The ReaxFF reactive force-field : development, applications and future directions

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method

Strong scaling of general-purpose molecular dynamics simulations on GPUs

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, J. Comp. Phys. 117, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., J. Comp. Phys. 227, 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3,375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5x.Comment: 30 pages, 14 figure

Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)

Multi-component polymer systems are important for the development of new materials because of their ability to phase-separate or self-assemble into nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction with a soft, coarse-grained polymer model is an established technique to investigate these soft-matter systems. Here we present an im- plementation of this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is suitable to simulate large system sizes with up to billions of particles, yet versatile enough to study properties of different kinds of molecular architectures and interactions. We achieve efficiency of the simulations commissioning accelerators like GPUs on both workstations as well as supercomputers. The implementa- tion remains flexible and maintainable because of the implementation of the scientific programming language enhanced by OpenACC pragmas for the accelerators. We present implementation details and features of the program package, investigate the scalability of our implementation SOMA, and discuss two applications, which cover system sizes that are difficult to reach with other, common particle-based simulation methods

Development and Validation of ReaxFF Reactive Force Field for Hydrocarbon Chemistry Catalyzed by Nickel

To enable the study of hydrocarbon reactions catalyzed by nickel surfaces and particles using reactive molecular dynamics on thousands of atoms as a function of temperature and pressure, we have developed the ReaxFF reactive force field to describe adsorption, decomposition, reformation and desorption of hydrocarbons as they interact with the nickel surface. The ReaxFF parameters were determined by fitting to the geometries and energy surfaces from quantum mechanics (QM) calculations for a large number of reaction pathways for hydrocarbon molecules chemisorbed onto nickel (111), (100) and (110) surfaces, supplemented with QM equations of state for nickel and nickel carbides. We demonstrate the validity and accuracy of ReaxFF by applying it to study the reaction dynamics of hydrocarbons as catalyzed by nickel particles and surfaces. For the dissociation of methyl on the (111), (100), and stepped (111) surfaces of nickel, we observe the formation of chemisorbed CH plus subsurface carbide. We observe that the (111) surface is the least reactive, the (100) surface has the fastest reaction rates, and the stepped (111) surface has an intermediate reaction rate. The importance of surface defects in accelerating reaction rates is highlighted by these results

Carbohydrate-derived amphiphilic macromolecules: a biophysical structural characterization and analysis of binding behaviors to model membranes.

The design and synthesis of enhanced membrane-intercalating biomaterials for drug delivery or vascular membrane targeting is currently challenged by the lack of screening and prediction tools. The present work demonstrates the generation of a Quantitative Structural Activity Relationship model (QSAR) to make a priori predictions. Amphiphilic macromolecules (AMs) "stealth lipids" built on aldaric and uronic acids frameworks attached to poly(ethylene glycol) (PEG) polymer tails were developed to form self-assembling micelles. In the present study, a defined set of novel AM structures were investigated in terms of their binding to lipid membrane bilayers using Quartz Crystal Microbalance with Dissipation (QCM-D) experiments coupled with computational coarse-grained molecular dynamics (CG MD) and all-atom MD (AA MD) simulations. The CG MD simulations capture the insertion dynamics of the AM lipophilic backbones into the lipid bilayer with the PEGylated tail directed into bulk water. QCM-D measurements with Voigt viscoelastic model analysis enabled the quantitation of the mass gain and rate of interaction between the AM and the lipid bilayer surface. Thus, this study yielded insights about variations in the functional activity of AM materials with minute compositional or stereochemical differences based on membrane binding, which has translational potential for transplanting these materials in vivo. More broadly, it demonstrates an integrated computational-experimental approach, which can offer a promising strategy for the in silico design and screening of therapeutic candidate materials

Scalable parallel molecular dynamics algorithms for organic systems

A scalable parallel algorithm, Macro-Molecular Dynamics (MMD), has been developed for large-scale molecular dynamics simulations of organic macromolecules, based on space-time multi-resolution techniques and dynamic management of distributed lists. The algorithm also includes the calculation of long range forces using Fast Multipole Method (FMM). FMM is based on the octree data structure, in which each parent cell is divided into 8 child cells and this division continues until the cell size is equal to the non-bonded interaction cutoff length. Due to constant number of operations performed at each stage of the octree, the FMM algorithm scales as O(N). Design and analysis of MMD and FMM algorithms are presented. Scalability tests are performed on three tera-flop machines: 1024-processor Intel Xeon-based Linux cluster, SuperMike at LSU, 1184-processor IBM SP4 Marcellus and the 512-processor Compaq AlphaServer Emerald at the U.S. Army Engineer Research and Development Center (ERDC) MSRC. The tests show that the Linux cluster outperforms the SP4 for the MMD application. The tests also show significant effects of memory- and cache-sharing on the performance

Anisotropic shock sensitivity for β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine energetic material under compressive-shear loading from ReaxFF-ℓg reactive dynamics simulations

We report here the predictions on anisotropy of shock sensitivity and of chemical process initiation in single crystal β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (β-HMX) using compressive shear reactive dynamics (CS-RD) model with ReaxFF-ℓg reactive force field. Analysis of resolved shear stress induced by uniaxial compression along three shock directions normal to (110), (011), and (010) planes leads to identify eight slip systems as candidates for shear deformation. For each of the eight slip systems, non-equilibrium reactive dynamics simulations were carried out to determine thermal, mechanical, and chemical responses to shear deformation. Shock direction normal to (010) plane exhibits large shear stress barriers arising from steric hindrance between molecules of adjacent layers leading to local dramatic energy and temperature increases under shear flow that in turn accelerate chemical bond breaking and initial product formation processes, promoting further molecular decomposition and eventually transition to detonation. This suggests that single crystal β-HMX is sensitive to shocks in direction normal to (010) plane. Shock directions normal to (110) and (011) planes reveal significantly less steric hindrance, leading to more modest energy and temperature increases followed by slower chemical reaction initiation. Thus, shock directions normal to (110) and (011) planes are less sensitive than shock direction normal to (010) plane, which agree with interpretations from currently available plate impact experiments on HMX. This validation of CS-RD and ReaxFF for characterizing sensitivity of single crystal energetic materials indicates that these methods can be applied to study sensitivity for more complex polymer bonded explosives and solid composite propellants having complex microstructures, corrugated interfaces, as well as defects