Universally Adaptable Multiscale Molecular Dynamics (UAMMD). A native-GPU software ecosystem for complex fluids, soft matter, and beyond
Description
We introduce UAMMD (Universally Adaptable Multiscale Molecular Dynamics), a novel software infrastructure tailored for mesoscale complex fluid simulations on GPUs. The UAMMD library encompasses a comprehensive range of computational schemes optimized for the GPU, spanning from molecular dynamics to immersed boundary fluctuating-hydrodynamics. Developed in CUDA/C++14, this header-only open-source software serves both as a simulation engine and as a library with a modular architecture, offering a vast array of independent modules, categorized as interactors (neighbor search, bonded, non-bonded and electrostatic interactions, etc.) and integrators (molecular dynamics, dissipative particle dynamics, smooth particle hydrodynamics, Brownian hydrodynamics and a rather complete array of Immersed Boundary -IB- schemes). UAMMD excels in schemes that couple particle-based elastic structures with continuum fields in different regions of the mesoscale. To that end, thermal fluctuations can be added in physically consistent ways, and fast modes can be eliminated to adapt UAMMD to different regimes (compressible or incompressible flow, inertial or Stokesian dynamics, etc.). Thus, UAMMD is extremely useful for coarse-grained simulations of nanoparticles, and soft and biological matter (from proteins to viruses and micro-swimmers). Importantly, all UAMMD developments are hand-to-hand validated against experimental techniques, and it has proven to quantitatively reproduce experimental signals from quartz-crystal microbalance, atomic force microscopy, magnetic sensors, optic-matter interaction and ultrasound.