Create graphene and other substrates for use in molecular dynamics simulations. A binary CLI utility grafen_cli and the library grafen are both available for use.

This is a pet project to help me set up simulation systems for my research. It is focused on formats used by Gromacs.

Usage

USAGE:
    grafen_cli [OPTIONS] <PATH> <X> <Y>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
        --std <Z>        Uniformly distribute positions along z. This value is
                         the deviation range (in nm) from the original position
                         of each residue.
    -t, --title <STR>    Title of system
        --z0 <Z>         Substrate position along z (nm)

ARGS:
    <PATH>    Output GROMOS file (the extension will be set to .gro)
    <X>       Size of system along the x axis (nm)
    <Y>       Size of system along the y axis (nm)

Library

See the documentation for usage examples.

Available Substrates

Spacings and translations for all substrates is currently hard-coded. Preferably this should be set in some configuration files or as an option input by the user during runtime.

Graphene

A monolayer of carbon atoms set in a hexagonal honeycomb structure. The spacing between every atom is 0.142 nm.

Silica

A monolayer of rigid SiO2 molecules set in a triclinic formation with with spacing 0.450 nm along both base vectors and an angle of 60 degrees between them.

License