Single-crystalline Mg tips

<p>This repository contains all input data for simulating the field-evaporation process of specifically<br> oriented single-crystalline APT tips with representing h.c.p. magnesium using TAPSim.</p> <p>Having conducted all simulations, it contains all detector hit information for all ions and each tip.</p> <p>The authors have also personally stored the trajectories of all ions for each tip. However,<br> given the size of these particular additional binary data (approx. 100 - 200GB), they have<br> --- as a compromise --- not yet been uploaded.&nbsp; They are available from the authors for free upon request.</p> <p><br> The individual components of the dataset are as follows, where the * is a placeholder/wildcard.</p> <p>*SX_DetectorHits.zip<br> The simulation results here specifically all detector hit maps for each tip and the input files for tapsim</p> <p>*.cif<br> The Crystallography Open Database file used to define the unit cell</p> <p>*MeshgenInput.tar.gz<br> The compressed txt-based inputfiles for MESHGEN with which the inputfiles for TAPSim<br> for each tip were generated.</p> <p>*TapsimInput.tar.gz<br> the compressed binary inputfiles for TAPSim which specify at which locations<br> the atoms and mesh supporting points are located</p> <p>*BaseAndTip.zip<br> The compressed PNG-renditions of where the tip ions and the base plate supporting points are located.<br> The potential Moire effects apparent in the images are likely related to us reducing the rendering resolution.</p> <p>*Everything.zip<br> The compressed PNG-renditions of where the tip ions, the base plate supporting points, and mesh points are located.</p> <p>*Meta.mat and *PRNG.txt<br> The MATLAB workspace variables which hold the orientation of each tip as a rotation matrix and<br> the seed of the random number generator. The rotation matrix is of active sense premultiplying<br> point position vectors from the VESTA output into their actual locations from which subsequently the tip was carved.<br> A few tip orientations did not run, this was solved by rotating them by an additional 0.5 deg random rotor<br> in space about the projected orientation, the corresponding individual rotation matrices are stored in individual *.mat files<br> with the corresponding tip ID in the filename each</p> <p>*.vesta<br> The Vesta inputfile with which sufficiently sized lattice point clouds were<br> written out to subsequently rotate them and carve into a tip.</p> <p>*DetectorHits.tar.gz<br> The compressed raw data in the default TAPSim format encoding where each<br> ion hit the detector surplus additional pieces of information.</p> <p>*.pl<br> Perl scripts with which to extract runtime profile information from the TAPSim command line output</p> <p>*.sh<br> Shell scripts used to execute the batch queue. Two scripts were used.<br> The first, &quot;run_queue_tapsim_job.sh&quot; $1 $2 fires off independent sequential TAPSIM simulations on existent data<br> The second &quot;run_single_tapsim_job.sh&quot; is called by the first script to fire this of.</p> <p>tapsim_r3225.zip<br> The source code used to execute the simulations</p> <p>The *.tar.gz files in the *.zip archives can be unpacked with the unpack_dataset.sh shell script specifically<br> 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.<br> Modification of the script might be necessary if file name of *.tar.gz archive has been changed...<br> Single *.tar.gz files in general can be most conveniently extracted with a Unix/Linux operating system via for instance the command:<br> tar -xvf nameofthefile.tar.gz<br> On Windows WinRAR can be used for decompression</p>