A GenIce2 format plugin to calculate radial distribution functions.
version 0.5.2
- PairList>=0.2.3
- GenIce2
% pip install genice2_rdf
% make install
Copy the files in genice2_rdf/formats/ into your local formats/ folder.
Usage:
% genice 1c -r 3 3 3 -w tip4p -f _RDF > 1c.rdf
% genice 1c -r 3 3 3 -w tip4p -f _RDF[OW:H=HW1=HW2] > 1c.rdf
% analice data.gro -O OW -H HW[12] -w tip3p -f _RDF[OW:HW1=HW2] > data.rdf
Options:
Atom name
Atom name and aliases chained with "=".
json Output in JSON format.
range=x Range of interest (0.9 nm)
binw=x Bin width (0.003 nm)
Options must be separated with colons.
You can specify the list of atom types to be calculated.
For example, in the following case, TIP4P water has four different atom
types (OW, HW1, HW2, and MW), so all the possible 10 combinations of
atom types will be examined.
% genice 1c -r 3 3 3 -w tip4p -f _RDF > 1c.rdf
If you just want the RDF of OW and H, and HW1 and HW2 should be
abbreviated by H, specify the option string like following.
% genice 1c -r 3 3 3 -w tip4p -f _RDF[OW:H=HW1=HW2] > 1c.rdf
% make test