Example dataset for openPMD-conform molecular dynamics data (MD domain extension)

This dataset results from the molecular dynamics (MD) simulation of the photon-sample interaction. The photons are propagated through the SASE1 beamline and the SPB-SFX instrument at European XFEL, with an initial energy of 5 keV. The sample is the two-nitrogenase iron protein (2nip) with 4348 atoms. The simulation is performed with a demo version of XMDYN. The datasets were rewritten from the original XMDYN output into an hdf5 format that complies with the openPMD metadata standard for particle and mesh data and the proposed domain extension of this standard for MD data. The dataset "pure_2nip_pmi_out.opmd.h5" conforms the openPMD metadata MD domain extension strictly, while the dataset "pure_2nip_pmi_out.opmd.ff.h5" stores form factor results additionally for SingFEL diffraction simulation. This dataset is part of the Deliverable D5.1 in Workpackage 5 (Virtual Neutron and X-ray Laboratory) of the Photon and Neutron Open Science Cloud (PaNOSC). This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 823852.<br>本数据集源自光子与样品相互作用的分子动力学（Molecular Dynamics, MD）模拟。光子以5 keV的初始能量，在欧洲X射线自由电子激光装置（European XFEL）的SASE1束线与SPB-SFX实验站内传播。本次模拟的样品为含4348个原子的二固氮酶铁蛋白（two-nitrogenase iron protein, 2nip），模拟过程采用XMDYN演示版完成。研究人员将原始XMDYN输出文件重构为符合openPMD元数据标准（适用于粒子与网格数据）及其针对分子动力学数据的拟议域扩展规范的HDF5格式数据集。其中，数据集"pure_2nip_pmi_out.opmd.h5"严格遵循openPMD元数据的分子动力学域扩展规范；而数据集"pure_2nip_pmi_out.opmd.ff.h5"则额外存储了用于SingFEL衍射模拟的形状因子结果。本数据集属于光子与中子开放科学云（Photon and Neutron Open Science Cloud, PaNOSC）第五工作包（虚拟中子与X射线实验室）的可交付成果D5.1。本项目获欧盟"地平线2020"研究与创新框架计划资助，资助协议编号为823852。