genice2-rdf

A GenIce2 format plugin to calculate radial distribution functions.

version 2.1

Requirements

• PairList>=0.2.11.1
• GenIce2>=2.1b2

Installation from PyPI

% pip install genice2-rdf

Manual Installation

System-wide installation

% make install

Private installation

Copy the files in genice2_rdf/formats/ into your local formats/ folder.

Usage

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

Test in place

% make test