Molecular Dynamics Simulations: Useful, yes. But Predictive?
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36 MATERIALS SCIENCE↗
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Validation of Computational Fluid Dynamics Simulations for Biological Performance Assessment in Hydropower units (Final Report)
The biological performance assessment (BioPA) toolset developed by Pacific Northwest National Laboratory (PNNL) estimates the relative biological performance of fish passage at a hydroelectric power turbine unit. The tool is based on the use of computational fluid dynamics (CFD) and fish biological response relationships. The recent release, BioPA-v3, is based on directly computed trajectory and collision of material Lagrangian particles using CFD simulation codes rather than the prior version that relies on Tecplot to compute streamtrace trajectories. Before modifying the toolset, a series of validation tests were performed at the various steps of modification in the toolset. Validation is a critical step of any numerical investigation that reflects the accuracy and reliability of the predicted results. It raises the confidence level of the user to use the modified version of the BioPA toolset. Several test cases were simulated and compared, where available, to observed data. The trajectory and collision of the small spherical and cylindrical particles in a water flume were compared to in-house experiments. The CFD predicted collision rate and flow field compared well with experimental observation for vane array and large cylinder as target bodies. Next, the CFD-predicted flow field and hydraulic performance of a laboratory-scale model of a Francis turbine was also successfully validated. Note that the trajectory of the particles is significantly affected by the flow field in such extreme conditions. In addition to the particle trajectories and flow field, the collision detection method employed in the CFD simulations was also successfully validated. The CFD predicted impact velocity, collision time, velocity, and trajectory of a sphere excellently matched with analytical value for a bouncing ball in the elastic collision. A similar approach was also tested and successfully validated for a collision of sphere with a 45° inclined plane. After successfully validating different cases, the BioPA toolset was modified to use direct output of the CFD prediction and the new version can be used in evaluating biological performance at hydroelectric turbines.
13 HYDRO ENERGY↗
Molecular dynamics simulation of self-rotation effects on ultra-precision polishing of single-crystal copper
Understanding the behaviors of the material removal mechanism of ultra-precision polishing process has been a critical issue of generating well-formed surface. In order to make clear the abrasive self-rotation effects on material removal at the atomic level, a three-dimensional molecular dynamics (MD) model is conducted to study the mechanics of ultra-precision polishing on single-crystal copper with a diamond abrasive and the effects of abrasive self-rotation velocity and direction. Morse potential energy function and EAM potential energy function are applied to model the copper/diamond and copper/copper interactions, respectively. The simulation results show that the deformation mechanism of single-crystal copper is due to the formation and movement of dislocations in the specimen. In addition, with the increasing of abrasive self-rotation velocity, the deformation mechanism falls from cutting to plowing regimes. The abrasive self-rotation velocity and direction have effects on the morphology and quality of the specimen surface, distribution and evolution of defects under the surface of the specimen. Also, the interatomic force between abrasive and specimen is studied to account for the effects of different polishing conditions.
36 MATERIALS SCIENCE↗
A Dynamic Simulation of the Indirect Land Use Implications of Recent Biofuel Production and Use in the United States.
The global indirect land use change (ILUC) implications of biofuel use in the United States of America (USA) from 2001 to 2010 are evaluated with a dynamic general equilibrium model. The effects of biofuels production on agricultural land area vary by year; from a net expansion of 0.17 ha per 1000 gallons produced (2002) to a net contraction of -0.13 ha per 1000 gallons (2018) in Case 1 of our simulation. In accordance with the general narrative about the implications of biofuel policy, agricultural land area increased in many regions of the world. However, oil-export dependent economies experienced agricultural land contraction because of reductions in their revenues. Reducing crude oil imports is a major goal of biofuel policy, but the land use change implications have received little attention in the literature. Simulations evaluating the effects of doubling supply elasticities for land and fossil resources show that these parameters can significantly influence the land use change estimates. Therefore, research that provides empirically-based and spatially-detailed agricultural land-supply curves and capability to project future fossil energy prices is critical for improving estimates of the effects of biofuel policy on land use.
