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At least 1,351 records · Page 75

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Abstract Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.

Chemistry↗

Aerodynamic simulation tests of RSI panels

The technique of mixing argon with air was used to simulate the temperature-time trajectory experienced by space shuttle vehicle insulation panels. Gap heating appears to be highly dependent upon gap design, it is relatively low for interlocking and tapered panel designs and significantly higher for a wider, unfilled gap design. The heating rate appears to be significantly higher at the windward facing edges of flush tiles and is aggravated at forward facing steps. This heating, however, is highly dependent on step heights relative to some characteristic thickness of the boundary layer.

Centolanzi, F. J.↗

Spectrum formation in supernovae - Numerical techniques

The study combines several novel techniques for spectrum simulation in the Eddington computer program which solves the comoving frame equation of transfer coupled with the statistical and radiative equilibrium equations. One of these is a generalization of the accelerated lambda iteration (ALI) scheme to include an approximate frequency-derivative operator. This greatly enhances the convergence rate of ALI in optically thick, high-velocity shear flows. Another is a partial linearization technique which is capable of efficiently solving a very large number of rate equations on a moderately sized computer. An expansion opacity and emissivity approximation is derived which makes it possible to determine the effect on the transfer and statistical equilibrium of a very large number of lines not explicitly represented in the frequency grid and additionally to treat line-blanketing from species not explicitly included in the rate equations. The utility of these techniques is illustrated with models of two supernovae.

Eastman, Ronald G.↗

Template Matching Approach to Signal Prediction

A new approach to signal prediction and prognostic assessment of spacecraft health resolves an inherent difficulty in fusing sensor data with simulated data. This technique builds upon previous work that demonstrated the importance of physics-based transient models to accurate prediction of signal dynamics and system performance. While models can greatly improve predictive accuracy, they are difficult to apply in general because of variations in model type, accuracy, or intended purpose. However, virtually any flight project will have at least some modeling capability at its disposal, whether a full-blown simulation, partial physics models, dynamic look-up tables, a brassboard analogue system, or simple hand-driven calculation by a team of experts. Many models can be used to develop a predict, or an estimate of the next day s or next cycle s behavior, which is typically used for planning purposes. The fidelity of a predict varies from one project to another, depending on the complexity of the simulation (i.e. linearized or full differential equations) and the level of detail in anticipated system operation, but typically any predict cannot be adapted to changing conditions or adjusted spacecraft command execution. Applying a predict blindly, without adapting the predict to current conditions, produces mixed results at best, primarily due to mismatches between assumed execution of spacecraft activities and actual times of execution. This results in the predict becoming useless during periods of complicated behavior, exactly when the predict would be most valuable. Each spacecraft operation tends to show up as a transient in the data, and if the transients are misaligned, using the predict can actually harm forecasting performance. To address this problem, the approach here expresses the predict in terms of a baseline function superposed with one or more transient functions. These transients serve as signal templates, which can be relocated in time and space against the signal background. One then has the ability to reconstruct a signal regardless of the precise timing of the transients. During operation, one applies the actual start times of spacecraft activities as they occur, and produces a reconstructed, accurate predict in real-time. This general approach is valid under two important conditions. First, the transients themselves must be time-invariant. Second, the transients must be reasonably consistent with respect to different operating points. Both of these assumptions are generally valid, but in the case of a complicated system with numerous types of overlapping transients, this approach may not be effective. Fortunately, there tend to be few transients in spacecraft telemetry of sensor quantities or low-level health and status information because these signals rarely reflect multiple different types of operation. Furthermore, if the predict is at least reasonably close to actual operation, the shift either in time, or in the operating point when the transient occurs - is likely to be small. The proposed approach considers three ways to recognize a transient. The first and most reliable is to use a different signal that identifies operating mode - often the transient will be correlated to a change in operating mode, and this change can usually be detected positively from discrete signals in spacecraft telemetry. If there is no useful mode signal, the second option is to identify the transient template by hand, and detect the onset of the transient using a curve-fitting approach. Finally, if one elects not to choose by hand, there is an option for automatic selection. This technique has been applied to sensor data from several JPL missions and industrial applications, demonstrating an improvement in accurate prediction of future behavior and early detection of system problems. This technique is applicable to practically any time-varying, quantitative sensor measurement.

Mackey, Ryan↗

Modeling techniques used in the communications link analysis and simulation system (CLASS)

CLASS (Communications Link Analysis and Simulation System) is a software package developed for NASA to predict the communication and tracking performance of the Tracking and Data Relay Satellite System (TDRSS) services. The modeling techniques used in CLASS are described. The components of TDRSS and the performance parameters to be computed by CLASS are too diverse to permit the use of a single technique to evaluate all performance measures. Hence, each CLASS module applies the modeling approach best suited for a particular subsystem and/or performance parameter in terms of model accuracy and computational speed.

