Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

• Published in: Computer physics communications Vol. 184; no. 5; pp. 1414 - 1425
• Main Authors: Fan, Zheyong, Siro, Topi, Harju, Ari
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.05.2013
• Subjects: CUDA; Graphics processing unit; Green–Kubo formula; Molecular dynamics simulation; Optimized algorithm; Performance evaluation; Thermal conductivity; Green–Kubo formula; CUDA; Performance evaluation; Optimized algorithm; Thermal conductivity; Molecular dynamics simulation; Graphics processing unit
• ISSN: 0010-4655; 1879-2944
• DOI: 10.1016/j.cpc.2013.01.008

Thermal conductivity is a very important property of a material both for testing theoretical models and for designing better practical devices such as more efficient thermoelectrics, and accurate and efficient calculations of thermal conductivity are very desirable. In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green–Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme, where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme, where a whole block is used for one particle and each thread in the block calculates one or several pair forces between the particle associated with the given block and its neighbor particle(s) associated with the given thread. For both schemes, two different classical potentials, namely, the Lennard-Jones potential and the rigid-ion potential are implemented. While the thread-scheme performs a little better for relatively large systems, the block-scheme performs much better for relatively small systems. The relative performance of the block-scheme over the thread-scheme also increases with the increasing cutoff radius. We validate the implementation by calculating lattice thermal conductivities of solid argon and lead telluride. The efficiency of our code makes it very promising to study thermal conductivity properties of more complicated materials, especially, materials with interesting nanostructures.