Create graphene and other substrates or system configurations for use in molecular dynamics simulations.

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

As of 0.10 requires Rust Nightly for nll and underscore_lifetimes features.

USAGE:
    grafen [OPTIONS]

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

OPTIONS:
    -d, --database <database>      Path to residue and component database
    -c, --conf <input_confs>...
            Path to input configuration files to add as components

    -o, --output <output>
            Output configuration file [default: conf.gro]

    -t, --title <title>            Title of output system

Substrate definitions are read from a JSON database. An example is provided in assets/database.json. This database contains a few residue and the following substrate definitions:

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

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.

A cylinder constructed of carbon atoms in the same structure as the above graphene.

The program supports reading configurations from disk and manipulating them in some ways. Currently read configurations can be extended by duplicating and cutting them, or cut into cylinders.

Such an example is included in the database.json file.

The database which is saved to disk can contain references to system configurations that it will read data from. If these paths are entered into the database as relative paths, they will be read as relative to the database location.

The program by default tries to read a database from disk. On Linux (and other non-OSX unix systems) it looks in a subdirectory to the locations specified by the XDG_DATA_HOME and XDG_DATA_DIRS (read-only) environment variables, or the $USER/.local/share directory. On OSX it looks in the same XDG-spec locations but also in the user and root Library/Application Support directories. On Windows in the directory set by the APPDATA environment variable.

See the documentation.

The program is unlicensed. See unlicense.org for details.