ChemicalCompositionProfile

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

Constructor for the ChemicalCompositionProfile 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

• 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()

Returns:

A dictionary containing the composition profile of each element as a percentage of the total composition

Return type:

dict

zValues()

Returns:

The positions of the bins associated with the density profile.

Return type:

PhysicalQuantity of type length

Usage Examples

Load an BulkConfiguration and calculate the chemical composition profile along the C-vector of the cell:

# Load the configuration for analysis
configuration = nlread('Si-Si3N4_interface.hdf5')[-1]

# Calculate the mass density profile along the C-vector of the cell.
composition_profile = ChemicalCompositionProfile(
    configuration,
    direction_index=2,
    resolution=2.0 * Angstrom,
    start_time=0.0 * fs
)

# Get the chemical composition and the positions of the bin centers.
chemical_composition = composition_profile.data()
bin_centers = composition_profile.zValues()

# Create the plot model
model = Plot.PlotModel(x_unit=Angstrom)
model.title().setText('Chemical composition')
model.xAxis().setLabel('C axis')
model.yAxis().setLabel('Element Percentage')
model.legend().setVisible(True)

# Add line for each element
for key in chemical_composition.keys():
    line = Plot.Line(bin_centers, chemical_composition[key])
    line.setLabel(f'Percentage of {key}')
    model.addItem(line)

# Set different colors for each line
Plot.Colors.applyToItems(model.items(plot_item_type=Plot.Line))

# Set the ranges and show the plot
model.setLimits()
Plot.show(model)

composition_profile.py Si-Si3N4_interface.hdf5

Notes

The fraction of each element within a bin is given as a percentage value with respect to the total number of atoms.