newanalysis.gfunction.RDF

class newanalysis.gfunction.RDF(modes, histo_min, histo_max, histo_dr, sel1_n, sel2_n, sel1_nmol, sel2_nmol, box_x, box_y=None, box_z=None, use_cuda=False, norm_volume=None)

Bases: object

class RDF

A container object for calculating radial distribution functions.

Methods

calcFrame

calcFrame(coor_sel1, coor_sel2, dip_sel1=None, dip_sel2=None,

printInfo

Print some information about the RDF container.

resetArrays

Reset histogram arrays to zero

scale

update_box

Update the box dimensions, when analysing NpT trajectories.

write

param filename .. name of the file to be written to. Each type of rdf will be written to a separate file:

with the ending specifying the type.
calcFrame(coor_sel1, coor_sel2, dip_sel1=None, dip_sel2=None, pre_coor_sel1_gpu=None, pre_coor_sel2_gpu=None, pre_dip_sel1_gpu=None, pre_dip_sel2_gpu=None)
calcFrame(coor_sel1, coor_sel2, dip_sel1=None, dip_sel2=None,

pre_coor_sel1_gpu=None, pre_coor_sel2_gpu=None, pre_dip_sel1_gpu=None, pre_dip_sel2_gpu=None)

Parameters:

  • numpy-array (coor_sel1 ..) –

  • selection (dip_sel2 .. numpy-array containing the dipoles of the second) –

  • selection –

  • selection –

  • arrays (pre-allocated) – PyCUDA GPU array objects obtained from drv.memalloc()

Pass the data needed to calculate the RDF for the current frame and do the calculation. Optionally, pre-allocated arrays on the GPU can be used. This is useful, if they are reused for more than one rdf calculation.

printInfo()

Print some information about the RDF container.

resetArrays()

Reset histogram arrays to zero

update_box(box_x, box_y, box_z)

Update the box dimensions, when analysing NpT trajectories.

write(filename='rdf')
Parameters:

file (filename .. name of the file to be written to. Each type of rdf will be written to a separate) – with the ending specifying the type.

Norm the calculated histograms and write them to the specified file.