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Data for paper "On the Crystal Structure of Colloidally Prepared Metastable Ag2Se Nanocrystals"

DOI

Content of the repository

  • search-data contains the relaxed structures sampled by ab initio random structure searching (AIRSS).
  • refined-structures contains the structures further relaxed using VASP and used for make the figure.
  • phonon contains the raw calculation data for the phonon calculations export from AiiDA file repository.
  • ag2se-calcs.aiida is an AiiDA export file containing all calculation performed and reported in paper with their full provenance. This file can be imported into an AiiDA instance (aiida-core >= 1.6.3). Raw data may also be access by simply unzipping the file. This file is hosted by Zenodo.
  • notebooks contains the notebooks for data analysis and visualisation.
  • figures contains the figures in the PNG and the SVG format. The SVG figures are generated using Inkscape.
  • antiPbCl2like_Ag2Se_laboratory.cif is the experimental structure generated using a Rietveld refinement of the anti-PbCl2-like structure to Ag2Se.

Importing data into a new AiiDA Database

The provenance data stored in the ag2se-calcs.aiida can be imported into a AiiDA database and allow the analysis in the notebooks folder to be reproduced. A few dependencies needs to be installed:

  • aiida-core>=1.6.3 is the mean package of the AiiDA framework.
  • aiida-vasp>2.0.1 contains the interface to VASP.
  • ase and pymatgen are needed for the analysis. ase==3.21 and pymatgen==2020.10.20 were used in this project, but other compatible version should work as well.
  • additional requires in the requirements.txt.

A few more steps are needed to step up a new AiiDA profile before importing the archive. Please follow the installation instructions on the offical documentation.

The magic "%aiida" can be enabled by a file aiida_magic_register.py in <home_folder>/.ipython/profile_default/startup:

if __name__ == '__main__':

    try:
        import aiida
        del aiida
    except ImportError:
        # AiiDA is not installed in this Python environment
        pass
    else:
        from aiida.tools.ipython.ipython_magics import register_ipython_extension
        register_ipython_extension()

Note that you may want to run ipython once so the profile folers are created. If not, just create them manually.

Once everything is in place, the following commands will import all data:

verdi archive import -G ag2se-paper -- ag2se-calcs.aiida

As each calculation/workflow is identified based on a unique ID (uuid), the analysis code in the notebook can be reused.