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.

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Nick Papior
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1 Bhumi A. Baraiya, 13 Nick Papior
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15 Fix Released

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download icon siesta-4.1-b4.tar.gz (md5, sig) Code, documentation and examples 22,085
last downloaded 24 hours ago
download icon siesta.pdf (md5, sig) Manual for Siesta 10,298
last downloaded 24 hours ago
download icon tbtrans.pdf (md5, sig) Manual for tbtrans 2,641
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download icon checksums.txt (md5) Checksums for the uploaded files 993
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Total downloads: 36,017

Release notes 


* 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.

* 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

* 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.


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.

- 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 Bhumi A. Baraiya  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/ 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 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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