https://github.com/capt-lappland/viamd

Visual Interactive Analysis of Molecular Dynamics

https://github.com/capt-lappland/viamd

Repository

Visual Interactive Analysis of Molecular Dynamics

https://github.com/Capt-Lappland/viamd/blob/master/

# VIAMD
Visual Interactive Analysis of Molecular Dynamics

VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed in collaboration with the Department for Media and Information Technology (LIU, Norrkping) and the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudementary script language that is used to declare operations which are performed over the frames of the trajectory.
The results can then be viewed in the different windows exposed in the application. 




## Status
[![Windows (MSVC 19)](https://github.com/scanberg/viamd/actions/workflows/windows.yml/badge.svg?branch=master)](https://github.com/scanberg/viamd/actions/workflows/windows.yml)
[![Ubuntu 20.04 (GCC 9)](https://github.com/scanberg/viamd/actions/workflows/ubuntu20.yml/badge.svg)](https://github.com/scanberg/viamd/actions/workflows/ubuntu20.yml)
[![Ubuntu 22.04 (GCC 11)](https://github.com/scanberg/viamd/actions/workflows/ubuntu22.yml/badge.svg)](https://github.com/scanberg/viamd/actions/workflows/ubuntu22.yml)
[![MacOS (Clang)](https://github.com/scanberg/viamd/actions/workflows/macos.yml/badge.svg)](https://github.com/scanberg/viamd/actions/workflows/macos.yml)

## Running VIAMD 

### Windows
For windows, we recommend to use the latest binary available on the [release page](https://github.com/scanberg/viamd/releases/).

### Ubuntu and MacOs
To [build](https://github.com/scanberg/viamd/wiki/0.-Building) VIAMD on your machine, you can follow the procedure described in details in the wiki for [Linux](https://github.com/scanberg/viamd/wiki/0.-Building#linux) and [MacOS](https://github.com/scanberg/viamd/wiki/0.-Building#mac).

## Documentation
Documentation about VIAMD is available on the github [wiki](https://github.com/scanberg/viamd/wiki). The two first chapters relate to the [visual](https://github.com/scanberg/viamd/wiki/1.-Visual) and [analysis](https://github.com/scanberg/viamd/wiki/2.-Analysis) features respectively, where we highlight the interactive part of software. The third chapter focus on the VIAMD [language](https://github.com/scanberg/viamd/wiki/3.-Language) used for scripting and the fourth chapter propose a serie of [tutorial](https://github.com/scanberg/viamd/wiki/4.-Tutorials) (under construction). 

A series of videos is available on [youtube](https://youtube.com/playlist?list=PLNx9MpJY8ffr9CeK7WefdOnuGRw_E5rSj&si=VatBHEwiL7jWyhPK).

## Update
If you want to stay informed about the latest update of VIAMD, please register your email address to the [form](https://forms.gle/fAxuWob8nMLcrS5h9). 

## Citations:
* General Framework:
  * R Sknberg, I Hotz, A Ynnerman, M Linares, VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics, J. Chem. Inf. Model. 2023, 63, 23, 73827391 https://doi.org/10.1021/acs.jcim.3c01033
  * R Sknberg, C Knig, P Norman, M Linares, D Jnsson, I Hotz, A Ynnerman, VIA-MD: Visual Interactive Analysis of Molecular Dynamics, 2018, Eurographics Proceedings, p. 1927

* Specific tool:
  * Selection tool: Robin Sknberg, Mathieu Linares, Martin Falk, Ingrid Hotz, Anders Ynnerman, MolFind-Integrated Multi-Selection Schemes for Complex Molecular Structures, 2019, The Eurographics Association, p. 17-21
  * Shape Space and Spatial Distribution Function: Robin Sknberg, Martin Falk, Mathieu Linares, Anders Ynnerman, Ingrid Hotz, Tracking Internal Frames of Reference for Consistent Molecular Distribution Functions, 2021, IEEE Transactions on Visualization and Computer Graphics, 28 (9), 3126-3137

## Financial Support
VIAMD has received constant financial support since 2018 from the Swedish e-Research center ([SeRC](https://e-science.se/)) and the [Wallenberg Foundation](https://www.wallenberg.org/en)

VIAMD is supported by [InfraVis](https://infravis.se/) for specific projets:
- Parser for LAMMPS file (2301-5217 / 140 hours)
- Interactice analysis of VeloxChem file (interactive analysis of orbitals and spectra plotting) (600 hours) 







## Acknowledgements

https://github.com/glfw/glfw

https://github.com/dougbinks/enkiTS

https://github.com/ocornut/imgui

https://github.com/epezent/implot

https://github.com/BalazsJako/ImGuiColorTextEdit

https://github.com/skaslev/gl3w

https://github.com/max0x7ba/atomic_queue

https://github.com/mlabbe/nativefiledialog

https://github.com/nothings/stb

#

Owner

GitHub Events