Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN

Area of Science:

• Computational physics
• X-ray science
• Molecular dynamics

Background:

• XMDYN is a molecular dynamics code for simulating ultrafast X-ray pulse interactions with atomic assemblies.
• It is part of the SIMEX simulation platform for computational single-particle imaging at the European XFEL.
• Efficient simulation of large atomic systems is crucial for understanding X-ray-matter interactions.

Purpose of the Study:

• To improve the computational performance of the XMDYN code.
• To enable efficient simulations of large, X-ray irradiated atomic assemblies.
• To support preparatory simulations for single-particle imaging experiments.

Main Methods:

• Incorporation of the existing tree-algorithm based Coulomb solver, PEPC, into XMDYN.
• Development and integration of a novel tree-algorithm based secondary ionization solver into XMDYN.
• Utilizing these enhanced solvers for molecular dynamics simulations.

Main Results:

• Successful integration of tree-algorithm solvers significantly boosts XMDYN's performance.
• Enables computationally efficient simulations for large atomic systems, including proteins and viruses.
• Provides a pathway for guiding experimental design in ultrafast X-ray science.

Conclusions:

• The enhanced XMDYN code offers a powerful tool for simulating X-ray interactions with complex biological systems.
• These advancements are vital for the future of single-particle imaging experiments at facilities like the European XFEL.
• The integration paves the way for more accurate and efficient computational studies in ultrafast X-ray science.