Enabling Real-Time Visualisations of Molecular Dynamics Properties in DL_POLY_4 (Proof of Concept)

Project reference: 1511

This project has the goal of extending the widely used DL_POLY_4 molecular dynamics software package to enable 3D visualisations of molecular simulations in real-time, representing a significant advance for the DL_POLY code. The project will involve extending the DL_POLY_4 source code and will see the exploitation of state-of-the-art visualization toolkits.

Project mentor: Alin Elena and Michael Lysaght

Site Co-ordinator: Simon Wong

Learning Outcomes

• The student will learn about visualization and how to exploit visualization software and toolkits on large-scale HPC systems.
• The student will learn about Qt5 and client/side and their usage for scientific visualization
• The student will learn how to run state-of-the-art parallel Molecular Dynamics software on heterogeneous HPC systems.

Student Prerequisites (compulsory)

• The student should have a good knowledge of C/C++.
• Qt5 and server/client, e.g. zeromq
• The student should be able to demonstrate a basic knowledge of 3D visualisation.
• The student should have some experience with numerical methods and technical computing in general

Student Prerequisites (desirable)

none

Training Materials

• Background reading on ZeroMQ: http://zeromq.org/
• Background reading onQt5 http://qt-project.org/
• Background reading on VTK: http://www.vtk.org/
• Background reading on DL_POLY_4: https://www.stfc.ac.uk/SCD/44516.aspx

Workplan

• Week 1: Training
• Week 2: Literature review
• Week 3: Enabling client/server side
• Week 4: Enabling client/server side
• Week 5: Enabling visualisation of 2D properties
• Week 6 Enabling visualisations of 3D properties
• Week 7: Performance analysis of the framework
• Week 8 Report writing.

Final Product Description

A version of the molecular dynamics code enabled for real-time visualizations of molecular dynamics simulations of materials and biomolecules.

Adapting the Project – Increasing the Difficulty

Initially the project will focus on a reliable client/server framework for data exchange between the MD engine and visualization app. Subsequently the project will concentrate on data visualiation received from application, 2D and 3D data using both qt and vtk contexts.

Adapting the Project – Decreasing the Difficulty

Focus on the more basic exploitations of visualization (2D properties), with less emphasis on the performance aspects.

Resources

Access to local supercomputing resources at ICHEC including HPC hardware and software (DL_POLY).

Organization

Irish Centre for High-End Computing