polypy.density¶

Density functions included with polypy. The Density class will determine generate a three dimensional grid that stores the total number of times that an atom spends within a xyz grid point during the simulation.

class polypy.density.Density(data, histogram_size=0.1, atom=None)[source]¶

Bases: object

The polypy.density.Density class evaluates the positions of all atoms in the simulation.

Parameters:	data (`polypy.read.Trajectory`) – Object containing the information from the HISTORY or ARCHIVE files. histogram_size (`float`, optional) – Specifies the spacing between histograms. atom (`str`, optional) – Specifies the atom to calculate the density for.

build_map()[source]¶: Constructs three dimensional grid of histogram_size * histogram_size * histogram_size. containing a count for how many times an atom passes through each histogram_size ** 3 cube.

find_limits()[source]¶: Determine the upper and lower limits of the simulation cell in all three dimensions.

one_dimensional_density(direction='x')[source]¶

Calculate the particle density within one dimensional histograms of a structure.

Parameters:	direction (`str`) – The dimension perpendicular to the histograms.
Returns:	Locations of histograms. y (`array_like`): Size of histograms. bin_volume (`float`): Volume of histograms.
Return type:	x (`array_like`)

two_dimensional_density(direction='x')[source]¶

Calculate the particle density within two dimensional pixels of a structure.

Parameters:	direction (`str`) – The dimension normal to the pixels.
Returns:	Locations of one dimension of the pixels. y (`array_like`): Locations of one dimension of the pixels. z (`array_like`): Size of pixels. bin_volume (`float`): Volume of pixels.
Return type:	x (`array_like`)

update_map(position)[source]¶: Determines the specific location of a given atom and adds it to the corresponding location in the three dimensional map of atomic positions.