__init__(self,
msys_model,
cms_model,
asl0,
asl1=None,
pos_type0='atom',
pos_type1='atom',
dr=0.1,
rmax=12.0)
(Constructor)
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This analyzer calculates the radial distribution function [RDF, also
known as g(r)] of specified positions in the system.
In general, we need two groups of positions. The first group are the
reference positions, whereas the second the distance group. For example,
say we want to calculate the RDF of the distances of water hydrogen atoms
with respect to water oxygen atoms, the first group will be all water
oxygen atoms' positions, and the second group all water hydrogen atoms'
positions. The reference and distance groups can be the same, for
example, in the case of the RDF of water oxygen atoms.
Each position doesn't have to be an atom's position, and it could be a
derived position such the center of mass of the molecule.
- Parameters:
asl0 (str) - Atom selection for the reference groupasl1 (str or None) - Atom selection for the distance group. If it's None,
it will default to asl0.pos_type0 (str) - Type of positions of the reference group: "atom" :
Use atom's position directly "com" : Use molecular
center of mass "coc" : Use molecular center of
charge "centroid": Use molecular centroidpos_type1 (str) - Type of positions of the distance group. Values are the same as
those of pos_type0dr (float) - Bin width in the unit of Angstromsrmax (float) - Maximum distance in the unit in Angstroms. The RDF will be
calculated until rmax.cms_model (cms.Cms)msys_model (msys.System) - Overrides:
object.__init__
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