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LBNL_DIATOMICS is a software package developed by P. Zarzycki (Lawrence Berkeley National Laboratory) for computing isotopic effects in diatomic molecules using mass-dependent spectroscopic parameters obtained experimentally or from first principles. The package provides a streamlined pipeline from the potential energy surface to the equilibrium constant of an isotopic exchange reaction.
BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.
DRACO (Diffusion ReACtiOn) is a diffusion and chemistry code designed to: 1) Operate on 3D with an unstructured grid defining an arbitrary geometry of interacting parts. 2) Generate its own meshes and use meshes created by other software. 3)Model the transport of any number of diffusing quantities: Concentrations, pressures, temperature, etc. 4) Allow diffusion coefficients to depend in an arbitrary way on concentration, temperature, position, time, etc. 5) Model general chemistry between concentrations with arbitrary reaction rates. 6) Allow arbitrary initial conditions, boundary conditions, and sources/sinks. 7) Allow all of the above to be specified by the user.
Many important chemical and physical phenomena involve dynamics on large number of electronic states. Thus, there is a critical need to develop methods to simulate dynamics in dense manifolds of states. Towards this end, we have: a) developed the multiple cloning in dense manifolds of states (MCDMS) method, which is capable of accurately modeling the quantum mechanical coherence between populations on a large number of electronic states, b) implemented MCDMS into the free, open-source PySpawn software package, c) developed graphics processing unit-accelerated algorithms modeling electron dynamics in light fields via Floquet time-dependent configuration interaction (F-TDCI), and d) critically compared different orbital bases in order to achieve an accurate and efficient F-TDCI expansion. This grant ended in August 2020, when our group moved to from Michigan State University to Stony Brook University, where this project continues under grant number DE-SC0021643.
Leaf level reflectance on each sample leaf was measured using a portable, full range (i.e. 0.35 to 2.5 microns) Spectra Vista Corporation (SVC) HR-1024i spectroradiometer, together with a leaf clip assembly with an internal, calibrated light source (SVC, Poughkeepsie, NY, USA). Each measurement was referenced against a LabSphere Spectralon (R) standard (LabSphere, Inc., North Sutton, NH, USA) to calculate leaf reflectance from the ratio of target and standard calibrated radiance measurements for each leaf. For each leaf, we collected two to five measurements over the leaf adaxial surface to calculate an average, depending on the leaf size and morphology. Spectral discontinuities in the detector overlap areas were corrected using the SVC instrument software prior to sample averaging and other quality control steps, as described previously (Serbin et al., 2014) using the R-FieldSpectra package (https://github.com/serbinsh/R-FieldSpectra). Refer to Serbin et al (2017) for the complete spectral reflectance dataset. We then calculated leaf spectral absorptance using the measured leaf reflectance following the approach of Wu et al., (2018), based on the original method derived by Shiklomanov et al., (2016) using the PEcAnRTM package (https://github.com/PecanProject/pecan/tree/develop/modules/rtm). This dataset contains one xlsx file, one csv file, and one pdf file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
A particular implementation of the programming structural synthesis system (PROSSS) is described. This software system combines a state of the art optimization program, a production level structural analysis program, and user supplied, problem dependent interface programs. These programs are combined using standard command language features existing in modern computer operating systems. PROSSS is explained in general with respect to this implementation along with the steps for the preparation of the programs and input data. Each component of the system is described in detail with annotated listings for clarification. The components include options, procedures, programs and subroutines, and data files as they pertain to this implementation. An example exercising each option in this implementation to allow the user to anticipate the type of results that might be expected is presented.
An exploratory study of the automatic generation and optimization of symbolic programs using DECOM - a prototypical requirement specification model implemented in pure LISP was undertaken. It was concluded, on the basis of this study, that symbolic processing languages such as LISP can support a style of programming based upon formal transformation and dependent upon the expression of constraints in an object-oriented environment. Such languages can represent all aspects of the software generation process (including heuristic algorithms for effecting parallel search) as dynamic processes since data and program are represented in a uniform format.
