Siesta 4.1-b2

Bug fix release of the 4.1 release series.

This contains bug-fixes found in the 4.1-b1 release.

Milestone information

Project:
Siesta
Series:
4.1
Version:
4.1-b2
Released:
2016-11-28  
Registrant:
Nick Papior
Release registered:
2016-11-28
Active:
No. Drivers cannot target bugs and blueprints to this milestone.  

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No blueprints or bugs assigned to you.
Assignees:
3 Alberto Garcia, 17 Nick Papior, 2 Ramon Cuadrado
Blueprints:
2 Implemented
Bugs:
20 Fix Released

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File Description Downloads
download icon siesta-4.1-b2.tar.gz (md5, sig) Code, documentation, and examples 5,641
last downloaded 24 hours ago
download icon siesta.pdf (md5, sig) Manual for Siesta 7,569
last downloaded 4 days ago
download icon tbtrans.pdf (md5, sig) Manual for tbtrans 6,129
last downloaded 8 days ago
Total downloads: 19,339

Release notes 

Please see the Manual for full details

*** Backward-compatibility issues:

    * The mixing routines have completely changed, hence the same
    convergence path cannot be expected. This, unfortunately, makes
    comparison difficult with prior versions. However, the final
    converged system should be transferable.

    * SIESTA now defaults to mixing the Hamiltonian instead of the
    density matrix. To revert to density-matrix mixing, use
    "SCF.Mix DM". The option to mix after the initial scf step is now
    'on' by default.

    * SIESTA now defaults to monitoring convergence for both the
    density matrix AND the Hamiltonian. To revert to only density
    matrix convergence, use: "SCF.H.Converge false"

    * A major number of fdf-flags concerning mixing
    parameters have changed to a more consistent naming scheme.
    However, all previous flags are still in effect but the newer
    flags have precedence. The previous flags are the default values
    for the newer flag-names.

    * Two additional files are created:
       H_DMGEN and
       H_MIXED
      these contain the Hamiltonian at various stages through the SCF.
      Currently they are intended for developers and may be removed in
      the final 4.1 release.
      You may delete these without problems.

*** New features

-- LDA+U (Javier Junquera)

    * Full incorporation of the LDA+U implementation in SIESTA
    * Two different LDA+U projectors available
    * Estimate the best U according to: Cococcioni and Gironcoli in PRB, 2005

-- Spin-Orbit coupling (Ramon Cuadrado)

    * On-site approximation for spin-orbit-coupling matrix elements.

-- MRRR method for diagonalization (Alberto Garcia)

    * This will typically be faster than divide-and-conquer algorithm
    and may be the future default. For Gamma-point calculations.

-- ELPA method for diagonalization (Alberto Garcia)

    * This provides better scalability compared to ScaLAPACK for large
    # of processors. For Gamma-point calculations.

-- Added interface to the PEXSI library for calculating the density
   matrix, DOS, and LDOS (Alberto Garcia)

    * This library provides massive parallelism and better
    scalability, but should only be used for very large systems.

-- SIESTA is now hybrid-parallelised (Nick R. Papior)

    * One may compile Siesta/Transiesta in serial, OpenMP, MPI, or
    MPI+OpenMP mode.

-- Re-write of non-equilibrium Green function code (Nick R. Papior)

    * N>=1 terminal support in transiesta
    * Improved convergence
    * Different ways of handling charge-reductions in SCF
    * All electrodes have settings _per electrode_ for full customization
    * Greatly reduced memory usage
    * Skewed axis are enabled for further reduction of complex systems
    * Implemented MUMPS method for inversion
    * Implemented LAPACK for inversion
    * Implemented BTD method for inversion (extremely fast)
    * Fully OpenMP threaded
    * Start directly from transiesta enabled
    * Temperature gradients as non-equilibrium a possibility

-- Complete rewrite of tbtrans utility (Nick R. Papior)

