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viamd

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Visual Interactive Analysis of Molecular Dynamics

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# VIAMD
Visual Interactive Analysis of Molecular Dynamics

VIAMD is an interactive analysis tool for molecular dynamics (MD) written in C/C++. VIAMD is developed at the PDC Center for High Performance Computing (KTH, Stockholm). It exposes a rudimentary scripting language for declaring operations performed across trajectory frames.
The results can then be viewed in the different windows exposed in the application. 

<img src="https://github.com/scanberg/viamd/assets/38646069/5651ef62-28bc-4f41-8234-75cf9ba85612" alt="This is an overview of the viamd software" width="800"/>

## 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 22.04 (GCC 11)](https://github.com/scanberg/viamd/actions/workflows/ubuntu22.yml/badge.svg)](https://github.com/scanberg/viamd/actions/workflows/ubuntu22.yml)
[![Ubuntu 24.04 (GCC 13)](https://github.com/scanberg/viamd/actions/workflows/ubuntu24.yml/badge.svg)](https://github.com/scanberg/viamd/actions/workflows/ubuntu24.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 using the latest binary available on the [release page](https://github.com/scanberg/viamd/releases/).

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

**NOTE:** To be able to run this, you will have to do some magic in a terminal to be able to run the app bundle since we do not have code signing.

```xattr -dr com.apple.quarantine viamd.app```

### Building for Ubuntu and macOS
To [build](https://github.com/scanberg/viamd/wiki/0.-Building) VIAMD on your machine, you can follow the procedure described in detail 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 first two 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 the software. The third chapter focuses on the VIAMD [language](https://github.com/scanberg/viamd/wiki/3.-Language) used for scripting, and the fourth chapter proposes a series 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 updates of VIAMD, please register your email address on the [form](https://forms.gle/fAxuWob8nMLcrS5h9).

## Citations:
* General Framework:
  * R Skånberg, I Hotz, A Ynnerman, M Linares, VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics, J. Chem. Inf. Model. 2023, 63, 23, 7382–7391 https://doi.org/10.1021/acs.jcim.3c01033
  * R Skånberg, C König, P Norman, M Linares, D Jönsson, I Hotz, A Ynnerman, VIA-MD: Visual Interactive Analysis of Molecular Dynamics, 2018, Eurographics Proceedings, p. 19–27

* Specific tool:
  * Selection tool: Robin Skånberg, 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 Skånberg, 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

<img src="https://raw.githubusercontent.com/scanberg/viamd/master/docs/images/serc.png" height="75" >
 &nbsp;&nbsp;&nbsp;
<img src="https://raw.githubusercontent.com/scanberg/viamd/master/docs/images/wallenberg.jpg" height="75" >
 &nbsp;&nbsp;&nbsp;
<img src="https://raw.githubusercontent.com/scanberg/viamd/master/docs/images/infravis.png" height="75" >

* VIAMD has received 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 currently supported as a development project in [InfraVis](https://infravis.se/)

## 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

#

<img src="https://github.com/user-attachments/assets/39b69b10-88a1-43a7-9d69-68513ac4e632" width="150" alt="This is the VIAMD logo" >

viamd

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