Model predictive control simulations with block-hierarchical differential–algebraic process models
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97 MATHEMATICS AND COMPUTING↗
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MISTIQS: An open-source software for performing quantum dynamics simulations on quantum computers
Not Available
97 MATHEMATICS AND COMPUTING↗
Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)]
The implementation of the GPU support in DFTB+, as described in Sec. III C of the original publication,1 was developed based on a previous unpublished implementation by Jacek Jakowski. In order to acknowledge his work on this first implementation, the authors of the original publication wish to include J. Jakowski as co-author. The scientific content of the original publication is not affected.
42 ENGINEERING↗
HPC-driven computational reproducibility in numerical relativity codes: a use case study with IllinoisGRMHD
Abstract Reproducibility of results is a cornerstone of the scientific method. Scientific computing encounters two challenges when aiming for this goal. Firstly, reproducibility should not depend on details of the runtime environment, such as the compiler version or computing environment, so results are verifiable by third-parties. Secondly, different versions of software code executed in the same runtime environment should produceconsistent numerical results for physical quantities. In this manuscript, we test the feasibility of reproducing scientific results obtained using theIllinoisGRMHDcode that is part of an open-source community software for simulation in relativistic astrophysics, theEinstein Toolkit. We verify that numerical results of simulating a single isolated neutron star withIllinoisGRMHDcan be reproduced, and compare them to results reported by the code authors in 2015. We use two different supercomputers: Expanse at SDSC, and Stampede2 at TACC. By compiling the source code archived along with the paper on both Expanse and Stampede2, we find thatIllinoisGRMHDreproduces results published in its announcement paper up to errors comparable to round-off level changes in initial data parameters. We also verify that a current version ofIllinoisGRMHDreproduces these results once we account for bug fixes which have occurred since the original publication.
Astronomy & Astrophysics↗
On-lattice kinetic Monte Carlo approaches for modeling molecular anisotropy in resveratrol crystallization
Stilbenes are a class of organic compounds with broad-ranging pharmaceutical and agricultural applications, which are typically isolated and purified through recrystallization. We are motivated by reducing experimental waste and optimizing yield via developing predictive simulations for processing-dependent crystal morphologies. Using resveratrol as a model stilbene system, we have developed an approach for simulating crystallization with molecular resolution using on-lattice kinetic Monte Carlo. In this work, we highlight modifications to the Stochastic Parallel PARticle Kinetic Simulator (SPPARKS) software package, which were essential to this application. Key enhancements include the incorporation of non-orthogonal cell shapes and monomer anisotropy approximations using bound hard spheres. This new SPPARKS application has been applied to resveratrol with attachment energy libraries obtained from density functional theory, resulting in excellent agreement with experimental morphology prediction.
crystallization↗
Kassiopeia: a modern, extensible C++ particle tracking package
Not Available
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver
The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a Fortran or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages -- Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.
electrostatics↗
El-CID: a filter for gravitational-wave electromagnetic counterpart identification
ABSTRACT As gravitational-wave (GW) interferometers become more sensitive and probe ever more distant reaches, the number of detected binary neutron star mergers will increase. However, detecting more events farther away with GWs does not guarantee corresponding increase in the number of electromagnetic counterparts of these events. Current and upcoming wide-field surveys that participate in GW follow-up operations will have to contend with distinguishing the kilonova (KN) from the ever increasing number of transients they detect, many of which will be consistent with the GW sky-localization. We have developed a novel tool based on a temporal convolutional neural network architecture, trained on sparse early-time photometry and contextual information for Electromagnetic Counterpart Identification (El-CID). The overarching goal for El-CID is to slice through list of new transient candidates that are consistent with the GW sky localization, and determine which sources are consistent with KNe, allowing limited target-of-opportunity resources to be used judiciously. In addition to verifying the performance of our algorithm on an extensive testing sample, we validate it on AT2017gfo – the only EM counterpart of a binary neutron star merger discovered to date – and AT2019npv – a supernova that was initially suspected as a counterpart of the GW event, GW190814, but was later ruled out after further analysis.
