pymatgen-analysis-diffusion

from pymatgen.core import Structure, Species, Lattice from pymatgen_analysis_diffusion.aimd.msd import MSDAnalyzer import numpy as np # 1. Create dummy structures to simulate a trajectory lattice = Lattice.cubic(10.0) species_list = [Species("Li"), Species("O")] * 4 # 8 atoms total # Generate a list of structures for the trajectory structures = [] for i in range(5): # Slightly perturb coordinates for each step coords = np.random.rand(8, 3) + i * 0.05 # Simulate some movement s = Structure(lattice, species_list, coords) structures.append(s) # Define simulation parameters time_step = 2.0 # Time step between structures in picoseconds (ps) step_skip = 1 # Use every step # 2. Initialize MSDAnalyzer for a specific species (e.g., Li) li_species = [Species("Li")] msd_analyzer = MSDAnalyzer( structures=structures, species=li_species, time_step=time_step, step_skip=step_skip ) # 3. Calculate diffusivity temperature = 300 # Kelvin diffusivity_data = msd_analyzer.get_diffusivity(temperature=temperature, initial_drift_correct=True) print(f"Calculated diffusivity for Li at {temperature}K:") print(f" Diffusivity: {diffusivity_data['diffusivity']:.2e} cm^2/s") print(f" Error: {diffusivity_data['error']:.2e} cm^2/s") # Optional: Get MSD data for plotting # time_points, msd_values = msd_analyzer.get_msd_plot() # print(f"First 5 MSD values: {msd_values[:5]}")