Siesta 4.1-b4

Bug fixes for the 4.1 beta release series.

NOTE: This release series is still a beta release. For production runs please use 4.0.2.

Milestone information

Project:
Siesta
Series:
4.1
Version:
4.1-b4
Released:
2018-11-07  
Registrant:
Nick Papior
Release registered:
2018-11-07
Active:
No. Drivers cannot target bugs and blueprints to this milestone.  

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14 Nick Papior
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Bugs:
15 Fix Released

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download icon siesta-4.1-b4.tar.gz (md5, sig) Code, documentation and examples 12,871
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download icon siesta.pdf (md5, sig) Manual for Siesta 7,847
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download icon tbtrans.pdf (md5, sig) Manual for tbtrans 1,831
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Total downloads: 23,210

Release notes 

Please note these BACKWARD COMPATIBILITY ISSUES:

* This release increases the size of the internal tables for two-center integrals used in
some matrix element calculations. This means that calculations are slightly more heavy,
but the accuracy is also superior. One can regain the *old* less accurate behaviour by
setting Compat.Matel.NRTAB to true in the fdf input file
(this is ONLY recommended for testing purposes).

* The default values for the MeshCutoff,
the maximum number of scf iterations,
and the variable SCFMustConverge have changed.

The list of changes over 4.1-b3 follows.

* Default changes:
    MeshCutoff has been increased to 300 Ry (from 100)
    MaxSCFIterations has been increased to 1000 (from 50)
    SCFMustConverge is now default true (from false)

* Added developer documentation found in Docs/developer
    Both ford (preferred) and Doxygen may be used

* Generally increased precision in many output files

* Lots of fixes and updates for the Lua/flook interaction

* Auxiliary supercell handling when reading DM matrices:
    Siesta can now read and convert nearly *any* DM matrix and make it
    match the used sparse pattern.

* Fixed minor inconsistencies when handling Bessel basis

* Updated all diagonalization routines
    - ELPA and MRRR for k-point sampling.
    - Less memory usage

* Fixed bug on reading *.ion* files (lp:1751723)

* Updated internal integration table sizes (slightly increased precision)

* PDOS files now also contain the fermi-level such that tools may easily
    align the energy to 0.

* Added more digits to dDmax which may be relevant when performing
    Spin-Orbit/Non-Collinear calculations.

* Fixed bug related to writing out non-collinear spin eigenvalues,
    and also for spin-orbit. (lp:1708634)

* Fixed parallel PDOS calculations of non-colinear and spin-orbit.
    (lp:1718162)

* Added calculated charges to the Lua interface (check the charges
    while running).

* Fixed lots of compilation issues related to the utilities
    (lp:1712317, lp:1712319, lp:1711850)

* Fix for reading a ghost basis (lp:1736455, lp:1738425)

* Fix when fdf-input lines are too long. Instead of discarding the
    remaining line, fdf now "dies" to inform users of possible erroneous
    input. (lp:1728281)

* Fixed Monkhorst-Pack displacements when the displacement was larger
    than 1 (lp:1721479)

* Fix for possible heap allocated arrays (Intel compilers) (lp:1704370)

* Ensured many files to be closed properly at the end of the runs.

* Added basic compiler information to the siesta/transiesta/tbtrans
    header (compiler output)

* Performing SOC calculations does not not require all species
    to have SOC contributions.

TranSiesta / TBtrans changes:

* Disk-space reduction when mixing non-periodic and periodic electrodes

* Now tiling is also enabled for Bloch expansions. This is actually faster
   than repetitions, so users should prefer tiling the electrodes

* TranSiesta is now intrinsic to the Siesta executable. An
   electrode should now be calculated using 'siesta --electrode'
   The TranSiesta executable still exists but is nothing but 'siesta --electrode'

* Many bug-fixes related to pivoting tables; this should only
   change the effective BTD matrices, and has no relevance to the
   accuracy of the calculations

* Huge performance increase in TBtrans in many different parts of the code

* Bug-fix for out-of-core calculations for spin-polarized TBT.Spin 2 calculations

* Fixed the default 2-terminal Poisson ramp. The ramp is now
   defaulted to be positioned in the central region.
     TS.Poisson ramp-central

* Small memory reduction by de-allocating unused siesta memory when
   entering transiesta.