Braun, W. R.↗

Elastic Bayesian Model Calibration

Functional data are ubiquitous in scientific modeling. For instance, quantities of interest are modeled as functions of time, space, energy, density, etc. Uncertainty quantification methods for computer models with functional response have resulted in tools for emulation, sensitivity analysis, and calibration that are widely used. However, many of these tools do not perform well when the computer model’s parameters control both the amplitude variation of the functional output and its alignment (or phase variation). This paper introduces a framework for Bayesian model calibration when the model responses are misaligned functional data. The approach generates two types of data out of the misaligned functional responses: (1) aligned functions so that the amplitude variation is isolated and (2) warping functions that isolate the phase variation. These two types of data are created for the computer simulation data (both of which may be emulated) and the experimental data. The calibration approach uses both types so that it seeks to match both the amplitude and phase of the experimental data. The framework is careful to respect constraints that arise, especially when modeling phase variation, and is framed in a way that it can be done with readily available calibration software. In conclusion, we demonstrate the techniques on two simulated data examples and on two dynamic material science problems: a strength model calibration using flyer plate experiments and an equation of state model calibration using experiments performed on the Sandia National Laboratories’ Z-machine.

97 MATHEMATICS AND COMPUTING↗

Ground-to-Flight Handling Qualities Comparisons for a High Performance Airplane

A flight test program was conducted in conjunction with a ground-based piloted simulation study to enable a comparison of handling qualities ratings for a variety of maneuvers between flight and simulation of a modern high performance airplane. Specific objectives included an evaluation of pilot-induced oscillation (PIO) tendencies and a determination of maneuver types which result in either good or poor ground-to-flight pilot handling qualities ratings. A General Dynamics F-16XL aircraft was used for the flight evaluations, and the NASA Langley Differential Maneuvering Simulator was employed for the ground based evaluations. Two NASA research pilots evaluated both the airplane and simulator characteristics using tasks developed in the simulator. Simulator and flight tests were all conducted within approximately a one month time frame. Maneuvers included numerous fine tracking evaluations at various angles of attack, load factors and speed ranges, gross acquisitions involving longitudinal and lateral maneuvering, roll angle captures, and an ILS task with a sidestep to landing. Overall results showed generally good correlation between ground and flight for PIO tendencies and general handling qualities comments. Differences in pilot technique used in simulator evaluations and effects of airplane accelerations and motions are illustrated.

Brandon, Jay M.↗

Exploring Applications of Machine Learning for Wildfire Monitoring and Detection using Unmanned Aerial Vehicles

Wildfires are increasing in frequency and severity around the world, including the United States. The losses caused by wildfires could be mitigated if high-risk areas, hotspots, and flare-ups could be monitored continuously, such as through the use of Unmanned Aerial Vehicles (UAVs). This paper documents exploratory efforts using machine learning to determine efficient flight paths for UAVs and to detect wildfires using image classification. On path planning, three machine learning techniques—Genetic Algorithm, Simulated Annealing, and Dynamic Programming—were explored. Genetic Algorithm was found to be an effective approach for path planning for wildfire monitoring and surveillance by UAVs. For a scenario of 25 locations in a circular arrangement, the algorithm was able to return the optimal path. The accuracy and execution time was found to be sensitive to the algorithm hyperparameters selected, which was especially evident in scenarios with hundreds or thousands of locations. Simulated Annealing was also found to be an effective approach for UAV path planning, with a major benefit of avoiding getting trapped in local minima and being straightforward to implement. Like Genetic Algorithm, the performance of Simulated Annealing was also found to be sensitive to the algorithm hyperparameters selected. By comparison, Dynamic Programming guarantees optimality for any number of locations, but it was found to be less practical in terms of execution time for scenarios with more than about a couple dozen locations. On wildfire detection, image classification using deep learning with a convolutional neural network was explored. Transfer learning was found to be a useful technique to efficiently train deep learning models. Also, it was determined that GPU processing can increase training speed by an order of magnitude, which enables significantly faster development. For a validation test set of 500 images, there were only two false negatives and zero false positives. These results demonstrate that detecting wildfires in static cameras using machine learning is feasible and establish a baseline for using images captured by UAVs in flight for wildfire detection.

