Notebooks

Here are some simple Jupyter Notebooks, showing how kinisi can be used to investigate mean-squared displacement and diffusion from a VASP Xdatcar file, centre of mass diffusion from an MDAnalysis universe, the Arrhenius behavior from an MDAnalysis universe, finite-size corrections using Yeh-Hummer analysis, and comparing with pymatgen and MDAnalysis.

• Finding the MSD uncertainties from a VASP file
• Diffusion coefficient from a VASP file
• Jump diffusion coefficient from a VASP file
• Diffusion coefficient of molecules using center of mass
• Investigation of an Arrhenius relationship
• Finite-size corrections with Yeh-Hummer
• Comparison with pymatgen
• Comparison with MDAnalysis
• Handling a poorly conditioned covariance matrix