Oladosu, Gbadebo A.↗
AladynPi – Adaptive Neural Network Molecular Dynamics Simulation Code with Physically Informed Potential: Computational Materials Mini-Application
This report provides an overview and description of commands used in the Computational Materials mini-application, AladynPi. AladynPi is an extension of a previously released mini-application, Aladyn (https://github.com/nasa/aladyn; Yamakov, V.I., and Glaessgen, E.H., NASA/TM-2018-220104). Aladyn and AladynPi are basic molecular dynamics codes written in FORTRAN 2003, which are designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory method. An input for the ANN is a set of structure coefficients, characterizing the local atomic environment of each atom, for which the atomic energy is obtained in the ANN inference process. In Aladyn, the ANN gives directly the energy of interatomic interactions. In AladynPi, the ANN gives optimized parameters for a predefined empirical function, known as bond-order-potential (BOP). The parameterized BOP function is then used to calculate the energy. AladynPi code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing manycore architectures based on graphic processing units (GPUs). The effort is supported by the High Performance Computing incubator (HPCi) project at NASA Langley Research Center.
Yamakov, Vesselin I.↗
Modeling Electron Injection at Semiconductor–Molecule Interfaces using First-Principles Dynamics Simulation: Effects of Nonadiabatic Coupling, Self-energy, and Surface Models
Excited electron transfer across semiconductor–molecule heterogeneous interfaces is central to various future electronic and optoelectronic devices. At the same time, first-principles modeling of such dynamical processes remains as a great challenge in theoretical chemistry and condensed matter physics for developing better understanding at the molecular scale. Excited electron transfer from a molecule to semiconductor surface is a particularly difficult case to model accurately, because the initial state of such an electron injection process often lies deep within the dense manifold of the conduction band states in the semiconductor. Nonadiabatic couplings and energy level alignments at such interfaces as well as the finite size error of the surface model all play important roles in numerical modeling of electron injection via first-principles theory. Here, using representative interfaces between a well-defined hydrogen-terminated Si(111) surface and series of covalently adsorbed conjugated molecules, we investigate the extent to which these theoretical and numerical considerations influence the description of electron injection at the semiconductor–molecule interface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
MRI Measurements and Granular Dynamics Simulation of Segregation of Granular Mixture
A counter intuitive axial segregation phenomenon in a rotating horizontal cylinder has recently captured attention of many researchers in different disciplines. There is a growing consensus that the interplay between the particle dynamics and the evolution of the internal structure during the segregation process must be carefully investigated. Magnetic resonance imaging (MRI) has been used to non-invasively obtain much needed dynamic/static information such as velocity and concentration profiles, and it has proven to be capable of depicting the evolution of segregation processes. Segregation in a rotating cylinder involves two processes: the first is to transport small particles in the radial direction to form a radial core, and the second is to transform the radial core into axially segregated bands. Percolation and/or "stopping" have been proposed as mechanisms for the radial segregation. As to mechanisms for axial band formation, much less is known. The difference in the dynamic angle of repose has been proposed to segregate different components in the axial direction. Recently, Hill and Kakalios have reported that particles mix or demix depending upon the competition between diffusion and preferential drift whose order can be determined by the dynamic angle of repose through the adjustment of the rotation rate. We claim that the dynamic angle of repose could be one of the causes, however, it fails to offer reasonable explanations for certain aspects of the axial migration. For example, we always observe that the radial segregation precedes the axial segregation and small particles migrate in the radial direction to form an axially extended radial core. It then transforms into axially segregated bands. By definition, the effects of the dynamic angle of repose are restricted near the free surface where the flowing layer is present. However, during the process of transforming from the radially segregated core to axially segregated bands, small particles located in the deep core region, which is untouched by the flowing layer, also completely disappear. Usually, the dynamics angle of repose are uniquely defined for individual species to characterize particle properties, and the dynamic angle of repose thus defined provides little information for the dynamic angle of repose of the mixture since the concentration ratio and the internal packing structure do not remain the same during the segregation processes. Under microgravity environment, the dynamics angle of repose argument does not hold since there is simply no flowing layer to influence/determine the preferred directions of segregation. We have thus designed an experiment so that the effects of the dynamic angle of repose can be minimized by filling the cylinder almost completely full. Small particles still formed a radial core and also migrated to form axial bands. As ground based experiments we have designed and conducted both 2D and 3D segregation experiments. The 2D experiments are performed using a thin cylinder (the gap between two end caps is about 5 mm) filled with different combinations of particles. The 3D experiments are conducted with a long cylinder of its length and diameter of 27cm and 7cm, respectively. Results of 2D experiments indicate that different mechanisms govern particle motion in regions near and far from the axis of rotation. Results of 3D experiments indicate that a series of collapses of microstructures of particle packing (micro-collapses) may be responsible for the creation of voids for small particles to migrate through in the axial direction. We have successfully eliminated the dynamic angle of repose as a cause for segregation, however, by almost completely filling the cylinder with the particles, we have lost an opportunity to investigate a possibility of particle "mobility" being a cause for segregation which requires a flowing surface but not the difference in the angle of repose. This is currently being investigated.
