https://github.com/pulkin/openmx-hks

A tool to read and operate OpenMX HKS (Kohn-Sham Hamiltonian) files
https://github.com/pulkin/openmx-hks

density-functional-theory hamiltonian kohn-sham matlab openmx physics python science solid-state-physics

Last synced: about 1 month ago
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A tool to read and operate OpenMX HKS (Kohn-Sham Hamiltonian) files

• Host: GitHub
• URL: https://github.com/pulkin/openmx-hks
• Owner: pulkin
• Created: 2017-03-06T12:31:38.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2021-01-12T18:14:55.000Z (about 4 years ago)
• Last Synced: 2024-01-30T04:08:20.276Z (12 months ago)
• Topics: density-functional-theory, hamiltonian, kohn-sham, matlab, openmx, physics, python, science, solid-state-physics
• Language: C
• Homepage:
• Size: 5.27 MB
• Stars: 11
• Watchers: 3
• Forks: 6
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
[![Build Status](https://dev.azure.com/gpulkin/openmx-hks/_apis/build/status/pulkin.openmx-hks?branchName=master)](https://dev.azure.com/gpulkin/openmx-hks/_build/latest?definitionId=1&branchName=master)

# openmx-hks

Parse the tight-binding Hamiltonian and other data from [OpenMX](http://www.openmx-square.org/)

and transform/output it into various formats.

Examples also include plotting

electronic band structure and calculating ballistic transport properties.

## Features

1. Portable: only `*.hks` file is required

2. Easy: minimal dependencies, straightforward options

3. Functional:

   - all data is parsed including the Hamiltonian, the overlap matrix,

     the Hartree potential, the Fermi level, the atomic structure and more;

   - adjusts energies;

   - exports Hamiltonian and overlap matrices into various formats

     (MATLAB, json, hdf5, sparse and dense);

   - exports structure into an XSF file;

  

## Download

From the [releases page](https://github.com/pulkin/openmx-hks/releases/tag/latest-build)

## Compile

Ubuntu example

Install dependencies

```bash

sudo apt-get install build-essential gcc-multilib libhdf5-dev

sudo ln -s /usr/lib/x86_64-linux-gnu/libhdf5_serial.so /usr/lib/x86_64-linux-gnu/libhdf5.so

```

Clone and make

```bash

mkdir openmx-hks

git clone https://github.com/pulkin/openmx-hks.git

cd openmx-hks

make -C src

```

## Examples

Extract Hamiltonian blocks into h5 file:

```bash

openmx-hks extract-hamiltonian your-hks-file.hks hamiltonian.h5

```

Extract atomic structure into xsf file:

```bash

openmx-hks extract-structure default.hks default.xsf bi,se

```

See the `examples` folder for other examples.

## Bugs

Report [here](https://github.com/pulkin/openmx-hks/issues)