Single-Crystalline Zr Tips

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. 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,<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本仓库存储了采用TAPSim（TAPSim）模拟特定取向单晶原子探针层析成像（Atom Probe Tomography, APT）针尖场蒸发过程的全部输入数据，模拟对象为代表密排六方（hexagonal close-packed, h.c.p.）结构的锆体系。 完成全部模拟后，本仓库还包含所有离子在各个针尖上的探测器命中信息。 作者还自行存储了每个针尖对应的所有离子的运动轨迹数据。但鉴于此类额外二进制数据体量较大（约100~200GB），作为折中方案暂未上传。有需求者可免费向作者索取该部分数据。 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：该压缩包内含所有针尖的探测器命中分布图模拟结果，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（MESHGEN）工具，以此生成各个针尖对应的TAPSim输入文件。 *TapsimInput.tar.gz：TAPSim的二进制压缩输入文件，用于指定原子与网格支撑点的空间位置。 *BaseAndTip.zip：包含针尖离子与基板支撑点位置的PNG渲染图压缩包。图像中可见的莫尔条纹大概率源于渲染分辨率的下调。 *Everything.zip：包含针尖离子、基板支撑点以及网格点位置的PNG渲染图压缩包。 *Meta.mat 与 *PRNG.txt：MATLAB（MATLAB）工作区变量文件，其中`Meta.mat`存储了以旋转矩阵形式表示的各针尖取向信息，`PRNG.txt`存储了随机数生成器的种子。该旋转矩阵为主动旋转矩阵，用于将VESTA（Vesta）输出的点位置向量转换为用于雕刻针尖的实际空间坐标。部分针尖的模拟任务未能正常执行，解决方法为沿其投影取向绕空间轴额外施加0.5°的随机旋转角，对应的单独旋转矩阵存储在文件名中带有对应针尖ID的*.mat文件中。 *.vesta：VESTA（Vesta）输入文件，用于生成足够大尺寸的晶格点云，以便后续进行旋转与针尖雕刻操作。 *DetectorHits.tar.gz：采用TAPSim默认格式存储的压缩原始数据，编码了每个离子的探测器命中位置以及额外附加信息。 *.pl：Perl（Perl）脚本，用于从TAPSim的命令行输出中提取运行时剖面信息。 *.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`，通过参数$1与$2启动现有数据集上的独立串行TAPSim模拟任务；其二为`run_single_tapsim_job.sh`，由前者调用以执行单个模拟任务。 tapsim_r3225.zip：用于执行模拟的源代码压缩包。 压缩包内的*.tar.gz文件可通过专用Shell脚本`unpack_dataset.sh`进行解压，执行格式为`unpack_dataset.sh $1 $2`，其中第一个参数$1为起始针尖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，则可能需要对该脚本进行修改。常规情况下，单个*.tar.gz文件可通过类Unix/Linux操作系统执行如下命令便捷解压：`tar -xvf 文件名.tar.gz`；在Windows系统中可使用WinRAR（WinRAR）工具完成解压。