On Strong Scaling and Open Source Tools for Analyzing Atom Probe Tomography Data

This repository contains supplemental results to the paper "On Strong Scaling and Open Source Tools
for Analyzing Atom Probe Tomography Data".

Specifically, the input parameter and result files from all synthetic benchmark studies.
The results file for all synthetic specimen benchmark studies are available from the
authors upon serious request.

The repository content is as follows:

Real world data:
Three triplets of *.tar.gz archive files document the settings and analysis files for the real world case studies
3013902 is the incipient specimen,
2763207 the intermediate specimen, and
3345501 the mature specimen.

Scripts.zip
Contains all batch scripts we used for performing the analyses as a queue

Synthetic data:

APTCrystallography.zip
Contains all results from the benchmarking of the reimplemented Vicente Araullo-Peters et al. method

FullVolumeTessellation.zip
Contains all results from the benchmarking of the Voro++ Voronoi volume tessellation method except for the HDF5/XDMF volume tessellation files of the 200 and 2000 million ion datasets

TwoPointStatistics.zip
Contains all results from benchmarking the computing of 2-point spatial statistics

TipSurfaceDescrSpatialStatistics.zip
Contains all results from benchmarking the alpha shape computation, descriptive spatial statistics, and clustering analyses

PARAPROBE.Results.2Mio.tar.gz
PARAPROBE.Results.20Mio.tar.gz
PARAPROBE.Results.200Mio.tar.gz
Contains all settings files and some results from benchmarking the hybrid implementation.

Unpack the individual repositories using tar through Linux console as follows:
tar -xvf <archivename>   
where <archivename> is a placeholder for the respective tar gz compressed archives within the ZIP file.
Alternatively WinRAR can be used on a Windows system.

We would kindly like to ask you to use the following repository
to access source code of PARAPROBE in the future:

https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe
https://paraprobe-toolbox.readthedocs.io/en/latest/

Only above repository will be updated in the future!
Only there new code additions and bugfixes are posted!
The examples folder of this repository contains a folder examples/tasks/paper14 which shows how
to run a workflow of paraprobe tools from this above repository to run analyses akin as reported in this paper.

Recommendations and bug reports to M. Kühbach are appreciated! Happy APT analyzing!

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The PARAPROBE source code version we used for analyzing the synthetic and real world APT
specimens in the paper used an earlier development version of the PARAPROBE tool, the source code
is here:

PARAPROBE_20190117_VersionUsedForPaper.zip

https://github.com/mkuehbach/PARAPROBE
https://paraprobe.readthedocs.io/en/latest/