1. 02 Jun, 2022 1 commit
  2. 01 Jun, 2022 1 commit
  3. 31 May, 2022 2 commits
  4. 30 May, 2022 3 commits
  5. 18 May, 2022 1 commit
  6. 10 May, 2022 3 commits
  7. 09 May, 2022 1 commit
  8. 05 May, 2022 3 commits
  9. 03 May, 2022 1 commit
  10. 29 Apr, 2022 21 commits
    • Nick R. Papior's avatar
      bug: fixed rebase · 943f9ccc
      Nick R. Papior authored
      943f9ccc
    • Nick R. Papior's avatar
      mnt: sorted BTD matrix output · 07087734
      Nick R. Papior authored
      It is not necessary for end-users to see
      the entire BTD format. Instead we only print
      the blocks in a sorted fashion. This is of course
      not *true* in the sense that internally the BTD is
      very different. However, it may give users a hint with
      a much reduced output for large matrices.
      07087734
    • Nick R. Papior's avatar
      mnt: removed unnecessary type(c_ptr) · be70d947
      Nick R. Papior authored
      be70d947
    • Nick R. Papior's avatar
    • Nick R. Papior's avatar
      mnt: fixed merged · dc182779
      Nick R. Papior authored
      dc182779
    • Nick R. Papior's avatar
      maint: reran all TS tests · b529f243
      Nick R. Papior authored
      Also ensured ts-deallocs does not interfere with regular
      Siesta runs.
      
      Updated copy_to_reference.sh script for TS tests.
      b529f243
    • Nick R. Papior's avatar
      maint: changed default unit to MB · 5e78d70b
      Nick R. Papior authored
      Also cleaned many empty spaces.
      
      The ts warning for non-bulk electrodes has been removed
      as well as the notice about increasing precision. It
      seems to just confuse users.
      
      Also, fixed the excess charge print-out which only had E-1
      which for initial SCF could be lower than 1.e-10 resulting
      in overflow when printing.
      
      Now init_electrode_HS has been moved to electrode_t%prepare_SE which
      superseedes the prior implementation.
      This means that basically everything that alters the electrode_t is
      handled in the ts_electrode.F90 code.
      
      Ran valgrind and fixed memory leaks upon siesta+tbtrans exit.
      Also, fixed some real memory leaks which was due to twice reading
      the electrode H and S. Certain arrays were just nullified instead
      of deallocated; xa, lasto and isc_off.
      
      Removed some output when creating the GF files. They didn't provide
      any details not already present in the output.
      5e78d70b
    • Nick R. Papior's avatar
      maint: enabled pivoting for metis output · 9b491021
      Nick R. Papior authored
      9b491021
    • Nick R. Papior's avatar
      e3006e30
    • Nick R. Papior's avatar
      bug: fixed SpPivot utility · 35a212be
      Nick R. Papior authored
      35a212be
    • Nick R. Papior's avatar
      maint: removed units for transmissions · b168394c
      Nick R. Papior authored
      This was an ancient leftover.
      b168394c
    • Nick R. Papior's avatar
      maint: fixed clean-up in tbtrans · 2c271465
      Nick R. Papior authored
      Fixed writing to a variable if that variable
      is in the argument list.
      One should not do
        write(var, *), 'tsaoeuhs', var
      
      Also fixed a potential variable overflow
      for TS.Analyze output.
      
      When TBT.dH was provided a non-existing file, it just
      continued without dH, this is not optimal.
      2c271465
    • Nick R. Papior's avatar
      enh: changed pretty-printed output for tbtrans and delta-H/SE · 7465cf94
      Nick R. Papior authored
      Also changed the calculation of ETA which should now be
      more precise for the first iteration.
      7465cf94
    • Nick R. Papior's avatar
      enh: added tscontour utility · cf707d57
      Nick R. Papior authored
      Now there is a utility tscontour which only
      reads in the chemical potential and the contours.
      
      This enables one to directly write-out the
      contours without reading in anything else.
      cf707d57
    • Nick R. Papior's avatar
      maint: fixed script tests to allow label= · ecd1f968
      Nick R. Papior authored
      This is nice for testing subsequent work by using
      label.
      
      Fixed delete/deallocations.
      ecd1f968
    • Nick R. Papior's avatar
      maint: finally cleaned the electrode type · e17969b8
      Nick R. Papior authored
      Now it is called electrode_t and all methods
      are contained for OO paradigm. This cleans the
      method quite a bit.
      
      Now we just need to adapt the changes to allow
      Elec as arguments (more clear than El).
      e17969b8
    • Nick R. Papior's avatar
      maint: removed writing E for every k-point · 2a5a3559
      Nick R. Papior authored
      Should be marginally faster.
      2a5a3559
    • Nick R. Papior's avatar
      enh: large refactor in ts+tbt methods · acabc49f
      Nick R. Papior authored
      Now we have eliminated many warnings related to
      temporary array creations. Even though the warnings were
      not effective (if using -fcheck=array-temps) they still
      impacted performance. I have thus cleaned a large fraction
      of them.
      
      Some of the same issues are also updated in transiesta
      
      I have also updated TriMat class for slightly better performance
      of index-look ups. I hope this should give better performance.
      There is now no if-statements in the index functions (and all
      are pure)
      
      I have filed questions related to temporary arrays here:
      https://gcc.gnu.org/bugzilla/show_bug.cgi?id=48655
      
      to figure out why I get better performance. I can't see
      why if there is no code change. Basically I have relied
      in many places about changing of dimensions for easier
      subroutine handling, but apparently when the ranks change,
      gfortran will try and create temporary arrays.
      
      Changed netcdf-parallel writes to be collective
      
      General recommendation is to use collective MPI-IO for
      best performance. In this case it also seems easy since
      it requires little change.
      
      This is hard to detect for low core counts and requires
      testing on larger machines.
      
      I.e. on my small laptop I do not see any performance
      increase.
      acabc49f
    • Nick R. Papior's avatar
      maint: ensured tbtrans cleans memory · ab2b34b8
      Nick R. Papior authored
      
      
      Now tbtrans cleans all memory by calling the
      appropriate reset functions.
      This meant a lot of added *_reset routines for
      the modules to ensure staticly memory is
      deallocated.
      So far I have no missing deallocates with
      valgrind.
      
      There are much edited code, but basically
      nothing has changed. Only added
      deallocates and ensured memory leaks are
      closed.
      Signed-off-by: Nick R. Papior's avatarNick Papior <nickpapior@gmail.com>
      ab2b34b8
    • Nick R. Papior's avatar
      enh: added missing features to byte_count · 0f072cd0
      Nick R. Papior authored
      Made use of byte_count in m_transiesta and m_tbtrans.
      Generally this means removing code (which is good)!
      
      Made only long integers accessible for calculating
      
      Allowed tbtrans to write out BTD matrices (and fixed
      it overwriting TS output).
      
      Added padding and worksize arrays for TBtrans memory
      estimation.
      0f072cd0
    • Nick R. Papior's avatar
      enh: streamlined tbtrans cdf stores · 53c32664
      Nick R. Papior authored
      
      
      All CDF files now use a common routine
      to store common data. This makes maintenance
      more easy.
      
      Added a byte_count module to accummulate
      bytes for determining file sizes.
      Signed-off-by: Nick R. Papior's avatarNick Papior <nickpapior@gmail.com>
      53c32664
  11. 01 Apr, 2022 1 commit
  12. 31 Mar, 2022 2 commits