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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 343 records · Page 19
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DOE OSTI2014

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix—required to propagate the electron dynamics—, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The role of the transition state in polyatomic reactions: Initial state-selected reaction probabilities of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction

Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H–H–CH{sub 3}-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

GPU-based simulation of the two-dimensional unstable structure of gaseous oblique detonations

In this paper, the two-dimensional structure of unstable oblique detonations induced by the wedge from a supersonic combustible gas flow is simulated using the reactive Euler equations with a one-step Arrhenius chemistry model. A wide range of activation energy of the combustible mixture is considered. Computations are performed on the Graphical Processing Unit (GPU) to reduce the simulation runtimes. A large computational domain covered by a uniform mesh with high grid resolution is used to properly capture the development of instabilities and the formation of different transverse wave structures. After the initiation point, where the oblique shock transits into a detonation, an instability begins to manifest and in all cases, the left-running transverse waves first appear, followed by the subsequent emergence of right-running transverse waves forming the dual-head triple point structure. This study shows that for low activation energies, a long computational length must be carefully considered to reveal the unstable surface due to the slow growth rate of the instability. For high activation energies, the flow behind the unstable oblique detonation features the formation of unburnt gas pockets and strong vortex-pressure wave interaction resulting in a chaotic-like vortical structure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Simulated evolution of fluorophores for light emitting diodes

Organic light emitting diodes based on fluorophores with a propensity for thermally activated delayed fluorescence (TADF) are able to circumvent limitations imposed on device efficiency by spin statistics. Molecules with a propensity for TADF necessarily have two properties: a small gap between the lowest lying singlet and triplet excited states and a large transition dipole moment for fluorescence. In this work, we demonstrate the use of a genetic algorithm to search a region of chemical space for molecules with these properties. This algorithm is based on a flexible and intuitive representation of the molecule as a tree data structure, in which the nodes correspond to molecular fragments. Our implementation takes advantage of hybrid parallel graphics processing unit accelerated computer clusters to allow efficient sampling while retaining a reasonably accurate description of the electronic structure (in this case, CAM-B3LYP/6-31G{sup ∗∗}). In total, we have identified 3792 promising candidate fluorophores from a chemical space containing 1.26 × 10{sup 6} molecules. This required performing electronic structure calculations on only 7518 molecules, a small fraction of the full space. Several novel classes of molecules which show promise as fluorophores are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Forces and stress in second order Møller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach

The forces acting on the atoms as well as the stress tensor are crucial ingredients for calculating the structural and dynamical properties of systems in the condensed phase. Here, these derivatives of the total energy are evaluated for the second-order Møller-Plesset perturbation energy (MP2) in the framework of the resolution of identity Gaussian and plane waves method, in a way that is fully consistent with how the total energy is computed. This consistency is non-trivial, given the different ways employed to compute Coulomb, exchange, and canonical four center integrals, and allows, for example, for energy conserving dynamics in various ensembles. Based on this formalism, a massively parallel algorithm has been developed for finite and extended system. The designed parallel algorithm displays, with respect to the system size, cubic, quartic, and quintic requirements, respectively, for the memory, communication, and computation. All these requirements are reduced with an increasing number of processes, and the measured performance shows excellent parallel scalability and efficiency up to thousands of nodes. Additionally, the computationally more demanding quintic scaling steps can be accelerated by employing graphics processing units (GPU’s) showing, for large systems, a gain of almost a factor two compared to the standard central processing unit-only case. In this way, the evaluation of the derivatives of the RI-MP2 energy can be performed within a few minutes for systems containing hundreds of atoms and thousands of basis functions. With good time to solution, the implementation thus opens the possibility to perform molecular dynamics (MD) simulations in various ensembles (microcanonical ensemble and isobaric-isothermal ensemble) at the MP2 level of theory. Geometry optimization, full cell relaxation, and energy conserving MD simulations have been performed for a variety of molecular crystals including NH{sub 3}, CO{sub 2}, formic acid, and benzene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Oxygen transport properties estimation by classical trajectory–direct simulation Monte Carlo

Coupling direct simulation Monte Carlo (DSMC) simulations with classical trajectory calculations is a powerful tool to improve predictive capabilities of computational dilute gas dynamics. The considerable increase in computational effort outlined in early applications of the method can be compensated by running simulations on massively parallel computers. In particular, Graphics Processing Unit acceleration has been found quite effective in reducing computing time of classical trajectory (CT)-DSMC simulations. The aim of the present work is to study dilute molecular oxygen flows by modeling binary collisions, in the rigid rotor approximation, through an accurate Potential Energy Surface (PES), obtained by molecular beams scattering. The PES accuracy is assessed by calculating molecular oxygen transport properties by different equilibrium and non-equilibrium CT-DSMC based simulations that provide close values of the transport properties. Comparisons with available experimental data are presented and discussed in the temperature range 300–900 K, where vibrational degrees of freedom are expected to play a limited (but not always negligible) role.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Nonlinear electronic excitations in crystalline solids using meta-generalized gradient approximation and hybrid functional in time-dependent density functional theory

