VibIR-Parallel-Compute

VibIR-Parallel-Compute: Enhancing Vibration and Infrared Analysis in High-Performance Computing Environments - Published in JOSS (2025)

https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute

Repository

A HPC-ready parallelized implementation of Vibration and Infrared computations from DFT simulations. https://morikawa-lab-osakau.gitlab.io/vibir-parallel-compute

https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute/blob/main/

# VibIR-Parallel-Compute

This packages is primarily about doing Vibration and Infrared computations and analysis. It is designed to be conducted in parallel and take advantage of multiple nodes available in High Performance Computing (HPC) environments. Aside from the primary computations, additional tools are provided to help with the analysis and post-processing.

## Getting started

### Installation

**via direct Pip**

Activate your python environment (`conda` or `virtualenv`) and install using `pip`:

```bash
pip install git+https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute.git
```

```{note}
This will install the latest version
```

**via Git**

Download the `git` repository and install:

```bash
git clone https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute.git
pip install vibir-parallel-compute/
```

This method allows you to retain a copy of the code and also to select a specific version you need. 

**Developer mode**

If you want to add new features or need to edit some portion of the code. You can install it using developer mode to save time on frequent reinstalls.

```bash
git clone https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute.git
pip install -e vibir-parallel-compute/
```

### Usage

A web manual is made available in https://morikawa-lab-osakau.gitlab.io/vibir-parallel-compute. Tutorials and examples are provided to help you get started.

## Developer notes

To succesfully run the `pytest` tests, there are a few prerequisites:

1. Python environment
2. Quantum Espresso executables (pw.x) and the pseudopotential file


### Common environment via Docker 

> Note: The docker container creation can be skipped if you already have an existing QE installation and virtual environment. Just change the necessary variables to the correct paths in your system. Also, we're using the [GBRV pseudopotentials](https://www.physics.rutgers.edu/gbrv/all_pbe_UPF_v1.5.tar.gz) in the input files so that need to be specifically available. See the necessary environmental variables in the ("Environment preparation")[#environment-preparation] section.

For the same environment, you can use the docker image provided in the `vibir-parallel-compute/docker/Dockerfile`:



```bash
# Create the docker image (imagename = vibirimage, about 1.6GB) 
docker build -t vibirimage .

# Create and run container (containername=vibircontainer)
docker run -it --name vibircontainer vibirimage

# (OPTIONAL) if exited and want to return to the session/container
# docker start vibircontainer
# docker exec -it vibircontainer /bin/bash
```

with `ls` you can see two directories, the `pyenv` containing the python virtual environment, and the `qe` containing the QE and pseudopotentials.

### Environment preparation

Here, we prepare the environment variables and the python environment for the tests.



```bash
# Download repository
git clone -b JOSS-branch https://gitlab.com/morikawa-lab-osakau/vibir-parallel-compute.git

# Package installation (change "pyenv" if you'd like to use your own venv)
source ~/pyenv/bin/activate
cd vibir-parallel-compute/
pip install .

# Export the necessary QE paths (adjust the paths accordingly, if you'll use your own QE installation)
export ESPRESSO_PSEUDO="/home/testuser/qe/pseudo"
export ESPRESSO_COMMAND="pw.x"
export ESPRESSO_TMPDIR="TMPDIR"
export ESPRESSO_BIN="/home/testuser/qe/bin"
export PATH=/home/testuser/qe/bin:$PATH
```

### Running pytest

```bash
# Run pytest
pytest -rP -vvv --durations=0  ./vibir_parallel_compute  
```


## Contributing

Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.

Owner

JOSS Publication

VibIR-Parallel-Compute: Enhancing Vibration and Infrared Analysis in High-Performance Computing Environments

Published

April 15, 2025

DOI

10.21105/joss.07855

Volume 10, Issue 108, Page 7855

Authors

Kurt Irvin M. Rojas
Department of Precision Engineering, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan

Yoshitada Morikawa
Department of Precision Engineering, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan, Research Center for Precision Engineering, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan

Ikutaro Hamada
Department of Precision Engineering, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan

Editor

Lucy Whalley

Tags

material science vibrational analysis infrared spectra

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