Nakagawa, M.↗
Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results
We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Equation of state of CH1.36: First-principles molecular dynamics simulations and shock-and-release wave speed measurements
In this paper, we report the computation and measurement of the equation of state of a plastic with composition CH 1.36 . The computational scheme employed is density functional theory based molecular dynamics, at the conditions: 1.8 g/cm 3 < ρ < 10 g/cm 3 , and 4000 K < T < 100 000 K. Experimental measurements are of the shock speeds in a geometry in which the plastic is directly abutting a different material, liquid deuterium, from which release wave behavior in the plastic can be deduced. After fitting our computed pressure and internal energy with a Mie-Grüneisen free energy model, we predict the principal shock Hugoniot and various shock-and-release paths and show that they agree with both recently published laser-shock data and our new data regarding the shock speeds on release. We also establish that, at least in the particular (ρ,T) range considered, the equation of state of this complex two-component material is well described by an equal pressure and temperature mixture of pure C and H equations of state with a composition-weighted additive-volume assumption. This observation, together with our fit to the limited-range simulation data, can form the basis for the construction of an accurate wide-range equation of state model for this plastic. Implications for its use as an ablator in inertial confinement fusion capsules are discussed.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Investigating the magnetovolume effect in isotropic body-centered-cubic iron using spin-lattice dynamics simulations
The understanding of the magnetovolume effect lacks explicit consideration of spin-lattice coupling at the atomic level, despite abundant theoretical and experimental studies throughout the years. This research gap is filled by the recently developed spin-lattice dynamics technique implemented in this study, which investigates the magnetovolume effect of isotropic body-centered-cubic (BCC) iron, a topic that has previously been subject to macroscopic analysis only. This approach demonstrates the magnetic anomaly followed by the volumetric changes associated with the effect, each characterized by the corresponding field-induced inflection temperature. The temperature of the heat capacity peaks is useful in determining the temperature for retarding the atomic volume increase. Moreover, this work shows the correlation between the effects of temperature and field strength in determining the equilibrium atomic volume of a ferromagnetic material under a magnetic field.
36 MATERIALS SCIENCE↗
Quantitative in-situ scanning electron microscope pull-out experiments and molecular dynamics simulations of carbon nanotubes embedded in palladium
In this paper, we present our results of experimental and numerical pull-out tests on carbon nanotubes (CNTs) embedded in palladium. We prepared simple specimens by employing standard silicon wafers, physical vapor deposition of palladium and deposition of CNTs with a simple drop coating technique. An AFM cantilever with known stiffness connected to a nanomanipulation system was utilized inside a scanning electron microscope (SEM) as a force sensor to determine forces acting on a CNT during the pull-out process. SEM-images of the cantilever attached to a CNT have been evaluated for subsequent displacement steps with greyscale correlation to determine the cantilever deflection. We compare the experimentally obtained pull-out forces with values of numerical investigations by means of molecular dynamics and give interpretations for deviations according to material impurities or defects and their influence on the pull-out data. We find a very good agreement of force data from simulation and experiment, which is 17 nN and in the range of 10–61 nN, respectively. Our findings contribute to the ongoing research of the mechanical characterization of CNT-metal interfaces. This is of significant interest for the design of future mechanical sensors utilizing the intrinsic piezoresistive effect of CNTs or other future devices incorporating CNT-metal interfaces.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Atomistic Insights into Nucleation and Formation of Hexagonal Boron Nitride on Nickel from First-Principles-Based Reactive Molecular Dynamics Simulations
Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni–B and Ni–N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.
