Commit c720664d authored by Philipp Geiger's avatar Philipp Geiger

Initial readme file.

parent 8088cd3e
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.. In ReStructured Text (ReST) indentation and spacing are very important (it is how ReST knows what to do with your
document). For ReST to understand what you intend and to render it correctly please to keep the structure of this
template. Make sure that any time you use ReST syntax (such as for ".. sidebar::" below), it needs to be preceded
and followed by white space (if you see warnings when this file is built they this is a common origin for problems).
.. Firstly, let's add technical info as a sidebar and allow text below to wrap around it. This list is a work in
progress, please help us improve it. We use *definition lists* of ReST_ to make this readable.
.. sidebar:: Software Technical Information
Name
Input dataset generator for neural network structure detection (NNSD)
Language
C++ / Python
Licence
`GPL <https://opensource.org/licenses/gpl-license>`_
Documentation Tool
ReST_ ???
Application Documentation
missing
Relevant Training Material
'Currently not available.'
Software Module Developed by
Philipp Geiger (TU Wien)
.. In the next line you have the name of how this module will be referenced in the main documentation (which you can
reference, in this case, as ":ref:`example`"). You *MUST* change the reference below from "example" to something
unique otherwise you will cause cross-referencing errors. The reference must come right before the heading for the
reference to work (so don't insert a comment between).
.. _n2stlib:
##############################################################
Input dataset generator for neural network structure detection
##############################################################
.. Let's add a local table of contents to help people navigate the page
.. contents:: :local:
.. Add an abstract for a *general* audience here. Write a few lines that explains the "helicopter view" of why you are
creating this module. For example, you might say that "This module is a stepping stone to incorporating XXXX effects
into YYYY process, which in turn should allow ZZZZ to be simulated. If successful, this could make it possible to
produce compound AAAA while avoiding expensive process BBBB and CCCC."
Over the last decade Behler-Parrinello symmerty functions [Behler2007]_ have been successfully applied to a wide variety of problems. Beside their key role in Neural Network Potential fitting they have also used for neural network based bond-order paramters [Geiger2013]_.
.. [Behler2007] J. Behler and M. Parrinello, Phys. Rev. Lett. 98, 146401 (2007)
.. [Geiger2013] P. Geiger and Ch. Dellago, J. Chem. Phys. 139, 164105 (2013)
Purpose of Module
_________________
.. Give a brief overview of why the module is/was being created, explaining a little of the scientific background and how
.. it fits into the larger picture of what you want to achieve. The overview should be comprehensible to a scientist
.. non-expert in the domain area of the software module.
.. This section should also include the following (where appropriate):
.. * Who will use the module? in what area(s) and in what context?
.. * What kind of problems can be solved by the code?
.. * Are there any real-world applications for it?
.. * Has the module been interfaced with other packages?
.. * Was it used in a thesis, a scientific collaboration, or was it cited in a publication?
.. * If there are published results obtained using this code, describe them briefly in terms readable for non-expert users.
.. If you have few pictures/graphs illustrating the power or utility of the module, please include them with
.. corresponding explanatory captions.
.. note::
TODO: refer to pilot project as described in the comment
.. If you are a post-doc who works in E-CAM, an obvious application for the module (or for the group of modules that
.. this one is part of) is your pilot project. In this case, you could point to the pilot project page on the main
.. website (and you must ensure that this module is linked there).
.. If needed you can include latex mathematics like
.. :math:`\frac{ \sum_{t=0}^{N}f(t,k) }{N}`
.. which won't show up on GitLab/GitHub but will in final online documentation.
Background Information
______________________
The accurate identification and classification of local ordered and disordered structures is an important task in atomistic computer simulations. Based on a neural network approach developed for the
calculation of energies and forces, the proposed method recognizes local atomic arrangements from a set of symmetry functions that characterize the environment around a given atom. The algorithm is simple and flexible and it does not rely on the definition of reference frame. Using the Lennard-Jones system as illustrative example, we show that the neural networks developed here detect amorphous and crystalline structures with high accuracy even in the case of complex atomic arrangements, for which conventional structure detection approaches are unreliable.
.. If the modifications are to an existing code base (which is typical) then this would be the place to name that
.. application. List any relevant urls and explain how to get access to that code. There needs to be enough information
.. here so that the person reading knows where to get the source code for the application, what version this information is
.. relevant for, whether this requires any additional patches/plugins, etc.
.. Overall, this module is supposed to be self-contained, but linking to specific URLs with more detailed information is
.. encouraged. In other words, the reader should not need to do a websearch to understand the context of this module, all
.. the links they need should be already in this module.
Building and Testing
____________________
.. Provide the build information for the module here and explain how tests are run. This needs to be adequately detailed,
.. explaining if necessary any deviations from the normal build procedure of the application (and links to information
.. about the normal build process needs to be provided).
Source Code
___________
.. Notice the syntax of a URL reference below `Text <URL>`_ the backticks matter!
.. Here link the source code *that was created for the module*. If you are using Github or GitLab and the `Gitflow Workflow
.. <https://www.atlassian.com/git/tutorials/comparing-workflows#gitflow-workflow>`_ you can point to your feature branch.
.. Linking to your pull/merge requests is even better. Otherwise you can link to the explicit commits.
.. * `Link to a merge request containing my source code changes
.. <https://github.com/easybuilders/easybuild-easyblocks/pull/1106>`_
.. There may be a situation where you cannot do such linking. In this case, I'll go through an example that uses a patch
.. file to highlight my source code changes, for that reason I would need to explain what code (including exact version
.. information), the source code is for.
.. You can create a similar patch file by (for example if you are using git for your version control) making your changes
.. for the module in a feature branch and then doing something like the following:
.. Don't forget the white space around the "literal block" (a literal block keeps all spacing and is a good way to
include terminal output, file contents, etc.)
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