Single-Crystalline Al Tips

This repository contains all input data for simulating the field-evaporation process of specifically<br> oriented single-crystalline APT tips with representing f.c.c. aluminium 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,<br> given the size of these particular additional binary data (approx. 100 - 200GB), they have<br> --- as a compromise --- not yet been uploaded. They are available from the authors for free upon request. <br> The individual components of the dataset are as follows, where the * is a placeholder/wildcard. *SX_DetectorHits.zip<br> The simulation results here specifically all detector hit maps for each tip and the input files for tapsim *.cif<br> The Crystallography Open Database file used to define the unit cell *MeshgenInput.tar.gz<br> The compressed txt-based inputfiles for MESHGEN with which the inputfiles for TAPSim<br> for each tip were generated. *TapsimInput.tar.gz<br> the compressed binary inputfiles for TAPSim which specify at which locations<br> the atoms and mesh supporting points are located *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. *Everything.zip<br> The compressed PNG-renditions of where the tip ions, the base plate supporting points, and mesh points are located. *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 *.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. *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. *.pl<br> Perl scripts with which to extract runtime profile information from the TAPSim command line output *.sh<br> Shell scripts used to execute the batch queue. Two scripts were used.<br> The first, "run_queue_tapsim_job.sh" $1 $2 fires off independent sequential TAPSIM simulations on existent data<br> The second "run_single_tapsim_job.sh" is called by the first script to fire this of. tapsim_r3225.zip<br> 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<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本仓库包含采用TAPSim模拟特定取向的面心立方（f.c.c.）铝单晶原子探针层析（Atom Probe Tomography, APT）针尖场蒸发过程所需的全部输入数据。 完成所有仿真后，本仓库还收录了所有离子及每根针尖的探测器击中信息。 作者还自行存储了每根针尖对应的所有离子的运动轨迹。但由于此类额外二进制数据体积庞大（约100~200GB），暂未上传至本仓库。如有需要，可向作者免费索取该部分数据。 本数据集的各个组成部分如下，其中*为通配符占位符： *SX_DetectorHits.zip：包含所有针尖的探测器击中映射图仿真结果，以及TAPSim的输入文件。 *.cif：用于定义晶胞的晶体学开放数据库（Crystallography Open Database, COD）文件。 *MeshgenInput.tar.gz：基于文本格式的压缩输入文件，用于MESHGEN工具，可由此生成每根针尖对应的TAPSim输入文件。 *TapsimInput.tar.gz：压缩的二进制输入文件，用于TAPSim，用于指定原子与网格支撑点的位置。 *BaseAndTip.zip：压缩的PNG格式图像，展示针尖离子与底板支撑点的位置分布。图像中出现的莫尔条纹大概率源于渲染分辨率的降低。 *Everything.zip：压缩的PNG格式图像，展示针尖离子、底板支撑点以及网格点的位置分布。 *Meta.mat 与 *PRNG.txt：存储MATLAB工作区变量的文件，其中前者以旋转矩阵形式存储每根针尖的取向信息，后者存储随机数生成器的种子。该旋转矩阵为主动旋转矩阵，可将VESTA输出的点位置向量前置相乘，转换为后续刻蚀针尖时的实际位置。部分针尖的初始取向未能顺利运行仿真，对此我们采用了绕投影取向在空间中额外旋转0.5°随机轴的方式进行修正，对应的单独旋转矩阵存储于以对应针尖ID命名的*.mat文件中。 *.vesta：VESTA输入文件，用于生成足够规模的格点云，以便后续进行旋转与刻蚀以制备针尖。 *DetectorHits.tar.gz：采用TAPSim默认格式存储的压缩原始数据，编码了每个离子击中探测器的位置及其他附加信息。 *.pl：Perl脚本，用于从TAPSim命令行输出中提取运行时性能分析信息。 *.sh：用于执行批量队列任务的Shell脚本，共包含两个脚本：其一为"run_queue_tapsim_job.sh"，通过传入参数$1、$2，在现有数据上启动独立的串行TAPSim仿真任务；其二为"run_single_tapsim_job.sh"，由前者调用以启动单个仿真任务。 tapsim_r3225.zip：用于执行仿真的源代码文件。 *.zip压缩包内的*.tar.gz文件可通过专用Shell脚本unpack_dataset.sh进行解压，使用格式为`unpack_dataset.sh $1 $2`，其中第一个参数$1为待解压的起始针尖ID，第二个参数$2为结束针尖ID。若*.tar.gz归档文件的文件名发生变更，可能需要对该脚本进行修改。单个*.tar.gz文件通常可在类Unix/Linux操作系统中通过如下命令便捷解压：`tar -xvf nameofthefile.tar.gz`；在Windows系统中则可使用WinRAR完成解压操作。