Single-crystalline Zr tips

This repository contains all input data for simulating the field-evaporation process of specifically
oriented single-crystalline APT tips with representing h.c.p. zirconium using TAPSim.

Having conducted all simulations, it contains all detector hit information for all ions and each tip.

The authors have also personally stored the trajectories of all ions for each tip. However,
given the size of these particular additional binary data (approx. 100 - 200GB), they have
--- as a compromise --- not yet been uploaded.  They are available from the authors for free upon request.

The individual components of the dataset are as follows, where the * is a placeholder/wildcard.

*SX_DetectorHits.zip
The simulation results here specifically all detector hit maps for each tip and the input files for tapsim

*.cif
The Crystallography Open Database file used to define the unit cell

*MeshgenInput.tar.gz
The compressed txt-based inputfiles for MESHGEN with which the inputfiles for TAPSim
for each tip were generated.

*TapsimInput.tar.gz
the compressed binary inputfiles for TAPSim which specify at which locations
the atoms and mesh supporting points are located

*BaseAndTip.zip
The compressed PNG-renditions of where the tip ions and the base plate supporting points are located.
The potential Moire effects apparent in the images are likely related to us reducing the rendering resolution.

*Everything.zip
The compressed PNG-renditions of where the tip ions, the base plate supporting points, and mesh points are located.

*Meta.mat and *PRNG.txt
The MATLAB workspace variables which hold the orientation of each tip as a rotation matrix and
the seed of the random number generator. The rotation matrix is of active sense premultiplying
point position vectors from the VESTA output into their actual locations from which subsequently the tip was carved.
A few tip orientations did not run, this was solved by rotating them by an additional 0.5 deg random rotor
in space about the projected orientation, the corresponding individual rotation matrices are stored in individual *.mat files
with the corresponding tip ID in the filename each

*.vesta
The Vesta inputfile with which sufficiently sized lattice point clouds were
written out to subsequently rotate them and carve into a tip.

*DetectorHits.tar.gz
The compressed raw data in the default TAPSim format encoding where each
ion hit the detector surplus additional pieces of information.

*.pl
Perl scripts with which to extract runtime profile information from the TAPSim command line output

*.sh
Shell scripts used to execute the batch queue. Two scripts were used.
The first, "run_queue_tapsim_job.sh" $1 $2 fires off independent sequential TAPSIM simulations on existent data
The second "run_single_tapsim_job.sh" is called by the first script to fire this of.

tapsim_r3225.zip
The source code used to execute the simulations

The *.tar.gz files in the *.zip archives can be unpacked with the unpack_dataset.sh shell script specifically
unpack_dataset.sh $1 $2 with the first argument $1 the start ID and the second argument $2 being the tip end ID to unpack.
Modification of the script might be necessary if file name of *.tar.gz archive has been changed...
Single *.tar.gz files in general can be most conveniently extracted with a Unix/Linux operating system via for instance the command:
tar -xvf nameofthefile.tar.gz
On Windows WinRAR can be used for decompression