 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
  2. 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
  3. 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
  4. 29 Jul, 2016 6 commits
  5. 28 Jul, 2016 1 commit
  6. 27 Jul, 2016 1 commit
  7. 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
  8. 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
  9. 22 Jul, 2016 1 commit
  10. 21 Jul, 2016 5 commits
  11. 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
  12. 11 Jul, 2016 1 commit
  13. 10 Jul, 2016 2 commits
  14. 09 Jul, 2016 2 commits
  15. 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
  16. 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
  17. 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
  18. 22 Jun, 2016 6 commits
    • Nick R. Papior's avatar
      5be9e0c2
    • Nick R. Papior's avatar
      Fixed LDA+U and non GGA-PBE calculations · 0987eafc
      Nick R. Papior authored
      - The LDA+U implementation explicitly calculated
        the pseudopotentials using GGA-PBE.
      
        This was hard-coded and now removed
      
        
      0987eafc
    • Nick R. Papior's avatar
      Removed vacuum point in electric field · de4ef8d1
      Nick R. Papior authored
      - Specifying the vacuum point was a testing purpose
        code. Which should have been removed at the merge
        r509.
      de4ef8d1
    • Nick R. Papior's avatar
      Streamlining the spin flags used · be5a7617
      Nick R. Papior authored
      - Future changes regarding the spin will introduce
        the spin components using a derived type containing
        all relevant information regarding the spin
        configuration of the calculation.
      
      
      - Now m_spin.F90 also contains a module t_spin
        containing the derived type.
      
        This derived type is as an initial attempt
        implemented in the vmat routine.
      
        Indeed the clarity of the interface is easier
        to recognize.
      be5a7617
    • Nick R. Papior's avatar
      Removed siesta hartree fix · 031ebbbc
      Nick R. Papior authored
      - This was not used consistently with transiesta.
      
        Hence it has been removed.
      
        Instead the user may use this flag:
          TS.SIESTA.Only .true.
        which stops transiesta after the initial siesta
        convergence.
        However, this will only take effect if the diagon
        method is used as an initial step.
      
      - Updated a few transiesta related fdf-flags so they
        fit with their intentional meaning in the calculation.
      031ebbbc
    • Nick R. Papior's avatar
      Improved printout of TS calculations upon error · c15acf44
      Nick R. Papior authored
      - When an inversion fails on the off-diagonal blocks
        a more descriptive message occurs now.
      
      - Changed a few variable names in some transiesta-related
        routines to make it easier to figure out what they meant.
      
      - Corrected comments on the stored scattering matrices in the
        Elec types.
      
      - Abstraction of the tbt_data.py bond-currents.
        Small insignificant change.
      
      - Fixed the projection <i|Gam|j> quantities because Gam was without
        factor \im. Now the correct value is stored in the nc file.
      
      - Allowed not-atom in the TBT.Atoms.Device block such that one may
        exactly remove certain atoms from the device region.
        These atoms have precedence over those defined as actual device atoms
        which is a bit counter intuitive... However, the main purpose is to
        allow defining the device region via downfolded atoms.
      c15acf44