We develop methods to calculate electron dynamics in crystalline solids in real-time time-dependent density functional theory employing exchange-correlation potentials which reproduce band gap energies of dielectrics; a meta-generalized gradient approximation was proposed by Tran and Blaha [Phys. Rev. Lett. 102, 226401 (2009)] (TBm-BJ) and a hybrid functional was proposed by Heyd, Scuseria, and Ernzerhof [J. Chem. Phys. 118, 8207 (2003)] (HSE). In time evolution calculations employing the TB-mBJ potential, we have found it necessary to adopt the predictor-corrector step for a stable time evolution. We have developed a method to evaluate electronic excitation energy without referring to the energy functional which is unknown for the TB-mBJ potential. For the HSE functional, we have developed a method for the operation of the Fock-like term in Fourier space to facilitate efficient use of massive parallel computers equipped with graphic processing units. We compare electronic excitations in silicon and germanium induced by femtosecond laser pulses using the TB-mBJ, HSE, and a simple local density approximation (LDA). At low laser intensities, electronic excitations are found to be sensitive to the band gap energy: they are close to each other using TB-mBJ and HSE and are much smaller in LDA. At high laser intensities close to the damage threshold, electronic excitation energies do not differ much among the three cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Quantum transport modelling of silicon nanobeams using heterogeneous computing scheme

We report the development of a powerful method for quantum transport calculations of nanowire/nanobeam structures with large cross sectional area. Our approach to quantum transport is based on Green's functions and tight-binding potentials. A linear algebraic formulation allows us to harness the massively parallel nature of Graphics Processing Units (GPUs) and our implementation is based on a heterogeneous parallel computing scheme with traditional processors and GPUs working together. Using our software tool, the electronic and quantum transport properties of silicon nanobeams with a realistic cross sectional area of ∼22.7 nm{sup 2} and a length of ∼81.5 nm—comprising 105 000 Si atoms and 24 000 passivating H atoms in the scattering region—are investigated. The method also allows us to perform significant averaging over impurity configurations—all possible configurations were considered in the case of single impurities. Finally, the effect of the position and number of vacancy defects on the transport properties was considered. It is found that the configurations with the vacancies lying closer to the local density of states (LDOS) maxima have lower transmission functions than the configurations with the vacancies located at LDOS minima or far away from LDOS maxima, suggesting both a qualitative method to tune or estimate optimal impurity configurations as well as a physical picture that accounts for device variability. Finally, we provide performance benchmarks for structures as large as ∼42.5 nm{sup 2} cross section and ∼81.5 nm length.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N{sup 2.6} for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20x to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The order of three lowest-energy states of the six-electron harmonium at small force constant

The order of low-energy states of six-electron harmonium is uncertain in the case of strong correlation, which is not a desired situation for the model system being considered for future testing of approximate methods of quantum chemistry. The computational study of these states has been carried out at the frequency parameter ω = 0.01, using the variational method with the basis of symmetry-projected, explicitly correlated Gaussian (ECG) lobe functions. It has revealed that the six-electron harmonium at this confinement strength is an octahedral Wigner molecule, whose order of states is different than in the strong confinement regime and does not agree with the earlier predictions. The results obtained for ω = 0.5 and 10 are consistent with the findings based on the Hund’s rules for the s{sup 2}p{sup 4} electron configuration. Substantial part of the computations has been carried out on the graphical processing units and the efficiency of these devices in calculation of the integrals over ECG functions has been compared with traditional processors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Molecular dynamics investigation of hexagonal boron nitride sputtering and sputtered particle characteristics

The sputtering of hexagonal boron nitride (h-BN) by impacts of energetic xenon ions is investigated using a molecular dynamics (MD) model. The model is implemented within an open-source MD framework that utilizes graphics processing units to accelerate its calculations, allowing the sputtering process to be studied in much greater detail than has been feasible in the past. Integrated sputter yields are computed over a range of ion energies from 20 eV to 300 eV, and incidence angles from 0° to 75°. Sputtering of boron is shown to occur at energies as low as 40 eV at normal incidence, and sputtering of nitrogen at as low as 30 eV at normal incidence, suggesting a threshold energy between 20 eV and 40 eV. The sputter yields at 0° incidence are compared to existing experimental data and are shown to agree well over the range of ion energies investigated. The semi-empirical Bohdansky curve and an empirical exponential function are fit to the data at normal incidence, and the threshold energy for sputtering is calculated from the Bohdansky curve fit as 35 ± 2 eV. These results are shown to compare well with experimental observations that the threshold energy lies between 20 eV and 40 eV. It is demonstrated that h-BN sputters predominantly as atomic boron and diatomic nitrogen, and the velocity distribution function (VDF) of sputtered boron atoms is investigated. The calculated VDFs are found to reproduce the Sigmund-Thompson distribution predicted by Sigmund's linear cascade theory of sputtering. The average surface binding energy computed from Sigmund-Thompson curve fits is found to be 4.5 eV for ion energies of 100 eV and greater. This compares well to the value of 4.8 eV determined from independent experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Rise of an argon bubble in liquid steel in the presence of a transverse magnetic field