Wildfire management↗

Using Hyperoptimized Tensor Networks and First-Principles Electronic Structure to Simulate the Experimental Properties of the Giant {Mn 84 } Torus

The single-molecule magnet {Mn 84 } is a challenge to theory because of its high nuclearity. Here, we directly compute two experimentally accessible observables, the field-dependent magnetization up to 75 T and the temperature-dependent heat capacity, using parameter-free theory. In particular, we use first-principles calculations to derive short- and long-range exchange interactions and compute the exact partition function of the resulting classical Potts and Ising spin models for all 84 Mn S = 2 spins to obtain observables. The latter computation is made possible by using hyperoptimized tensor network contractions, a technique developed to simulate quantum supremacy circuits. We also synthesize the magnet and measure its heat capacity and magnetization, observing qualitative agreement between theory and experiment and identifying an unusual bump in the heat capacity and a plateau in the magnetization. Our work also identifies some limitations of current theoretical modeling in large magnets, such as sensitivity to small, long-range exchange couplings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct numerical simulations of a reacting mixing layer with chemical heat release

In order to study the coupling between chemical heat release and fluid dynamics, direct numerical simulations of a chemically reacting mixing layer with heat release are performed. The fully compressible equations as well as an approximate set of equations that is asymptotically valid for low-Mach-number flows are treated. These latter equations have the computational advantage that high-frequency acoustic waves have been filtered out, allowing much larger time steps to be taken in the numerical solution procedure. A detailed derivation of these equations along with an outline of the numerical solution technique is given. Simulation results indicate that the rate of chemical product formed, the thickness of the mixing layer, and the amount of mass entrained into the layer all decrease with increasing rates of heat release.

Mcmurtry, P. A.↗

Non-propagating structures and propagating waves in solar wind turbulence revealed by simulations and observations

Structures and waves are common features of solar wind turbulence at various scales. The interplay between structures and waves is important for processes such as the turbulent energy cascade, plasma heating, and particle scattering. Our understanding of turbulence has been advanced by not only new space missions and numerical simulations, but also techniques that have been developed to interpret the rapidly growing turbulence data. We review basic models of turbulence with a specific focus on the analysis methods for understanding magnetic structures and waves. MHD and kinetic waves in single-spacecraft time series measurements can be identified through mode decomposition or their characteristic polarization signatures. The structures in this paper are considered as zero-frequency, non-propagating or convected modes embedded in the solar wind. The synergy between observations and simulations is most evident in the application of spatial-temporal analysis to multi-spacecraft observation and turbulence simulations. The spatial-temporal analysis has greatly improved our understanding of structures and waves in turbulence. We conclude by discussing prospects for future research.

79 ASTRONOMY AND ASTROPHYSICS↗

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A manipulator system designed for Free-Flying Teleoperator Spacecraft

A preliminary design of a manipulator system, applicable to a Free-Flying Teleoperator Spacecraft operating in conjunction with the Shuttle or Tug, is presented. The manipulator arm incorporates two 4-ft segments to the wrist with actuators located at the shoulder, elbow, and wrist. The wrist provides three degrees-of-freedom through pitch, yaw and continuous roll joints. An interchangeable end effector provides multiple task performance and satellite worksite versatility. A tip force of 10 lbs and a torque of 15 ft-lbs is provided. Man-in-the-loop simulations, using both unilateral and bilateral control techniques, were conducted. Based upon the simulation, a new, but relatively simple, control technique was proposed for the manipulator system.

Tewell, J. R.↗

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

Classical molecular dynamics simulates the time evolution of molecular systems through the phase space spanned by the positions and velocities of the constituent atoms. Molecular-level thermodynamic, kinetic, and structural data extracted from the resulting trajectories provide valuable information for the understanding, engineering, and design of biological and molecular materials. The cost of simulating many-body atomic systems makes simulations of large molecules prohibitively expensive, and the high-dimensionality of the resulting trajectories presents a challenge for analysis. Driven by advances in algorithms, hardware, and data availability, there has been a flare of interest in recent years in the applications of machine learning – especially deep learning – to molecular simulation. Furthermore, these techniques have demonstrated great power and flexibility in both extracting mechanistic understanding of the important nonlinear collective variables governing the dynamics of a molecular system, and in furnishing good low-dimensional system representations with which to perform enhanced sampling or develop long-timescale dynamical models. It is the purpose of this article to introduce the key machine learning approaches, describe how they are married with statistical mechanical theory into domain-specific tools, and detail applications of these approaches in understanding and accelerating biomolecular simulation.

74 ATOMIC AND MOLECULAR PHYSICS↗

SIDSIM (Sub-Interval Distribution-function in Simulation) [SWR-17-22]