I proposed to continue a cooperative research project with Dr. David S. McKay concerning image analysis of tracks. Last summer we showed that we could measure track densities using the Oxford Instruments eXL computer and software that is attached to an ISI scanning electron microscope (SEM) located in building 31 at JSC. To reduce the dependence on JSC equipment, we proposed to transfer the SEM images to UHCL for analysis. Last summer we developed techniques to use digitized scanning electron micrographs and computer image analysis programs to measure track densities in lunar soil grains. Tracks were formed by highly ionizing solar energetic particles and cosmic rays during near surface exposure on the Moon. The track densities are related to the exposure conditions (depth and time). Distributions of the number of grains as a function of their track densities can reveal the modality of soil maturation. As part of a consortium effort to better understand the maturation of lunar soil and its relation to its infrared reflectance properties, we worked on lunar samples 67701,205 and 61221,134. These samples were etched for a shorter time (6 hours) than last summer's sample and this difference has presented problems for establishing the correct analysis conditions. We used computer counting and measurement of area to obtain preliminary track densities and a track density distribution that we could interpret for sample 67701,205. This sample is a submature soil consisting of approximately 85 percent mature soil mixed with approximately 15 percent immature, but not pristine, soil.
As the operation of large systems becomes ever more dependent on extensive automation, the need for an effective solution to the problem of design and validation of the underlying software becomes more critical. Large systems possess much detailed structure, typically hierarchical, and they are hybrid. Information processing at the top of the hierarchy is by means of formal logic and sentences; on the bottom it is by means of simple scalar differential equations and functions of time; and in the middle it is by an interacting mix of nonlinear multi-axis differential equations and automata, and functions of time and discrete events. The lecture will address the overall problem as it relates to flight vehicle management, describe the middle level, and offer a design approach that is based on Differential Geometry and Discrete Event Dynamic Systems Theory.
As the operation of large systems becomes ever more dependent on extensive automation, the need for an effective solution to the problem of design and validation of the underlying software becomes more critical. Large systems possesses much detailed structure, typically hierarchical, and they are hybrid. Information processing at the top of the hierarchy is by means of formal logic and sentences; on the bottom it is by means of simple scalar differential equations and functions of time; and in the middle it is by an interacting mix of nonlinear multi-axis differential equations and automata, and functions of time and discrete events. The lecture will address the overall problem as it relates to flight vehicle management, describe the middle level, and offer a design approach that is based on Differential Geometry and Discrete Event Dynamic Systems Theory.
CTAEMS MDP Optimal Planner is a problem-solving software designed to command a single spacecraft/rover, or a team of spacecraft/rovers, to perform the best action possible at all times according to an abstract model of the spacecraft/rover and its environment. It also may be useful in solving logistical problems encountered in commercial applications such as shipping and manufacturing. The planner reasons around uncertainty according to specified probabilities of outcomes using a plan hierarchy to avoid exploring certain kinds of suboptimal actions. Also, planned actions are calculated as the state-action space is expanded, rather than afterward, to reduce by an order of magnitude the processing time and memory used. The software solves planning problems with actions that can execute concurrently, that have uncertain duration and quality, and that have functional dependencies on others that affect quality. These problems are modeled in a hierarchical planning language called C_TAEMS, a derivative of the TAEMS language for specifying domains for the DARPA Coordinators program. In realistic environments, actions often have uncertain outcomes and can have complex relationships with other tasks. The planner approaches problems by considering all possible actions that may be taken from any state reachable from a given, initial state, and from within the constraints of a given task hierarchy that specifies what tasks may be performed by which team member.
An improved approach to the mathematical modeling of feedback control of thermal networks has been devised. Heretofore software for feedback control of thermal networks has been developed by time-consuming trial-and-error methods that depend on engineers expertise. In contrast, the present approach is a systematic means of developing algorithms for feedback control that is optimal in the sense that it combines performance with low cost of implementation. An additional advantage of the present approach is that a thermal engineer need not be expert in control theory. Thermal networks are lumped-parameter approximations used to represent complex thermal systems. Thermal networks are closely related to electrical networks commonly represented by lumped-parameter circuit diagrams. Like such electrical circuits, thermal networks are mathematically modeled by systems of differential-algebraic equations (DAEs) that is, ordinary differential equations subject to a set of algebraic constraints. In the present approach, emphasis is placed on applications in which thermal networks are subject to constant disturbances and, therefore, integral control action is necessary to obtain steady-state responses. The mathematical development of the present approach begins with the derivation of optimal integral-control laws via minimization of an appropriate cost functional that involves augmented state vectors. Subsequently, classical variational arguments provide optimality conditions in the form of the Hamiltonian equations for the standard linear-quadratic-regulator (LQR) problem. These equations are reduced to an algebraic Riccati equation (ARE) with respect to the augmented state vector. The solution of the ARE leads to the direct computation of the optimal proportional- and integral-feedback control gains. In cases of very complex networks, large numbers of state variables make it difficult to implement optimal controllers in the manner described in the preceding paragraph.
