polypy.analysis

Analysis functions

class polypy.analysis.OneDimensionalChargeDensity(histogram_positions, atom_densities, atom_charges, histogram_volume, timesteps)

Bases: object

The polypy.analysis.OneDimensionalChargeDensity class converts one dimensional number densitie into the charge density, electric field and electrostatic potential.

Parameters:

• histogram_positions (array_like) – Histogram locations.
• atom_densities (list) – List of histograms.
• atom_charges (list) – List of atom charges.
• histogram_volume (float) – Volume of the histograms.
• timesteps (float) – Simulation timestep.

calculate_charge_density()

Calculates the charge density in one dimension.

Returns:Charge density. Return type:charge_density (array_like)

calculate_electric_field()

Calculates the electric field.

Returns:Electric field. Return type:e_field (array_like)

calculate_electrostatic_potential()

Calculates the electrostatic potential.

Returns:Electrostatic potential. Return type:potential (array_like)

polypy.analysis.conductivity(charge_carriers, volume, diff, temperature, hr)

Calculate the ionic conductivity.

Parameters:

• charge_carriers (float) – Number of charge carriers.
• volume (float) – Average cell volume.
• diff (float) – Diffusion coefficient.
• temperature (float) – Temperature.
• hr (float) – Haven ratio.

Returns:

Ionic conductivity.

Return type:

conductivity (float)

polypy.analysis.system_volume(data)

Calculate the volume at each timestep and return a volume as function of time.

Parameters:data (polypy.read.Trajectory) – polypy Trajectory object. Returns:Volume as a function of timestep. step (array_like): Timestep. Return type:volume (array_like)

polypy.analysis.two_dimensional_charge_density(atoms_coords, atom_charges, bin_volume, timesteps)

Calculates the charge density in two dimensions.

Parameters:

• atoms_coords (list) – List of atomic coordinates
• atom_charges (list) – List of atomic charges
• bin_volume (float) – Volume of histograms

Returns:

Charge density.

Return type:

charge_density (array_like)