Opendda: a Novel High-Performance Computational Framework for the Discrete Dipole Approximation

Abstract

This work presents a highly optimized computational framework for the Discrete Dipole Approximation, a numerical method for calculating the optical properties associated with a target of arbitrary geometry that is widely used in atmospheric, astrophysical and industrial simulations. Core optimizations include the bit-fielding of integer data and iterative methods that complement a new Discrete Fourier Transform (DFT) kernel, which efficiently calculates the matrixvector products required by these iterative solution schemes. The new kernel performs the requisite 3-D DFTs as ensembles of 1-D transforms, and by doing so, is able to reduce the number of constituent 1-D transforms by 60% and the memory by over 80%. The optimizations also facilitate the use of parallel techniques to further enhance the performance. Complete OpenMP-based shared-memory and MPI-based distributed-memory implementations have been created to take full advantage of the various architectures. Several benchmarks of the new framework indicate extremely favorable performance and scalability.

Calculations of the mass absorption cross sections for carbonaceous nanoparticles modeling soot

“…In this respect, the PDI method thus differs from the usual implementations of the Discrete Dipole Approximation (DDA) method [22,23] that are rather based on the scattering of dipoles on a regular cartesian grid to allow use of fast Fourier transform algorithms. Note that despite this arbitrary discretization of the volume of the nanostructure under consideration, DDA approaches are much often used in the literature especially because of the wide dissemination of corresponding open source codes [24,[29][30][31], in contrast to the PDI method for which no general code is available. As the exact atomic positions are often not known in many carbonaceous structures, especially the soot systems investigated here, the PDI method thus could appear irrelevant at first sight.…”

Understanding the photothermal effect of gold nanostars and nanorods for biomedical applications

“…DDA calculations were performed using OpenDDA soware, running on a Linux system. 49 The size and shape of the gold nanostructures were assumed to be identical to the TEM images and the gold nanostructures were described by 3D Cartesian coordinates. Typically, GNRs were modelled as cylinders with hemispherical caps, lying along the x-axis.…”

Surface-enhanced Raman spectroscopy for biomedical diagnostics and imaging

“…The most commonly used DDA code is DDSCAT, written in FORTRAN 90, which includes functions of various target geometries and periodic structures [174]. Recently, C based codes as well as Matlab based codes have been published [173,[175][176].…”