The Trajectory Software Applications 6.0 for the Dec Alpha platform has an implementation of the Jacchia-Lineberry Upper Atmosphere Density Model used in the Mission Control Center for International Space Station support. Previous trajectory software required an upper atmosphere to support atmosphere drag calculations in the Mission Control Center. The Functional operation will differ depending on the end-use of the module. In general, the calling routine will use function-calling arguments to specify input to the processor. The atmosphere model will then compute and return atmospheric density at the time of interest.
The Solar Dynamics Observatory (SDO) mission, which is part of the Living With a Star program, was successfully launched and deployed from its Atlas V launch vehicle on February 11, 2010. SDO is an Explorer-class mission now operating in a geosynchronous orbit (GEO). The basic mission is to observe the Sun for a very high percentage of the 5-year mission (10-year goal) with long stretches of uninterrupted observations and with constant, high-data-rate transmission to a dedicated ground station located in White Sands, New Mexico. A significant portion of SDO's launch mass was propellant, contained in two large tanks. To ensure performance with this level of propellant, a slosh analysis was performed. This paper provides an overview of the SDO slosh analysis, the on-orbit experience, and the lessons learned. SDO is a three-axis controlled, single fault tolerant spacecraft. The attitude sensor complement includes sixteen coarse Sun sensors, a digital Sun sensor, three two-axis inertial reference units, two star trackers, and four guide telescopes. Attitude actuation is performed either using four reaction wheels or eight thrusters, depending on the control mode, along with single main engine which nominally provides velocity-change thrust. The attitude control software has five nominal control modes: three wheel-based modes and two thruster-based modes. A wheel-based Safehold running in the Attitude Control Electronics (ACE) box improves the robustness of the system as a whole. All six modes are designed on the same basic proportional-integral-derivative attitude error structure, with more robust modes setting their integral gains to zero. To achieve and maintain a geosynchronous orbit for a 2974-kilogram spacecraft in a cost effective manner, the SDO team designed a high-efficiency propulsive system. This bi-propellant design includes a 100-pound-force main engine and eight 5-pound-force attitude control thrusters. The main engine provides high specific impulse for the maneuvers to attain GEO, while the smaller Attitude Control System (ACS) thrusters manage the disturbance torques of the larger main engine and provide the capability for much smaller orbit adjustment burns. SDO's large solar profile produces a large solar torque disturbance and momentum buildup. This buildup drives the frequency of momentum unloads via ACS thrusters. SDO requires 1409 kilograms (which is approximately half the launch mass) of propellant to achieve and maintain the GEO orbit while performing the momentum unloads for 10 years.
