Toposwarm Data

Dataset of topological low-symmetry organic compounds, as identified by a high throughput framework based on tight-binding calculations on neutral compounds. Currently containing information on 1-dimensional periodic systems. The HDF5 files are split up according to number of atoms per unit cell. Each HDF5 file, contains groups corresponding to POSCAR files. Each group has the associated metadata (# of atoms, nx, ny, lx,ly, width, symmetry…), stored as HDF5 attributes. Since objects or files cannot be stored in HDF5 files, each POSCAR file is loaded as an ase.atoms.Atoms object and then this object is broken into 4 arrays (“symbols”, “pbc”, “cell”, “positions”) and stored in HDF5 datasets in the POSCAR group. To access the POSCAR information, create an ase.atoms.Atoms object with the 4 datasets as the initial attributes. Work performed at the Center for Nanoscale Materials, an Office of Science user facility, and supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This material is based upon work supported by Laboratory Directed Research and Development (LDRD) funding from Argonne National Laboratory, provided by the Director, Office of Science, of the U.S. Department of Energy under Contract No. DE-AC02-06CH11357.

本数据集为拓扑低对称性有机化合物数据集，其通过基于中性化合物紧束缚计算（tight-binding calculations）的高通量框架识别得到。当前数据集仅包含一维周期性体系的相关信息。数据集以HDF5文件存储，文件按单胞内原子数目进行划分。每个HDF5文件内包含与POSCAR文件对应的组，每个组均存储有相关元数据（原子数、nx、ny、lx、ly、宽度、对称性等），并以HDF5属性的形式保存。由于HDF5文件无法直接存储对象或文件，我们将每个POSCAR文件加载为原子模拟环境（Atomic Simulation Environment, ASE）的Atoms对象，随后将该对象拆解为四个数组："symbols"、"pbc"、"cell"、"positions"，并将其存储于对应POSCAR组的HDF5数据集中。若需读取POSCAR相关信息，可通过这四个数据集作为初始属性构建ase.atoms.Atoms对象。本工作依托纳米尺度材料中心（Center for Nanoscale Materials）完成，该中心为美国能源部（U.S. Department of Energy）科学办公室下属的用户设施，相关研究受美国能源部科学办公室基础能源科学办公室合同号DE-AC02-06CH11357资助。本研究同时获得阿贡国家实验室（Argonne National Laboratory）实验室导向研究与发展（Laboratory Directed Research and Development, LDRD）项目资金支持，该资助由美国能源部科学办公室主任根据合同号DE-AC02-06CH11357提供。