Large-scale Ferrofluid Simulations on Graphics Processing Units

We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism of computations. For an ensemble consisting of one million of ferromagnetic particles, the performance of the proposed algorithm on a Tesla M2050 GPU demonstrated a computational-time speed-up of four order of magnitude compared to the performance of the sequential All-Pairs (AP) algorithm on a single-core CPU, and two order of magnitude compared to the performance of the optimized AP algorithm on the GPU. The accuracy of the scheme is corroborated by comparing the results of numerical simulations with theoretical predictions

Classical molecular simulations of complex industrially-important systems on the Intel Paragon

Advances in parallel supercomputing now make possible molecular-based engineering and science calculations that will soon revolutionize many technologies, such as those involving polymers and those involving aqueous electrolytes. We have developed a suite of message-passing codes for classical molecular simulation of such complex fluids and amorphous materials and have completed a number of demonstration calculations of problems of scientific and technological importance with each. In this overview paper we will outline the techniques for classical molecular simulation of these industrially-important systems on the Inter Paragon and we will summarize some of the important scientific and technical results of the varied applications, including the following: (1) Parallel codes for quatemion dynamics using techniques for handling long-range Coulombic forces allow study of ion pairing in supercritical aqueous electrolyte solutions. Ion pairing lies at the heart of technological problems with corrosion and solids deposition in industrial processes utilizing high temperature water. (2) Non-equilibrium, multiple time step molecular dynamics lets us investigate the rheology of molecular fluids. Such calculations enable the molecular-based design of new synthetic lubricants of importance in the automotive engines of the future. (3) Chain molecule Monte Carlo simulations in the Gibbs ensemble now permit calculation of phase equilibrium of long-chain molecular systems. With complementary equilibrium molecular dynamics (with multiple time steps) we have been able to gain fundamental insight into the technologically-important problem of liquid-liquid phase separation in polymer blends

Lattice Boltzmann simulations of anisotropic particles at liquid interfaces

Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while still resolving the microscopic structure of a large number of particles and of the local hydrodynamics. Due to its high degree of locality, the lattice Boltzmann method, when combined with a molecular dynamics solver and parallelized on modern supercomputers, provides a tool that allows such studies. Still, running simulations on hundreds of thousands of cores is not trivial. We report on our practical experiences when employing large fractions of an IBM Blue Gene/P system for our simulations. Then, we extend our model for spherical particles in multicomponent flows to anisotropic ellipsoidal objects rendering the shape of e.g. clay particles. The model is applied to a number of test cases including the adsorption of single particles at fluid interfaces and the formation and stabilization of Pickering emulsions or bijels.Comment: 10 pages, 5 figures; ParCFD 2011 proceedings contributio

Phase behavior and molecular scale dynamics of confined fluids using new atomistic simulation techniques: CRADA No. 1140 close-out report

The Mobil-nCUBE-Sandia CRADA No. 1140 was aimed at developing the tools and capabilities to model fluid phase behavior and flow in pores--ultimately leading to a better understanding of these phenomena. In this CRADA close-out report the collaboration`s original goals are revisited, the course of the CRADA is traced, and the technical accomplishments of the CRADA are presented

A parallel computing-visualization framework for polycrystalline minerals

In this report, we have reported some preliminary results in the development of a parallel computing-visualization framework for large-scale molecular dynamics simulations of polycrystals of minerals, which are geophysically relevant for Earth’s mantle. First, we have generated the input configurations of atoms belonging to various grains distributed in the space in a way, which resembles the polycrystalline structure of the minerals. The Input configuration is developed using Voronoi geometry. Thus generated polycrystalline system is simulated using the PolyCrystal Molecular Dynamics algorithm. Performance tests conducted using up to 256 processors and a couple of millions of atoms have shown that the computation time per MD step remains under 20 seconds. The other important part is the development of an efficient visualization system to interactively explore the massive three dimensional and time-dependent datasets produced by MD simulations. Some results are presented for the simulation of two-grain structure. The proposed framework is expected to be useful in simulations of more realistic and complex rheological (mechanical) properties of important Earth forming mineral phases under different conditions of stresses and temperatures

Understanding Dynamics of Polymers Under Confinement: A Molecular Dynamics and Neutron Scattering Study