Liu, Song↗
Start-to-end beam dynamics simulation of double triangular current profile generation in Argonne Wakefield Accelerator
Double triangular current profile (DT) gives a high transformer ratio which is the determining factor of the performance of collinear wakefield accelerator. This current profile can be generated using the emittance exchange (EEX) beam line. Argonne Wakefield Accelerator (AWA) facility plans to generate DT using the EEX beam line. We conducted start-to-end simulation for the AWA beam line using PARMELA code. Also, we discuss requirements of beam parameters for the generation of DT.
43 PARTICLE ACCELERATORS↗
Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces
In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory reproduces the excess accumulation of ethane at the interface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A new hydrocarbon empirical potential in angle bending calculation for the molecular dynamics simulation
Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Role of interfaces on the mechanical response of accumulative roll bonded nanometallic laminates investigated via dislocation dynamics simulations
Unraveling the effects of continuous dislocation interactions with interfaces, particularly at the nanometer length scales, is key to a broader understanding of plasticity, to material design and to material certification. To this end, this work proposes a novel discrete dislocation dynamics-based model for dislocation interface interactions tracking the fate of residual dislocation on interfaces. This new approach is used to predict the impact of dislocation/interface reactions on the overall mechanical behavior of accumulative roll bonded nanometallic laminates. The framework considers the dynamic evolution of the interface concurrent with a large network of dislocations, thus, accounting for the local short and long range effects of the dislocations under the external boundary conditions. Specifically, this study focuses on two-phase Fe/Cu nanometallic laminates, and investigates the role of the underlying elastic and plastic contrast of the Fe and the Cu layers on the composite response of the material. Moreover, the role of initial microstructures, resulting from processing is also investigated. Subsequently, the model is used to examine the effect of layer thickness and interface orientation relationship on the residual stresses of the relaxed microstructure. The associated mechanical response of these laminates are compared when loaded under normal direction compression, as well as shear compression. Finally, this work predicts a dominant effect of the layer thickness, as compared to the interface orientation relationship, on the macroscopic response and on the residual stresses of these nanolaminates, while the local dislocation transmission propensity through the interface is significantly influenced by the corresponding orientation relationship.
36 MATERIALS SCIENCE↗
Quantum-Based Molecular Dynamics Simulations Using Tensor Cores
Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix–matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born–Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born–Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Study of the effects of metalloid elements (P, C, B) on Fe-based amorphous alloys by ab initio molecular dynamics simulations
In order to understand the effects of the metalloid elements M (M: P, C, B) on the atomic structure, glass formation ability (GFA) and magnetic properties of Fe-based amorphous alloys, Fe{sub 80}P{sub 13}C{sub 7}, Fe{sub 80}P{sub 14}B{sub 6} and Fe{sub 80}B{sub 14}C{sub 6} amorphous alloys are chosen to study through first-principle simulations in the present work. The atomic structure characteristic of the three amorphous alloys is investigated through the pair distribution functions (PDFs) and Voronoi Polyhedra (VPs) analyses. The PDFs and VPs analyses suggest that the GFA of the three alloys dropped in the order of Fe{sub 80}P{sub 13}C{sub 7}, Fe{sub 80}P{sub 14}B{sub 6}, and Fe{sub 80}B{sub 14}C{sub 6}, which is well consistent with the experimental results. The density of state (DOS) of the three amorphous alloys is calculated to investigate their magnetic properties. Based on the DOS analysis, the average magnetic moment of Fe atom in Fe{sub 80}P{sub 13}C{sub 7} and Fe{sub 80}P{sub 14}B{sub 6} amorphous alloys can be estimated to be 1.71 μ{sub B} and 1.70 μ{sub B}, respectively, which are in acceptable agreement with the experimental results. However, the calculated average magnetic moment of Fe atom in Fe{sub 80}B{sub 14}C{sub 6} amorphous alloy is about 1.62 μ{sub B}, which is far less than the experimental result.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