genice2-cif 2.1.1

CIF reader plugin for GenIce.

genice2-cif

A loader plugin for GenIce2 to read CIF file or to obtain structures in Zeolite DB.

version 2.1.1

Requirements

• cif2ice>=0.3.0
• GenIce2
• validators

Installation from PyPI

% pip install genice2-cif

Manual Installation

System-wide installation

% make install

Private installation

Copy the files in genice2_cif/formats/ into your local formats/ folder.

Usage

* To convert a local cif file to Gromacs format,

    % genice2 cif[RHO.cif] > RHO.gro
    % genice2 cif[ice.cif:O=O] > RHO.gro   # Specify the tetrahedral atom type ()

  * Options:

    * filename: A CIF file.
    * O=M:      Regards the atom type M as the position of a water molecule.
                (Default is "TS" (Tetrahedral hypothetical element "T" or "S"ilica, and "O" is ignored.))

* Some zeolites share the network topology with low-density ices. If you want to retrieve a zeolite ITT structure from [IZA structure database](http://www.iza-structure.org/databases) to prepare a low-density ice, try the following command:

    % genice2 zeolite[ITT] > ITT.gro

Test in place

% make test