Making Waves on Mira

Estimated reading time: 8 minutes

“Our work demonstrates that, in nanoscale systems, one has to think about van der Waals forces in terms of interactions between waves instead of interactions between particles,” Tkatchenko said.

The MBD model is the first to demonstrate the importance of collective charge density fluctuations, rather than the sum of local fluctuations, in describing non-bonded interactions between nanostructures. The MBD model also uses a first-principles-based approach—meaning it relies on fundamental physics rather than being shaped by experimental data—which allows researchers to simulate systems in detail that may be difficult or impossible to observe in the laboratory.

“They applied and tested their van der Waals model on a diverse set of nanostructures with many shapes and sizes,” said Alvaro Vazquez-Mayagoitia, ALCF assistant computational scientist.

Validating the model required extremely powerful computation. Among the nanostructures simulated were proteins, as well as carbon-based nanostructures that are incredibly strong and popular for material applications, including 1-D carbyne-like nanowires, 2-D graphene sheets and 3-D carbon nanotubes comprised of a few thousand of atoms each.

A few thousand atoms may not sound like a lot for a supercomputer, but for first-principles simulations, it’s not the number of atoms that are the computational burden—it’s their electrons. The determination of the electronic structures is extremely computational intensive. Mira computes up to 10 quadrillion calculations per second, and thousands of its processors run in parallel to simulate a near-realistic electronic structure at the nanoscale.

“The theory we used can be partitioned to run many simultaneous calculations at one time,” DiStasio said. “Mira is well-designed for running these interdependent calculations very efficiently.”

Unlike nanostructures, which are static simulations, the team’s dynamic liquid water simulations take many continuous weeks on several thousand processors to model structural changes in response to different solutes and high temperatures and pressures.

By working closely with Alvaro Vazquez-Mayagoitia and other ALCF staff, DiStasio’s team modified their codes to run efficiently on Mira’s HPC environment. Vazquez-Mayagoitia assisted in porting and adapting the first-principles Quantum ESPRESSO (QE) code to Mira. The improvements to the QE software followed a twofold strategy: better use of Mira’s processors and reduction of interprocessor communication. New multi-threaded OpenMP routines and use of asynchronous communications, which reduce delays by allowing some processors to transmit data while others continue computing, enabled a speed up of QE simulations by up to 40 percent.

“For ALCF, it is a priority to support science projects by understanding what they need to get their simulations done using big computers,” Alvaro said. “By assisting projects with modernizing their open source codes, we accelerate new discoveries that can benefit people around the globe.”

Now, they want to take the MBD model and integrate it with the dynamic water simulations, which could significantly improve the accuracy and predictive ability of simulations important to aqueous ion batteries, drug delivery across cell membranes and hydrogen fuel cells, among many other systems.

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