openmaterials.ai / codes / pymatgen-analysis-diffusion
A pymatgen add-on for MD of ionic conductors: probability densities and van Hove functions, beside the MSD, Arrhenius and Nernst-Einstein analysis in pymatgen.
D = <[dr(t)]^2> / (2dt) from the mean squared displacement, an Arrhenius plot across temperatures, then sigma = rho z^2 F^2 D / (RT) at 300 K. Li-excess Li6.25PS5.25Cl0.75 gave 14 mS/cm and 211 meV (Deng 2016).
A linear fit of the MSD against 2dt gives D at each temperature. log D against 1/T gives the activation energy Ea and the extrapolated D at 300 K (Deng 2016).
The Nernst-Einstein relation converts D300K to sigma300K with the molar density of mobile ions and their charge, z = +1, at T = 300 K (Deng 2016).
P(r) on a 3D grid counts alkali ions per grid point over the run, normalized over the cell. Isosurfaces show the low-energy sites and the paths between them (Deng 2016).
The self part Gs(r,t) tracks how far an ion moves in time t. The distinct part Gd(r,t) shows when a vacated site is refilled, a sign of correlated motion (Deng 2016).
A FireWorks workflow relaxes, builds the supercell, runs NVT AIMD at several temperatures under a WallTimeHandler and stores snapshots in MongoDB (Deng 2016).
AIMD at 800 to 1400 K analyzed with pymatgen: pristine c-Na3PS4 gives 1.1e-4 mS/cm and 537 meV, one Na+ interstitial 1.06 mS/cm and 256 meV, 6.25% Sn doping 10.7 mS/cm and 171 meV. Zhu 2015
AIMD between 600 and 1300 K, with diffusivities fitted by pymatgen tools, predicted 0.94 mS/cm and 317 meV at room temperature. The synthesized compound measured 0.4 mS/cm and 356 meV. Richards 2016
Enumerate orderings of the disordered cell with enumlib via pymatgen, relax the lowest.
NVT Nose-Hoover runs at several temperatures, 2 fs steps, cells of at least 10 A.
Fit the MSD against 2dt per temperature, then an Arrhenius plot for Ea and D at 300 K.
Nernst-Einstein conductivity, probability density isosurfaces, van Hove functions.