79 ASTRONOMY AND ASTROPHYSICS↗
Constraining galaxy–halo connection with high-order statistics
ABSTRACT We investigate using three-point statistics in constraining the galaxy–halo connection. We show that for some galaxy samples, the constraints on the halo occupation distribution parameters are dominated by the three-point function signal (over its two-point counterpart). We demonstrate this on mock catalogues corresponding to the Luminous red galaxies (LRGs), Emission-line galaxies (ELGs), and quasars (QSOs) targeted by the Dark Energy Spectroscopic Instrument (DESI) Survey. The projected three-point function for triangle sides less up to 20 h−1 Mpc measured from a cubic Gpc of data can constrain the characteristic minimum mass of the LRGs with a preci sion of 0.46 per cent. For comparison, similar constraints from the projected two-point function are 1.55 per cent. The improvements for the ELGs and QSOs targets are more modest. In the case of the QSOs, it is caused by the high shot-noise of the sample, and in the case of the ELGs, it is caused by the range of halo masses of the host haloes. The most time-consuming part of our pipeline is the measurement of the three-point functions. We adopt a tabulation method, proposed in earlier works for the two-point function, to significantly reduce the required compute time for the three-point analysis.
79 ASTRONOMY AND ASTROPHYSICS↗
DSPS: Differentiable stellar population synthesis
ABSTRACT Models of stellar population synthesis (SPS) are the fundamental tool that relates the physical properties of a galaxy to its spectral energy distribution (SED). In this paper, we present DSPS: a python package for SPS. All of the functionality in DSPS is implemented natively in the JAX library for automatic differentiation, and so our predictions for galaxy photometry are fully differentiable, and directly inherit the performance benefits of JAX, including portability onto GPUs. DSPS also implements several novel features, such as i) a flexible empirical model for stellar metallicity that incorporates correlations with stellar age, ii) support for the Diffstar model that provides a physically-motivated connection between the star formation history of a galaxy (SFH) and the mass assembly of its underlying dark matter halo. We detail a set of theoretical techniques for using autodiff to calculate gradients of predictions for galaxy SEDs with respect to SPS parameters that control a range of physical effects, including SFH, stellar metallicity, nebular emission, and dust attenuation. When forward modelling the colours of a synthetic galaxy population, we find that DSPS can provide a factor of 5 speed-up over standard SPS codes on a CPU, and a factor of 300-400 on a modern GPU. When coupled with gradient-based techniques for optimization and inference, DSPS makes it practical to conduct expansive likelihood analyses of simulation-based models of the galaxy–halo connection that fully forward model galaxy spectra and photometry.
79 ASTRONOMY AND ASTROPHYSICS↗
FORECASTOR – II. Simulating galaxy surveys with the Cosmological Advanced Survey Telescope for Optical and UV Research
The Cosmological Advanced Survey Telescope for Optical and UV Research (CASTOR) is a planned flagship space telescope, covering the blue-optical and UV part of the spectrum. Here, we introduce the CASTOR image simulator, a python GalSim package-based script capable of generating mock CASTOR images from an input catalogue. We generate example images from the CASTOR Wide, Deep, and Ultra-Deep surveys using simulated lightcones from the Santa Cruz semi-analytic model. We make predictions for the performance of these surveys by comparing galaxies that are extracted from each image using Source Extractor to the input catalogue. We find that the Wide, Deep, and Ultra-Deep surveys will be 75 per cent complete for point sources down to $\sim 27$, 29, and 30 mag, respectively, in the UV, u, and g filters, with the UV-split and u-split filters reaching a shallower depth. With a large area of $\sim 2200$ deg$^2$, the Wide survey will detect hundreds of millions of galaxies out to $z\sim 4$, mostly with $M_\ast \gtrsim 10^{9}\,{\rm M}_{\odot }$. The Ultra-Deep survey will probe to $z\sim 5$, detecting galaxies with $M_\ast \gtrsim 10^{7}{\rm M}_{\odot }$. These galaxy samples will enable precision measurements of the distribution of star formation in the cosmic web, connecting the growth of stellar mass to the assembly of dark matter haloes over two thirds of the history of the Universe, and other core goals of CASTOR’s legacy surveys. These image simulations and the tools developed to generate them will be a vital planning tool to estimate CASTOR’s performance and iterate the telescope and survey designs prior to launch.
79 ASTRONOMY AND ASTROPHYSICS↗
Switching-Cycle-Based Startup for Grid-tied Inverters
This paper presents a novel switching cycle-based startup approach that eliminates the need for voltage sensors and phase-locked loops. Here, the proposed method surpasses the bandwidth limitations inherent in traditional PLL-based synchronization techniques and attains grid synchronization of the inverter within two switching cycles. Despite the absence of voltage sensors and PLLs, this synchronization is achieved without inrush currents. Furthermore, the startup method does not necessitate the addition of any hardware or an increase in software complexity. Simulation and experimental results are presented to verify the effectiveness of the proposed method.
