Single-crystalline Mg 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. magnesium 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本仓库包含了使用TAPSim模拟以六方密排（hexagonal close-packed, h.c.p.）镁为结构表征的特定取向单晶原子探针层析（Atom Probe Tomography, APT）针尖场蒸发过程的全部输入数据。本仓库已完成全部模拟工作，包含所有离子在各针尖上的全部探测器击中数据；作者还自行存储了各针尖的所有离子轨迹数据。但鉴于此类额外二进制数据体量庞大（约100~200GB），作为折中方案暂未上传，使用者可通过向作者申请免费获取该部分数据。 本数据集的具体组成如下，其中*为占位符/通配符： *SX_DetectorHits.zip：包含各针尖的全部探测器击中分布图等模拟结果与TAPSim输入文件的压缩包； *.cif：用于定义晶胞的晶体学开放数据库（Crystallography Open Database）文件； *MeshgenInput.tar.gz：基于文本的MESHGEN压缩输入文件，用于生成各针尖对应的TAPSim输入文件； *TapsimInput.tar.gz：TAPSim的压缩二进制输入文件，用于指定原子与网格支撑点的位置； *BaseAndTip.zip：包含针尖离子与基板支撑点位置的PNG渲染图压缩包。图像中可见的潜在摩尔纹效应，大概率与我们降低渲染分辨率有关； *Everything.zip：包含针尖离子、基板支撑点与网格点位置的PNG渲染图压缩包； *Meta.mat与*PRNG.txt：存储各针尖取向（以旋转矩阵形式）与随机数生成器种子的MATLAB工作区变量文件。该旋转矩阵为主动前置乘法矩阵，可将VESTA输出的点位置矢量转换为实际空间位置，后续基于该位置刻蚀制备针尖； 部分针尖取向的模拟未能正常运行，我们通过将其绕投影取向在空间中额外旋转0.5°的随机转轴解决了该问题，对应的独立旋转矩阵存储于文件名包含对应针尖ID的*.mat文件中； *.vesta：VESTA输入文件，用于导出足够大的晶格点云，以便后续旋转并刻蚀为针尖； *DetectorHits.tar.gz：采用TAPSim默认格式存储的压缩原始数据，编码了各离子的探测器击中位置与额外附加信息； *.pl：用于从TAPSim命令行输出中提取运行时配置信息的Perl脚本； *.sh：用于执行批量任务队列的Shell脚本。本次共使用两类脚本：其一为`run_queue_tapsim_job.sh`，通过参数$1、$2对已有数据启动独立的串行TAPSIM模拟任务；其二为`run_single_tapsim_job.sh`，由首个脚本调用以启动单个模拟任务； tapsim_r3225.zip：用于执行模拟的源代码压缩包； 上述*.tar.gz格式文件可通过专用Shell脚本unpack_dataset.sh进行解压，解压命令格式为`unpack_dataset.sh $1 $2`，其中$1为待解压的起始针尖ID，$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； 通常而言，单个*.tar.gz文件可通过类Unix/Linux操作系统的下述命令便捷解压：`tar -xvf nameofthefile.tar.gz`；在Windows系统中可使用WinRAR完成解压。