* Fixed the box Poisson for N-electrode calculations when using
   skewed electrodes. Thanks to Azar Ostovan and Thomas Frederiksen.

* Fixed tbtrans setup for bias-window-only calculations. Now the contours
   are correctly interpreted.

* Fixed tbtrans AVCEIG output.

* Change TBtrans DOS output such that there is no normalization

* Enabled tbtrans 1-orbital calculations in the BTD matrices.

* Fixed sign-convention changes in orbital-currents. Now they are
   checked and works together with sisl (>0.9).

* Allowed external GF files for the self-energies. This is mainly beneficial
   for TBtrans as we can add external electrodes *anywhere* in the device.
   Say Buttiker-probes.

* Bugfix when the left electrode was set to -|V|/2 (the default |V|/2 is
   unaffected).

* Added much more output to the TBT*.nc files; electrode information is now
   complete, and also the BTD matrices are written.

* Enabled tbtrans -fdf TBT.Analyze which runs all pivoting schemes, this
   may be very beneficial to run with tbtrans before performing calculations.
   Choosing the correct pivoting scheme can be really important!

* Enabled output file on tbtrans command line:
     tbtrans --out TBT.out RUN.fdf
   is (more or less) equivalent to:
     tbtrans RUN.fdf > TBT.out

* Made Fermi charge correction more aggressive for faster convergence.

* TBtrans can now calculate DM, COOP and COHP curves. They are calculated
   in the supercell picture and can thus be analyzed cross-boundary as well.
   They are calculated both from the Green function and the spectral function.
   The coming >0.9.3 release of sisl will enable this analysis.

* Fixed TBtrans DOS (Green) calculations when performing k-point calculations. There
   can be small differences when comparing Green function DOS between this version
   and prior versions. The bug is only present when time-reversal-symmetry is applied.

Changelog 

View the full changelog

The changelog is present in the tar-ball and comes in two variants. Each changelog is with respect to the 4.0 version.

Files:
- CHANGES, a subset of all commits and their commit logs
- CHANGES_DETAILED, a complete detailed list of commits logs

0 blueprints and 15 bugs targeted

Bug report Importance Assignee Status
1718162 #1718162 Spin-coupled DOS and PDOS does not work in parallel 3 High Nick Papior  10 Fix Released
1736455 #1736455 Floating orbitals, reading User.Basis 4 Medium Nick Papior  10 Fix Released
1751723 #1751723 user basis option not working with 4.1 4 Medium Nick Papior  10 Fix Released
1786218 #1786218 Spurious output when running Siesta with i-PI 4 Medium Nick Papior  10 Fix Released
1787939 #1787939 PDOS compatibility fmpdos.f 4 Medium Nick Papior  10 Fix Released
1799991 #1799991 Incorrect .RHO density file origin on using Grid.CellSampling 4 Medium Nick Papior  10 Fix Released
1800652 #1800652 Bug in Pulay - Guarenteed reduction mixing scheme 4 Medium Nick Papior  10 Fix Released
1708634 #1708634 Writing EIG files for non-colinear and spin-orbit 5 Low Nick Papior  10 Fix Released
1728281 #1728281 fdf input ignores too long input lines 5 Low Nick Papior  10 Fix Released
1739610 #1739610 MD runs and supercell changes 5 Low Nick Papior  10 Fix Released
1711850 #1711850 Tests/Makefile have `show` target but `list` is commented 6 Wishlist Nick Papior  10 Fix Released
1712317 #1712317 Util/build_all.sh does not build all due to BUG 6 Wishlist Nick Papior  10 Fix Released
1712319 #1712319 Contents of Util/README is old 6 Wishlist Nick Papior  10 Fix Released
1738425 #1738425 ion.nc files are missing for ghost atoms 1 Undecided Nick Papior  10 Fix Released
1751723 #1751723 user basis option not working with 4.1 1 Undecided   10 Fix Released
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