Hi all,
I am very new to pymatgen and I am trying to use the diffussion analyzer to plot the MSD curves and compute the ionic conductivity from VASP AIMD outputs. However, I am getting MSDs that are oscillating with time but I expect the MSDs to increase with time. Although VASPKIT gives the correct MSDs but it cannot compute the ionic conductivity.
Below is the code I am using:
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Analyze AIMD results, calculate MSD and conductivity
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import os
from pymatgen.core.trajectory import Trajectory
from pymatgen.io.vasp.outputs import Xdatcar
from pymatgen.core import Structure
from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer
import numpy as np
import pickle
Read the XDATCAR file and get a series of structural information
traj = Trajectory.from_file( ‘XDATCAR’ )
Instantiate the DiffusionAnalyzer class
and initialize this class with the from_structures method; 1600 is the temperature, 1 is the vtime step (POTIM = 1), 1 is the number of interval steps
diff = DiffusionAnalyzer.from_structures(traj, ‘K’ , 1600 , 2 , 5 )
Plotting msd using the built-in plot_msd method to draw MSD images
diff.plot_msd()
Export MSD data to a file by calling the export_msdt() method
diff.export_msdt(filename=‘pymatgen_msd.dat’)
Next, get the ion mobility directly, the unit is mS/cm
C = diff.conductivity
D = diff.diffusivity
with open ( ‘Ionic_Conductivity_results.dat’ , ‘w’ ) as f:
f.write( ‘# AIMD result for K-ion\n’ )
f.write( ‘temp\tconductivity\tDiffusivity\n’ )
f.write(‘d\t.4f\t%.5e\n’ % (1600, C, D))