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STEMsalabim
===========

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The *STEMsalabim* software aims to provide accurate scanning transmission electron microscopy (STEM) image simulation of
a specimen whose atomic structure is known. It implements the frozen lattice multi-slice algorithm as described in
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great detail in the book `Advanced computing in electron microscopy <http://dx.doi.org/10.1007/978-1-4419-6533-2>`_ by
Earl J. Kirkland.

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While there are multiple existing implementations of the same technique, at the time of this writing none of them is
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suitable for leveraging massive parallelization available on high-performance computing (HPC) clusters, making it
possible to simulate large supercells and parameter sweeps in reasonable time.
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The purpose of *STEMsalabim* is to fill this gap by providing a multi-slice implementation that is well parallelizable
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both within and across computing nodes, using a mixture of threaded parallelization and message passing interface (MPI).


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.. toctree::
    :maxdepth: 2
    :caption: Getting Started

    install
    usage
    visualization

.. toctree::
    :maxdepth: 2
    :caption: More information

    general
    parameters
    file_formats
    http_reporting
    faq
    whats_new
    citing
    articles
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Contact us!
===========

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*STEMsalabim* is a relatively young software package and was not heavily tested outside the scope of our group.
We are glad to help you getting your simulations to run.
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Please contact **strl-stemsalabim [at] lists.uni-marburg.de** for support or feedback.
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Credits
=======

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  * We acknowledge the creators of the supplementary libraries that *STEMsalabim* depends on.
  * We would also like to acknowledge the creators of `STEMsim <http://dx.doi.org/10.1007/978-1-4020-8615-1_36>`_,
    which we used as a reference implementation to test *STEMsalabim*.
  * Once again, we would like to highlight the book
    `Advanced computing in electron microscopy <http://dx.doi.org/10.1007/978-1-4419-6533-2>`_ by Earl J. Kirkland for
    its detailed description of the implementation of multi-slice algorithms.
  * *STEMsalabim* was written in the `Structure & Technology Research Laboratory <https://www.uni-marburg.de/wzmw/strl>`_
    of the `Philipps-Universität Marburg <https://www.uni-marburg.de/>`_ with financial support by
    the `German Research Foundation <http://www.dfg.de/en/>`_
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+--------------------------------+----------------------------------------------+
| Philipps-Universität Marburg   | Structure & Technology Research Laboratory   |
+================================+==============================================+
| |image0|                       | |image1|                                     |
+--------------------------------+----------------------------------------------+

.. |image0| image:: images/umr.png
.. |image1| image:: images/strl.jpg