Tags give the ability to mark specific points in history as being important
  • 5.0.0   STEMsalabim 5.0.0 release
    5b74f120 · Version 5.0.0 release ·
    Release 5.0.0

    STEMsalabim 5.0.0

    February 28th, 2019


    The parameters application.verbose and simulation.skip_simulation are deprecated now. The groups adf/adf_intensities, cbed/cbed_intensities, and adf/center_of_mass now have a dimension for energy loss. It is usually 1 unless plasmon scattering feature is used.

    Highlights ^^^^^^^^^^

    • Speed improvements by increasing the grid sizes to match efficient FFT sizes. Note, that this may result in a higher simulation grid density than specified in grating.density parameter!
    • Alternative parallelization scheme, see :ref:parallelization-scheme. When appropriate, different MPI procs now calculate different frozen phonon configurations / defoci in parallel. This reduces the required amount of communication between the processors.
    • Automatic calculation of center of mass of the CBEDs for all ADF points. The COMs are calculated when adf.enabled = true and stored in the NC file next to adf/adf_intensities in adf/center_of_mass. Unit is mrad.
    • New executables ssb-mkin and ssb-run. The former prepares an input NC file from which the latter can run the simulation. This has multiple advantages. See :ref:simulation-structure for more information.
    • Single plasmon scattering.

    Other changes ^^^^^^^^^^^^^

    • Removed application.verbose parameter.
    • Removed simulation.skip_simulation.
    • Ability to disable thermal displacements via frozen_phonon.enable = false parameter.
    • Fixed a serious bug with the integrated defocus averaging.
    • Input XYZ files can now contain more than one space or TAB character for column separation.
    • Removed Doxygen documentation and doc string comments.
    • Default FFTW planning is now FFTW_MEASURE. This improves startup times of the simulation slightly.
    • Changed the chunking of the adf/adf_intensities and cbed/cbed_intensities variables for faster write speed.
    • Added AMBER/slice_coordinates variable to the output file, that contains the z coordinate of the upper boundary of each slice in nm.
    • Removed HTTP reporting and CURL dependency.
    • Significant code refactoring and some minor bugs fixed.
    • Improved documentation.
  • 4.0.2
    a438aec7 · Version 4.0.2 ·
  • 4.0.1
    d97839ba · Version 4.0.1 ·
    Release 4.0.1

    STEMsalabim 4.0.1

    March 21st, 2018

    • Bugfixes
  • 4.0.0
    Release 4.0.0

    STEMsalabim 4.0.0

    March 9th, 2018


    I'm releasing this version as 4.0.0, but neither the input nor output files changed. The parameter precision has become deprecated and there is a parameter tmp-dir. Please see the documentation.

    • Removed option for double precision. When requested, this may be re-introduced, but it slowed down compilation times and made the code significantly more complicated. The multislice algorithm with all its approximations, including the scattering factor parametrization, is not precise enough to make the difference between single and double precision significant.
    • Improved the Wave class, so that some important parts can now be vectorized by the compiler.
    • Introduced some more caches, so that performance could greatly be improved. STEMsalabim should now be about twice as fast as before.
    • Results of the MPI processors are now written to temporary files and merged after each configuration is finished. This removes many MPI calls which tended to slow down the simulation. See the --tmp-dir parameter.
    • Moved the Element, Atom, and Scattering classes to their own (isolated) library libatomic. This is easier to maintain.
    • Simplified MPI communication by getting rid of serialization of C++ objects into char arrays. This is too error-prone anyway.
    • Added compatibility with the Intel parallel studio (Compilers, MKL for FFTs, Intel MPI). Tested with Intel 17 only.
    • Some minor fixes and improvements.
  • 3.1.4
    bc8586e6 · Version 3.1.4 ·
    Release 3.1.4

    STEMsalabim 3.1.4

    • Finished Gitlab and Readthedocs integration
    • made all the tests pass
  • 3.1.3
    Release 3.1.3

    STEMsalabim 3.1.3

    • Added Gitlab CI logic
    • Improved documentation
    • Fixed CMake bugs
  • 3.1.1
    Release 3.1.1

    STEMsalabim 3.1.1

    • Fixed Sphinx build process to be compatible with Read the docs
  • 3.1
    Release 3.1

    STEMsalabim 3.1.0

    • Added GPL-3 License and changed copyright header in all files
    • Added min required libconfig version to documentation
    • Added FindPackageHandleStandardArgs to the custom FindXX.cmake files
    • Replaced the date.h library by some custom code, a step towards Intel compiler compatibility.
  • 3.0.2
    Release 3.0.2

    STEMsalabim 3.0.2

    • Improved the custom CMake files to make the build process easier.
  • 3.0.1
    e3a22bf3 · Version number bump ·
    Release 3.0.1

    STEMsalabim 3.0.1

    • Added gperftools support
    • fixed serious bug with the --defocus command line parameter being ignored.
  • 3.0.0
    Release 3.0.0

    STEMsalabim 3.0.0

    • Reworked input/output file format.
    • Reworked CBED storing. Blank areas due to bandwidth limiting are now removed.
    • Changes to the configuration, mainly to defocus series.
    • Compression can be switched on and off via config file now.
    • Prepared the project for adding a Python API in the future.
    • Added tapering to smoothen the atomic potential at the edges as explained in I. Lobato, et al, Ultramicroscopy 168, 17 (2016) <https://www.sciencedirect.com/science/article/pii/S030439911630081X>_.
    • Added analysis scripts for Python and MATLAB to the Si 001 example.
  • 2.0.0
  • 2.0.0-beta2
  • 2.0.0-beta
    d536d13a · Added Whats new section ·
  • 1.0   This is the initial release version
  • 1.0b   The first official beta version to the stable 1.0