42 ENGINEERING↗
Open Power System Datasets and Open Simulation Engines: A Survey Toward Machine Learning Applications
A major factor behind the success of machine learning (ML) models in multiple domains is the availability and accessibility of large, labeled, and well-organized datasets for training and benchmarking. In comparison, power grid datasets face three major challenges: (i) real-world data is often restricted by regulatory constraints, privacy reasons, or security concerns, making it difficult to obtain and work with; (ii) synthetic datasets, which are created to address these limitations, often have incomplete information and are released using specialized tools, making them inaccessible to the broader community; and, (iii) input-output datasets are difficult to generate through simulation for non-experts because open-source simulators are not known outside the power system community. This survey addresses these challenges by serving as an entry point to publicly available datasets and simulators for researchers venturing in this area. We review the current landscape of open-source power network data, machine models, consumer demand profiles, renewable generation data, and inverter models. We also examine open-source power system simulators, which are crucial for generating high-quality, high-fidelity power grid datasets. We aim to provide a foundation for overcoming data scarcity and advance towards a structured web of datasets and simulators to support the development of ML for power systems.
42 ENGINEERING↗
Chapter 18: Learning and Tracking Ad Hoc Fiducial Markers in Spatial Augmented Reality
We describe a spatial augmented reality system with a tangible user interface used to control computer simulations of complex systems. In spatial augmented reality, the user’s physical space is augmented with projected imagery, blending real objects with projected information, and a tangible user interface enables users to manipulate physical objects as controllers for interactive visualizations. Our system learns ad hoc objects in the user’s environment as fiducial markers (i.e., objects that are visually recognized and tracked). When combined with simulation and visualization tools, these interfaces allow the user to control simulations or ensembles of simulations via physical objects using apt metaphors. While other research has leveraged the use of depth cameras, our system enables the use of standard cameras in readily available smartphones and webcams and has an implementation that runs completely in JavaScript in the web browser. We discuss the prerequisite object-recognition requirements for such tangible user interfaces and describe computer-vision and machine-learning algorithms meeting those requirements. We conclude by presenting example applications, which are also available online.
energy distribution↗
Modeling of a Parabolic Trough Solar Field for Acceptance Testing: A Case Study
As deployment of parabolic trough concentrating solar power (CSP) systems ramps up, the need for reliable and robust performance acceptance test guidelines for the solar field is also amplified. Project owners and/or EPC contractors often require extensive solar field performance testing as part of the plant commissioning process in order to ensure that actual solar field performance satisfies both technical specifications and performance guaranties between the involved parties. Performance test code work is currently underway at the National Renewable Energy Laboratory (NREL) in collaboration with the SolarPACES Task-I activity, and within the ASME PTC-52 committee. One important aspect of acceptance testing is the selection of a robust technology performance model. NREL1 has developed a detailed parabolic trough performance model within the SAM software tool. This model is capable of predicting solar field, sub-system, and component performance. It has further been modified for this work to support calculation at subhourly time steps. This paper presents the methodology and results of a case study comparing actual performance data for a parabolic trough solar field to the predicted results using the modified SAM trough model. Due to data limitations, the methodology is applied to a single collector loop, though it applies to larger subfields and entire solar fields. Special consideration is provided for the model formulation, improvements to the model formulation based on comparison with the collected data, and uncertainty associated with the measured data. Additionally, this paper identifies modeling considerations that are of particular importance in the solar field acceptance testing process and uses the model to provide preliminary recommendations regarding acceptable steady-state testing conditions at the single-loop level.
14 SOLAR ENERGY↗
Stochastic analysis of surface metrology
The design and evaluation of the expected performance of optical systems require sophisticated and reliable information about the surface topography for planned optical elements before they are fabricated. Modern x-ray source facilities are reliant upon the availability of optics with unprecedented quality (surface slope accuracy <0.1 μrad). The problem is especially complex in the case of x-ray optics, particularly for the X-ray Surveyor under development and other missions. The high angular resolution and throughput of future x-ray space observatories requires hundreds of square meters of high-quality optics. The uniqueness of the optics and limited number of proficient vendors makes the fabrication extremely time consuming and expensive, mostly due to the limitations in accuracy and measurement rate of metrology used in fabrication. Here, we discuss improvements in metrology efficacy via comprehensive statistical analysis of a compact volume of metrology data. The data are considered stochastic, and a statistical model called invertible time-invariant linear filter (InTILF) is developed now for two-dimensional (2-D) surface profiles to provide compact description of the 2-D data in addition to one-dimensional data treated so far. The InTILF model captures stochastic patterns in the data and can be used as a quality metric and feedback to polishing processes, avoiding high-resolution metrology measurements over the entire optical surface. The modeling, implemented in our BeatMark™ software, allows simulating metrology data for optics made by the same vendor and technology. The data are vital for reliable specification for optical fabrication, to be exactly adequate for the required system performance.