The rise of gaseous bubbles in viscous liquids is a fundamental problem in fluid physics, and it is also a common phenomenon in many industrial applications such as materials processing, food processing, and fusion reactor cooling. In this work, the motion of a single argon gas bubble rising in quiescent liquid steel under an external magnetic field is studied numerically using a Volume-of-Fluid method. To mitigate spurious velocities normally generated during numerical simulation of multiphase flows with large density differences, an improved algorithm for surface tension modeling, originally proposed by Wang and Tong [“Deformation and oscillations of a single gas bubble rising in a narrow vertical tube,” Int. J. Therm. Sci. 47, 221–228 (2008)] is implemented, validated and used in the present computations. The governing equations are integrated by a second-order space and time accurate numerical scheme, and implemented on multiple Graphics Processing Units with high parallel efficiency. The motion and terminal velocities of the rising bubble under different magnetic fields are compared and a reduction in rise velocity is seen in cases with the magnetic field applied. The shape deformation and the path of the bubble are discussed. An elongation of the bubble along the field direction is seen, and the physics behind these phenomena is discussed. The wake structures behind the bubble are visualized and effects of the magnetic field on the wake structures are presented. A modified drag coefficient is obtained to include the additional resistance force caused by adding a transverse magnetic field.

42 ENGINEERING↗
DOE OSTI2017

Rapid sampling of stochastic displacements in Brownian dynamics simulations

Here, we present a new method for sampling stochastic displacements in Brownian Dynamics (BD) simulations of colloidal scale particles. The method relies on a new formulation for Ewald summation of the Rotne-Prager-Yamakawa (RPY) tensor, which guarantees that the real-space and wave-space contributions to the tensor are independently symmetric and positive-definite for all possible particle configurations. Brownian displacements are drawn from a superposition of two independent samples: a wave-space (far-field or long-ranged) contribution, computed using techniques from fluctuating hydrodynamics and non-uniform fast Fourier transforms; and a real-space (near-field or short-ranged) correction, computed using a Krylov subspace method. The combined computational complexity of drawing these two independent samples scales linearly with the number of particles. The proposed method circumvents the super-linear scaling exhibited by all known iterative sampling methods applied directly to the RPY tensor that results from the power law growth of the condition number of tensor with the number of particles. For geometrically dense microstructures (fractal dimension equal three), the performance is independent of volume fraction, while for tenuous microstructures (fractal dimension less than three), such as gels and polymer solutions, the performance improves with decreasing volume fraction. This is in stark contrast with other related linear-scaling methods such as the force coupling method and the fluctuating immersed boundary method, for which performance degrades with decreasing volume fraction. Calculations for hard sphere dispersions and colloidal gels are illustrated and used to explore the role of microstructure on performance of the algorithm. In practice, the logarithmic part of the predicted scaling is not observed and the algorithm scales linearly for up to 4×10 6 particles, obtaining speed ups of over an order of magnitude over existing iterative methods, and making the cost of computing Brownian displacements comparable to the cost of computing deterministic displacements in BD simulations. Finally, a high-performance implementation employing non-uniform fast Fourier transforms implemented on graphics processing units and integrated with the software package HOOMD-blue is used for benchmarking.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Large scale Brownian dynamics of confined suspensions of rigid particles

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217–296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its “square” root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contraction

Here, we present a reduced scaling formulation of the state specific complete active space second-order perturbation method (CASPT2) requiring O( N 4 ) operations and O( N 2 ) memory for a fixed active space, where N is proportional to system size. Motivated by the properties of the Kronecker sum, we introduce the supporting subspace technique (SST), which decomposes the CASPT2 linear equations into two parts: a single-reference MP2 energy term using dressed orbitals, plus a reduced linear system with dimension scaling as O( N 2 ). Together with Laplace quadrature, the SST allows us to reformulate CASPT2 using a MP2 energy computation and Fock builds. By further applying the tensor hyper-contraction (THC) approximation, the MP2-like term can be computed with O( N 4 ) operations, and the remainder can be solved with O( N 3 ) operations using the preconditioned conjugate gradient method. This is the first application of THC in the context of multi-reference methods. We also developed an efficient implementation of the method by utilizing graphical processing units and exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method against conventional CASPT2 for reactions in the gas phase. We apply the new method to Menshutkin S N 2 reactions in carbon nanotubes, demonstrating the feasibility of CASPT2 calculations with O(100) atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