Analysis Module

The analysis package provides tools for computing structural, dynamical, and interfacial properties from molecular dynamics simulations.

Distribution Functions

cemd.analysis.compute_rdf()

Calculate the Radial Distribution Function (RDF) g(r), and its derivatives G(r) and n(r).

Silicate Network

cemd.analysis.analyze_silicates()

Entry point for analyzing silicate network structures.

Diffusion

cemd.analysis.msd(univ, atom_type[, dt, ...])	Calculate the diffusion coefficient in a bulk solution from the mean squared displacement (MSD).
cemd.analysis.msd_profile(univ, atom_type[, ...])	Calculate a profile of diffusion coefficients at a liquid/solid interface.
cemd.analysis.diffusion_coefficient(df_msd)	Calculate the diffusion coefficients for a bulk solution from an MSD DataFrame.
cemd.analysis.diffusion.diffusion_coefficient_profile(df_msd)	Calculate the spatial diffusion coefficient profile from an MSD MultiIndex DataFrame.
cemd.analysis.diffusion.plot_msd(df_msd)	Plot the MSD values from a pandas DataFrame.
cemd.analysis.diffusion.plot_diffusion_profile(...)	Plot the spatial diffusion coefficient profile from a pandas DataFrame.

Bond Correlation

cemd.analysis.tcf.bondcorr(universe, ...[, ...])	Calculate the time correlation function (TCF) of a bond.
cemd.analysis.tcf.lifetime(odf, corrtime)	Calculate the bond lifetime by fitting the time correlation function.

Interface Properties

cemd.analysis.density_profile(universe, ...)	Create a DataFrame with the average density of atoms of given types along a given axis.
cemd.analysis.density_map(univ, atom_types, ...)	Create a 2D density map of atoms within a specified distance of an interface.
cemd.analysis.electrostatic_potential(...)	Calculate charge distribution, electric field, and electrostatic potential.
cemd.analysis.density.find_interfaces_coordinates(...)	Calculate the solid/liquid interface coordinates for an interfacial system.
cemd.analysis.density.shift_profile(...[, ...])	Shift the coordinates of a 1D density profile.