DensityProfile

class DensityProfile(md_trajectory, start_time=None, end_time=None, resolution=None, atom_selection=None, direction_index=None, time_resolution=None, info_panel=None)

Constructor for the DensityProfile object.

Parameters:

  • md_trajectory (MDTrajectory | AtomicConfiguration) – The MDTrajectory or configuration to calculate the density profile for.

  • start_time (PhysicalQuantity of type time) – The start time.
    Default: 0.0 * fs

  • end_time (PhysicalQuantity of the type time) – The end time.
    Default: the last time frame.

  • resolution (PhysicalQuantity of type length) – The bin size, which determines the resolution of the profile.
    Default: 2.0 * Angstrom

  • atom_selection (PeriodicTableElement | str | list of ints) – Only include contributions from this atom selection. The atoms can be selected by element i.e. PeriodicTableElement, tag or a list of atomic indices.
    Default: All elements are considered

  • direction_index (int) – The index of the cell vector along which the profile should be calculated. Can only be an element of [0, 1, 2].
    Default: 2

  • time_resolution (PhysicalQuantity of type time) – The time interval between snapshots in the MD trajectory that are included in the analysis.

  • info_panel (InfoPanel (Plot2D)) – Info panel to show the calculation progress.
    Default: No info panel

data()

Return the density profile.

zValues()

Return the positions of the bins associated with the density profile.

Usage Examples

Load an MDTrajectory and calculate the mass density profile along the A-vector of the cell:

md_trajectory = nlread('alumina_trajectory.nc')[-1]

# Calculate the mass density profile along the A-vector of the cell.
density_profile = DensityProfile(md_trajectory,
                                 direction_index=0)

# Get the mass density in gram/ccm and the positions of the bin centers.
mass_density = density_profile.data().inUnitsOf(kiloGram/Meter**3)/1000.0
bin_centers  = density_profile.zValues().inUnitsOf(Angstrom)

# Plot the data using pylab.
import pylab

pylab.plot(bin_centers, mass_density,
           label='Mass density of alumina along A-vector')
pylab.xlabel('a (Angstrom)')
pylab.ylabel('d(a) (g/cm**3)')
pylab.legend()

pylab.show()

density_profile.py