Crate bader

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 with adaptions for multi-threading.

Supported Platforms

• Linux
• Os X
• Windows

Installing the binary

Cargo

$ cargo install bader

From Source

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/bca executable.

$ git clone https://github.com/adam-kerrigan/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/bca ~/bin

Using the library

Add the following to your Cargo.toml: bader = "0.4.8"

Minimum Supported Rust Version (MSRV)

This crate is guaranteed to compile on stable Rust 1.56.1 and up.

Usage

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.

$ bca 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.

$ bca charge-density.cube -s spin-density.cube

For a detailed list of usage options run

$ bca --help

Output

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’.

License

MIT

Modules

analysis

Performs analysis of the VoxelMap to find the partitioned charge, assigned atom and other relevant properties.

arguments

For parsing command-line arguments.

atoms

Contains Atoms for storing the relevant data on the atoms in the calculation. Also contains Lattice and for storing information about the cell in which the density is stored.

errors

Provides custom errors types.

grid

Contains Grid for managing the movement around the grid on which the density is stored.

io

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.

methods

Contains the methods for partioning the density, finding maxima and calculating the Laplacian for voxel based grids.

progress

Provides a visible and hidden implementation of the trait ProgressBar.

utils

Misc functions mainly for vector and matrix manipulation.

voronoi

Calculates the Voronoi vectors, and their alpha values for the weight method, for lattices. Also useful for periodic minimum distances.

voxel_map

Provides the BlockingVoxelMap and VoxelMap for storing the maxima and weights of partioned voxels.