An incredibly fast, multi-threaded, Bader charge partitioning binary and library. Based on methods presented in Yu Min and Trinkle Dallas R. 2011 J. Che.m Phys. 134 064111 and W Tang et al 2009 J. Phys.: Condens. Matter 21 084204 with adaptions for multi-threading.
- Os X
$ cargo install bader
To check out the lastest features not in the binaries yet you can compile from source. To do this run the following, which will create the ./target/release/bader executable.
$ git clone https://github.com/kerrigoon/bader-rs $ cd bader-rs $ cargo build --verbose --release
From here you can either move or link the binary to folder in your path.
$ mv ./target/release/bader ~/bin
Add the following to your Cargo.toml:
bader = "0.2.2"
This crate is guaranteed to compile on stable Rust 1.40.0 and up. It might compile with older versions but that may change in any new patch release. To test this crate requires Rust 1.42.0 and above.
The program takes a charge density file as input and performs Bader analysis of the data. Currently it supports density in VASP or cube formats. It is recommended to run VASP calculations with LAECHG = .TRUE. to print the core density and self-consistent valence density. These can then be passed as reference files to the program using the -r, --reference flag where they will be summed.
$ bader CHGCAR -r AECCAR0 -r AECCAR2
VASP charge density files containing spin densities will output the the partitioned spin also. To achieve this for cube files requires using the --spin flag to pass a second file to treat as the spin density.
$ bader charge-density.cube -s spin-density.cube
For a detailed list of usage options run
$ bader --help
The program outputs two files, ACF.dat & BCF.dat. The Atomic Charge File (ACF.dat) contians the charge (and spin) information for each atom and the Bader Charge File (BCF.dat) contains the information about each Bader volume. The BCF file also includes the atom number in the number column formatted as 'atom number: bader volume'.
Builds the clap::App and parses command-line arguments.
Contains Density for managing the reference density for partioning. Also stores structures for moving around the grid on which the density is stored.
Handles the File I/O for both the density file and result files. Provides a FileFormat trait to be implemented by modules designed to cover a specific file format of a density file.
Misc functions mainly for vector and matrix manipulation.
Calculates the Voronoi vectors, and their alpha values for the weight method, for lattices. Also useful for periodic minimum distances.
Provides the VoxelMap for storing the maxima and weights of partioned voxels.