Time-series simulation is a technique used to estimate the energy delivery of a power generation system with output that changes under changing conditions. Such variable resources include photovoltaic energy systems that experience different levels of sunlight or wind farms with changing wind patterns. As distributed generation from these variable resources continues to flourish, having improved software tools to accurately measure, model, and estimate phenomena of interest to grid integration, in addition to energy output, will be crucial for safeguarding smooth integration and operation of these energy systems. Currently, time-series simulations assume conditions and power output are constant over the duration of a time-step (steady-state assumption). NREL researchers improve the accuracy with a new simulation software called SIDSIM (Sub-Interval Distribution Simulation) that replaces this steady value (solar or wind resource) with a distribution function that has a maximum value, a minimum value, and a shape to the curve within each time-step. The distribution function used for modeling varying values in the SIDSIM software is a novel equation and presents advantageous new benefits over the conventional methods. The first advantage comes in the ability to determine maximum instantaneous power within a time-step. This enables better protection of a system from overcurrent issues and it also allows for better forecasting and reservation of transmission capacity; such capabilities are essential for energy system integration. Second, a distribution function helps to determine the amount of energy loss due to “clipping” in cases where the photovoltaic direct current (DC) system capacity exceeds the inverter capacity, the AC interconnect capacity, or any other limiting component or threshold value. It improves estimates of battery throughput by allowing both charge and discharge of a battery within the duration of a time-step. Third, it provides a more refined estimate of utility-bill impacts by considering the delivered power may be higher than the site load or lower than the regular average power estimates that are made using a quasi-steady-state assumption. SEE ALSO OSTI ID 1,361,018

Walker, Andy↗

Using Monte-Carlo Simulations to Study the Disk Structure in Cygnus X-1

As the first dynamically determined black hole X-ray binary system, Cygnus X-1 has been studied extensively. However, its broad-band spectra in hard state with BeppoSAX is still not well understood. Besides the soft excess described by the multi-color disk model (MCD), the power- law component and a broad excess feature above 10 keV (disk reflection component), there is also an additional soft component around 1 keV, whose origin is not known currently.We propose that the additional soft component is due to the thermal Comptonization process between the s oft disk photon and the warm plasma cloud just above the disk.i.e., a warm layer. We use Monte-Carlo technique t o simulate this Compton scattering process and build several table models based on our simulation results.

Yao, Y.↗

Superresolution Full-polarimetric Imaging for Radio Interferometry with Sparse Modeling

We propose a new technique for radio interferometry to obtain superresolution full-polarization images in all four Stokes parameters using sparse modeling. The proposed technique reconstructs the image in each Stokes parameter from the corresponding full-complex Stokes visibilities by utilizing two regularization functions: the ℓ {sub 1} norm and the total variation (TV) of the brightness distribution. As an application of this technique, we present simulated linear polarization observations of two physically motivated models of M87 with the Event Horizon Telescope. We confirm that ℓ {sub 1}+TV regularization can achieve an optimal resolution of ~25%–30% of the diffraction limit λ/D{sub max}, which is the nominal spatial resolution of a radio interferometer for both the total intensity (i.e., Stokes I) and linear polarizations (i.e., Stokes Q and U). This optimal resolution is better than that obtained from the widely used Cotton–Schwab CLEAN algorithm or from using ℓ {sub 1} or TV regularizations alone. Furthermore, we find that ℓ {sub 1}+TV regularization can achieve much better image fidelity in linear polarization than other techniques over a wide range of spatial scales, not only in the superresolution regime, but also on scales larger than the diffraction limit. Our results clearly demonstrate that sparse reconstruction is a useful choice for high-fidelity full-polarimetric interferometric imaging.

79 ASTRONOMY AND ASTROPHYSICS↗

Application of Land Surface Data Assimilation to Simulations of Sea Breeze Circulations

A technique has been developed for assimilating GOES-derived skin temperature tendencies and insolation into the surface energy budget equation of a mesoscale model so that the simulated rate of temperature change closely agrees with the satellite observations. A critical assumption of the technique is that the availability of moisture (either from the soil or vegetation) is the least known term in the model's surface energy budget. Therefore, the simulated latent heat flux, which is a function of surface moisture availability, is adjusted based upon differences between the modeled and satellite- observed skin temperature tendencies. An advantage of this technique is that satellite temperature tendencies are assimilated in an energetically consistent manner that avoids energy imbalances and surface stability problems that arise from direct assimilation of surface shelter temperatures. The fact that the rate of change of the satellite skin temperature is used rather than the absolute temperature means that sensor calibration is not as critical. The sea/land breeze is a well-documented mesoscale circulation that affects many coastal areas of the world including the northern Gulf Coast of the United States. The focus of this paper is to examine how the satellite assimilation technique impacts the simulation of a sea breeze circulation observed along the Mississippi/Alabama coast in the spring of 2001. The technique is implemented within the PSUNCAR MM5 V3-5 and applied at spatial resolutions of 12- and 4-km. It is recognized that even 4-km grid spacing is too coarse to explicitly resolve the detailed, mesoscale structure of sea breezes. Nevertheless, the model can forecast certain characteristics of the observed sea breeze including a thermally direct circulation that results from differential low-level heating across the land-sea interface. Our intent is to determine the sensitivity of the circulation to the differential land surface forcing produced via the assimilation of GOES skin temperature tendencies. Results will be quantified through statistical verification techniques.

Mackaro, Scott↗