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In this paper a new algorithm for fast serial and parallel dynamics simulation of space robots as characterized by serial chain systems with a floating base is presented.
Computational fluid dynamics (CFD) enables modeling, analysis, and visualization of phenomena that would usually be impossible or extremely expensive to measure experimentally.
The presence of fault gouge has considerable influence on slip properties of tectonic faults and the physics of earthquake rupture. The presence of fluids within faults also plays a significant role in faulting and earthquake processes. In this study, we present 3-D discrete element simulations of dry and fluid-saturated granular fault gouge and analyze the effect of fluids on stick-slip behavior. Fluid flow is modeled using computational fluid dynamics based on the Navier-Stokes equations for an incompressible fluid and modified to take into account the presence of particles. Analysis of a long time train of slip events shows that the (1) drop in shear stress, (2) compaction of granular layer, and (3) the kinetic energy release during slip all increase in magnitude in the presence of an incompressible fluid, compared to dry conditions. We also observe that on average, the recurrence interval between slip events is longer for fluid-saturated granular fault gouge compared to the dry case. This observation is consistent with the occurrence of larger events in the presence of fluid. It is found that the increase in kinetic energy during slip events for saturated conditions can be attributed to the increased fluid flow during slip. Finally, our observations emphasize the important role that fluid flow and fluid-particle interactions play in tectonic fault zones and show in particular how discrete element method (DEM) models can help understand the hydromechanical processes that dictate fault slip.
The wood duck (Aix sponsa) is a common and important cavity-nesting duck in North America; however, we know very little about how changes in vital rates influence population growth rate (λ). We used estimates of fertility and survival of female wood ducks from our nest-box studies in South Carolina, Alabama, and Georgia, USA, to create a stage-based matrix population model. We conducted perturbation analyses and ranked elasticity values to examine the relative importance of 17 component vital rates to λ. Female survival is influenced by nest success, so we recognized this female heterogeneity in our analyses. Four vital rates showed the greatest importance to λ. Analytic elasticities were greatest for breeding season and nonbreeding season survival of females that nested successfully, followed by nest success and female recruitment to the breeding population. Differences in female quality were important to λ. Next, we used process variation of vital rates and conducted life-stage simulation analyses (LSA) followed by variance decomposition to determine the amount of variation in λ explained by each vital rate. Female recruitment to the breeding population explained 57.7% of the variation in λ followed by nest success (11.4%), and breeding and nonbreeding season survival of females that nested successfully (9.3% and 9.4%, respectively). Together these 4 vital rates explained 88% of the variation in λ. Mean asymptotic population growth rate (λ = 0.80 ± 0.08 [SD]) from LSA revealed a declining population. Recruitment of females hatched from nest boxes was insufficient to sustain the nest-box population. Furthermore, including yearling (SY) females that were produced outside of nest boxes (i.e., immigrants) increased recruitment rates 1.5 to 2 times more than when only SY females recruited from nest boxes were included. Future research that examines how emigration and immigration interact with survival and reproduction to influence local population dynamics of wood ducks will be important for identifying the value of nest-box programs to wood duck conservation and management.
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A method, called beatification, is presented for rapidly extracting weakly nonlinear Hamiltonian systems that describe the dynamics near equilibria of systems possessing Hamiltonian form in terms of noncanonical Poisson brackets. The procedure applies to systems like fluids and plasmas in terms of Eulerian variables that have such noncanonical Poisson brackets, i.e., brackets with nonstandard and possibly degenerate form. A collection of examples of both finite and infinite dimensions is presented.
Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.
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Trivalent rare-earth elements (REEs) readily incorporate in Ca-bearing minerals such as calcite (CaCO3), a phenomenon with important implications for the use of REEs as biogeochemical tracers as well as for environmental remediation. Despite substantial efforts, determining the incorporation modes of trivalent REEs in calcite has remained challenging due to their presence in multiple coordination environments. This is particularly problematic for the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. In this work, ab initio molecular dynamics (AIMD) simulations of Nd3+ incorporated in calcite were performed to resolve its incorporation modes. Nd3+ and Ca2+ have very similar ionic radii but the additional positive charge requires a charge compensation scheme (CCS). Five CCSs were considered in AIMD simulations, and the resulting atomic trajectories were then used to compute EXAFS spectra for direct fitting to a published experimental spectrum. The results of the fits indicated that Nd3+ incorporates at the Ca2+ site in calcite in a mixture of six- and seven-fold coordination environments and through three main incorporation modes: associated with a protonated nearest-neighbor Ca2+ vacancy, incorporated as NdOH2+, and charge compensated by a remote species (on the spatial scale probed by EXAFS). The incorporation of Nd3+ in calcite via multiple modes was consistent with previous work, but the AIMD-EXAFS approach allowed for resolving the nature, proportion, and structure of the different coordination environments.
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The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.