The current study probes the structure, dynamics, and rheological behavior of associating polymers including ionomers in melts and solutions as well as conjugated polymers confined into nanoparticles, using molecular dynamics (MD) simulations and neutron scattering techniques. The study focuses on two families of associative polymers, ion containing macromolecules and conjugated polymers. Polymers that consist of ionizable groups along their backbone found uses in a broad range of applications. Examples include light weight energy storage and generation systems, and biomedical applications, where the polymers act as ion exchange membranes, and actuators. The ionic groups tend to form clusters that are in the core of many of the applications. Understanding the relationship of cluster properties and the structure and dynamics of ionizable polymers is crucial to optimize current applications and develop new materials with controlled transport, mechanical stability, and desired response to external stimuli. The first part of the study focuses on understanding the structure and dynamics of polystyrene sulfonate melts as the distribution of the ionizable groups varies with random, precise (number of carbons between ionizable groups is exact), and blocky distributions along the backbone, using atomistic MD simulations. We find that the shape and size distribution of clusters as well as the number of unique chains associated with each cluster are affected by the distribution of the ionic groups. The dynamics of the polymer and the mobility of the counterions are affected by both the number and size of the clusters as well as the number of polymer chains associated with each cluster. Following the understanding of the effects of the clusters on polymer melts, the study proceeds to probe the effects of nonlinear elongational flow on associating polymer melts, which are processed into viable materials under elongational flows. This effort contains two components a coarse grain, and an atomistic MD studies. We find that the response of the melts to elongational flows results from the evolution of both the ionic clusters and Van der Waals domains. The coarse grain study shows that clusters break and reform continuously as the chain stretches heterogeneously in the presence of elongational flow. The atomistic study provides details regarding the effect of chain and cluster rearrangements on the response to the flow. Following melts studies, the work probed the segmental motion of slightly sulfonated polystyrene in cyclohexane solutions using the quasi-elastic neutron scattering technique. We find constraint dynamics at larger length scales however the polymer remains mobile on smaller length scales. Adding a small amount of alcohol is enough to release the constraints within the ionic clusters and results in an increase in segmental polymer motion on all length scales. The last part of the study focused on understanding the effects of the number of rigid luminescent polymer molecules, their chemistries, and initial orientation, on the structure and dynamics of soft nanoparticles (referred to as “polydots”). We find that increasing the number of chains confined affects the internal conformation of the polymer chains where side chains substituting the polymer backbone affect the polydots’ shape and stability. Similar to a single macromolecule polydots, these NPs exhibit a glass-like dynamics with relaxation times in a range of microseconds

The rheology of chain molecules under shear

The rheology of chain molecules is a subject that comprises a wide variety of complex physical phenomena, challenging scientific questions, and fundamentally important practical applications. Computer simulation, molecular dynamics in particular, is a powerful tool to provide insight into these subjects on a molecular level. In this work, nonequilibrium molecular dynamics (NEMD) is employed to study linear and branched alkane chains in the melt state under transient and steady-state shearing conditions. This study focuses on three isomers of C30H62 (n-triacontane, squalane, and 9-n-octyldocosane) as well as a linear short-chain polyethylene (C100H202)- A transferable united atom potential is used to model these alkane chains, and the simulations of planar Couette flow are performed using the SLLOD algorithm and a multitimestep simulation technique implemented on massively parallel computer architectures. The strain rates studied in this work (108-1012 s-1) are extremely difficult to study experimentally yet typical of the severe conditions commonly found in engines and other machinery. Compared to experiment, NEMD and the united atom model underpredict the kinematic viscosities of n-triacontane and 9-n-octyldocosane but accurately predict the values for squalane (within 15%) at temperatures of 311 and 372 K. In addition, the predicted kinematic viscosity index values for both 9-n-octyldocosane and squalane are in quantitative agreement with experiment and represent the first such predictions by molecular simulation. Thus, this same general potential model and computational approach can be used to predict this important lubricant property for potential lubricants prior to their synthesis, offering the possibility of simulation guided lubricant design. Simulations of C100H202 under steady-state shearing conditions reveal a pronounced minimum in the hydrostatic pressure at an intermediate strain rate that is associated with a minimum in the intermolecular potential energy as well as transitions in the strain-rate-dependent behavior of several other viscous and structural properties of the system. Upon onset of shear, the stress overshoot curves calculated for C100 are in good quantitative agreement with Doi-Edwards theory if the terminal relaxation time is assumed to have the same strain-rate dependence as the calculated self-diffusion coefficient in the flow direction. This shear-enhanced diffusion offers a possible mechanism for strain-rate-dependent relaxation times in the fast flows of polymers