42 ENGINEERING↗
SU-E-J-56: Dosimetric Impact of Patient Roll Variability in Peripheral-Lung SBRT
Purpose: Positional variation about the patient longitudinal axis may introduce deleterious effects to clinical treatment plans, the effects of which are exacerbated by hypo-fractionated treatment regimens. Our goal is to evaluate the dosimetric impact of rotational setup error in stereotactic body radiation therapy (SBRT) for peripherally-located lung lesions. Methods: Six patients who had been treated for peripheral lung lesions using varying SBRT techniques were analyzed. Each patient's planning CT was processed using custom in-house software to simulate 1, 3, and 5 degree roll in both directions about their longitudinal axis. The original plan was fused and re-calculated. Agreement between planned and error-simulated dose distributions was quantified using 3%, 3mm criteria for the 3-dimensional gamma metric, and changes in target coverage and adjacent normal anatomy were also quantified. Results: Increased rotational setup error resulted in reduced target coverage, with changes in equivalent uniform dose ranging from −1.24% to −6.11% for simulated roll greater than or equal to 3 degrees, increasing with magnitude of error and skewed for roll directed toward the involved side. Changes to normal tissue metrics are linearly related to simulated roll, with rib D(1cc) changes ranging from −4.23% to 3.27% relative to the original treatment plan. Error-simulated dose distributions demonstrate agreement by the gamma metric in the planned target of 72.56%, 81.02%, and 99.52% for 5, 3, and 1 degree simulated roll scenarios, respectively. Corresponding agreement for the regional dose in excess of 50% of the maximum were 65.71%,70.77%, and 97.88%. Conclusion: This study suggests that the ability to detect and compensate for rotational positioning variations beyond a threshold level may improve care for patients with peripherally-located lesions beyond that which may be accomplished using only translational axes. Positional error of one degree of roll had little influence, though three or more degrees of error introduced significant discrepancy.
60 APPLIED LIFE SCIENCES↗
SU-E-T-443: Geometric Uncertainties in Eye Plaque Dosimetry for a Fully Loaded 16 Mm COMS Plaque
Purpose: To determine the effect of geometric uncertainties in the seed positions in a COMS eye plaque on the central axis (CAX) dose. Methods: A Silastic insert was placed into a photopolymer 3D printed 16 mm COMS plaque, which was then positioned onto a custom-designed PMMA eye phantom. High resolution 3D images were acquired of the setup using a Siemens Inveon microPET/CT scanner. Images were acquired with the plaque unloaded and loaded with IsoAid I-125 seed shells (lack of silver core to minimize metal artifacts). Seed positions and Silastic thickness beneath each slot were measured. The measured seed coordinates were used to alter the seed positions within a standard 16 mm COMS plaque in Plaque Simulator v5.7.3 software. Doses along the plaque CAX were compared for the original and modified plaque coordinates using 3.5 mCi seeds with treatment times set to deliver 70 Gy to tumour apexes of 3.5, 5, and 10 mm height. Results: The majority of seeds showed length-wise displacement, and all seeds showed displacement radially outward from the eye center. The average radial displacement was 0.15 mm larger than the expected 1.4 mm offset, approximately half of which was due to increased Silastic thickness beneath each slot. The CAX doses for the modified seed positions were consistently lower for all tumour heights due to geometric displacement of the seeds; dose differences were found to increase to a maximum of 2.6% at a depth of ∼10 mm, after which they decreased due to the inverse square dose fall-off minimizing this effect. Conclusion: This work presents initial results of a broader dosimetric uncertainty evaluation for fully loaded COMS eye plaques and demonstrates the effects of seed positioning uncertainties. The small shifts in seed depths had noticeable effects on the CAX doses indicating the importance of careful Silastic loading. Funding provided by Alberta Cancer Foundation Grant #26655, Vanier Canada Graduate Scholarship, and Alberta Innovates Health Sciences Graduate Studentship.
60 APPLIED LIFE SCIENCES↗