    * Made tbtrans a stand-alone utility for user-defined tight-binding method
    * EXTREME SCALE version (BTD-only)
      - Memory consumption _only_ dependent on "device" region
    * N>=1 electrode support
    * Region projections for transmission through "eigenstates"
    * Custom change of the self-energies
    * k -> k' transmissions
    * Interpolation of bias Hamiltonians
    * Bond-currents
    * Fully OpenMP threaded and/or MPI parallelized
    * DOS and bulk transmission for electrodes
    * Gf-DOS/spectral-DOS for device region

-- Mixing routines rewritten (Nick R. Papior)

    * New mixing schemes Pulay (Guarenteed Reduction)
    * Custom mixing restart options (full user customizability)

-- Added more constraints (Nick R. Papior)

    * Constraints are verbose and many new ways of using constraints exists

-- NetCDF4 file format for siesta -> parallel IO (Nick R. Papior)

    * Provides a standard intrinsically grouped file for retaining
    nearly all siesta related information in one file.

-- Enabled convergence control of density-, energy density matrices,
   Hamiltonian and energy.

-- LUA scripting in siesta (Nick R. Papior)

    * This is an experimental feature

-- Gate calculations (Nick R. Papior)

    * Charge and Hartree gate

-- Utilities (Nick R. Papior)

    * All make-files are now prepared to enable parallel builds
      - this makes compilation *MUCH* faster. For example:
         make -j4
        will compile using 4 cores.
    * Grimme utility
      - easy creation of FDF block for Grimme parameters
    * SpPivot, pivot sparsity pattern using several different routines
    * TS/** different utilities related to transiesta

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

2 blueprints and 20 bugs targeted

Blueprint Priority Assignee Delivery
Optimization of projector application Optimization of projector application 3 Medium Alberto Garcia  11 Implemented
Revamp of the CML subsystem Revamp of the CML subsystem 3 Medium Alberto Garcia  11 Implemented
Bug report Importance Assignee Status
1642438 #1642438 Linear kick in MD/CG runs 2 Critical Nick Papior  10 Fix Released
1642438 #1642438 Linear kick in MD/CG runs 2 Critical Nick Papior  10 Fix Released
1622526 #1622526 Bug in switch-off option for MRRR 3 High Alberto Garcia  10 Fix Released
1623415 #1623415 The initial and reported magnetic m_y moment is wrong in some subroutines 3 High Ramon Cuadrado  10 Fix Released
1623420 #1623420 Initial spin polarization is not correctly reported in the output file 3 High Ramon Cuadrado  10 Fix Released
1627041 #1627041 libncdf.a compilation error with only INCFLAGS 3 High Nick Papior  10 Fix Released
1630849 #1630849 DM is never reused! 3 High Nick Papior  10 Fix Released
1639779 #1639779 used-atoms and electrode check 3 High Nick Papior  10 Fix Released
1640137 #1640137 GeometryConstraints not work for 4.1 verlet MD 3 High Nick Papior  10 Fix Released
1643589 #1643589 program crashes when not using default LDA+U parameters 3 High Nick Papior  10 Fix Released
1619437 #1619437 g95 compiler failing 4 Medium Nick Papior  10 Fix Released
1625725 #1625725 "PAO.BasisType nodes" does not work properly with siesta 4.0 4 Medium Nick Papior  10 Fix Released
1633039 #1633039 VCA Utility fails with the interpolation scheme 4 Medium Nick Papior  10 Fix Released
1627936 #1627936 dc_lapack in generated arch.make (in 4.1-b1) 5 Low Nick Papior  10 Fix Released
1638726 #1638726 consistency check of chemical potential and bias applied 5 Low Nick Papior  10 Fix Released
1638815 #1638815 SCF.Mix with non-supported key does not fail 5 Low Nick Papior  10 Fix Released
1639812 #1639812 TS.Poisson with a file, not working in SERIAL 5 Low Nick Papior  10 Fix Released
1640813 #1640813 Crash when using tree timer in TranSIESTA 5 Low Nick Papior  10 Fix Released
1641573 #1641573 Slab dipole correction for 1-electrode 5 Low Nick Papior  10 Fix Released
1630827 #1630827 DipoleCorrection is always true for slab 6 Wishlist Nick Papior  10 Fix Released
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