NASA’s Orbital Debris Program Office (ODPO) maintains various returned spacecraft materials, capabilities, and facilities used for in situ and laboratory measurements that directly support orbital debris environmental models. In situ measurements include the analysis of exposed and returned hardware surfaces. These surfaces serve as passive sensors for the small-sized micrometeoroid and orbital debris (MMOD) flux below the sensitivity of ground-based radar and optical sensors. Various instruments and techniques are used to determine the size and depth of selected impact features, and – if feasible – the composition of the projectile material. Analysis of the impactor residues enables the differentiation of MM and OD for debris below 1 mm to support modeling the OD environment. In addition, projectiles identified as OD can be further differentiated in low-, medium-, and high- density impactors based on chemical analyses. In addition to in situ measurements, the ODPO has also worked in collaboration with the U.S. Space Force Space Systems Command (formerly the U.S. Air Force Space and Missile Systems Center), the Aerospace Corporation, and the University of Florida on a laboratory-based hypervelocity impact test, DebriSat, conducted at the Air Force Arnold Engineering Development Complex in 2014. The resulting data from this impact test series are being analyzed to assess the fragments’ sizes/masses, materials/densities, shapes, and other parameters of interest. The DebriSat project provides the data needed to update NASA’s breakup models and size estimation models using the simulated orbital breakup of a modern, low Earth orbit spacecraft. Ultimately, over 200,000 fragments from this impact test will be stored at NASA Johnson Space Center (JSC) and further analyzed by the ODPO. This project will also use machine learning techniques to infer physical parameters of fragments embedded in the soft-catch foam used in the impact experiment. Applied to X-ray imagery of the foam panels, these techniques promise to minimize human-in-the-loop processes for fragment extraction and physical characterization. A brief overview of this project and data collected will be presented. Lastly, the ODPO provides various capabilities hosted at NASA JSC for optical inspections and measurements using a variety of techniques and scientific instrumentation to support both in situ and laboratory measurements. The ODPO’s Optical Measurement Center (OMC) is an advanced facility for photometric and spectroscopic laboratory measurements of targets, including fragments from the DebriSat project. The OMC simulates telescopic observations by using space-like illumination conditions and source-target-sensor orientation techniques. Additionally, the OMC is uniquely equipped to acquire pseudo-bidirectional reflectance distribution data for broadband photometric measurements, thus removing aspect angle dependencies that can affect target size estimates using the optical size estimation model. Narrow-band surface material characterization using spectroscopic instrumentation gives insight into how the albedo parameter – also important in the optical size estimation model – may vary depending on the state of the material. The OMC also performs simulations of photometric measurements using optical ray-tracing software to model the OMC optical throughput. In addition to the OMC, the ODPO houses a start-of-the-art Fragment Analysis Facility that uses multiple microscopic inspection instruments to support in situ measurements and material characterization. An overview of both facilities will be highlighted in this paper.
NASA’s Orbital Debris Program Office (ODPO) maintains various returned spacecraft materials, capabilities, and facilities used for in situ and laboratory measurements that directly support orbital debris environmental models. In situ measurements include the analysis of exposed and returned hardware surfaces. These surfaces serve as passive sensors for the small-sized micrometeoroid and orbital debris (MMOD) flux below the sensitivity of ground-based radar and optical sensors. Various instruments and techniques are used to determine the size and depth of selected impact features, and – if feasible – the composition of the projectile material. Analysis of the impactor residues enables the differentiation of MM and OD for debris below 1 mm to support modeling the OD environment. In addition, projectiles identified as OD can be further differentiated in low-, medium-, and high- density impactors based on chemical analyses. In addition to in situ measurements, the ODPO has also worked in collaboration with the U.S. Space Force Space Systems Command (formerly the U.S. Air Force Space and Missile Systems Center), the Aerospace Corporation, and the University of Florida on a laboratory-based hypervelocity impact test, DebriSat, conducted at the Air Force Arnold Engineering Development Complex in 2014. The resulting data from this impact test series are being analyzed to assess the fragments’ sizes/masses, materials/densities, shapes, and other parameters of interest. The DebriSat project provides the data needed to update NASA’s breakup models and size estimation models using the simulated orbital breakup of a modern, low Earth orbit spacecraft. Ultimately, over 200,000 fragments from this impact test will be stored at NASA Johnson Space Center (JSC) and further analyzed by the ODPO. This project will also use machine learning techniques to infer physical parameters of fragments embedded in the soft-catch foam used in the impact experiment. Applied to X-ray imagery of the foam panels, these techniques promise to minimize human-in-the-loop processes for fragment extraction and physical characterization. A brief overview of this project and data collected will be presented. Lastly, the ODPO provides various capabilities hosted at NASA JSC for optical inspections and measurements using a variety of techniques and scientific instrumentation to support both in situ and laboratory measurements. The ODPO’s Optical Measurement Center (OMC) is an advanced facility for photometric and spectroscopic laboratory measurements of targets, including fragments from the DebriSat project. The OMC simulates telescopic observations by using space-like illumination conditions and source-target-sensor orientation techniques. Additionally, the OMC is uniquely equipped to acquire pseudo-bidirectional reflectance distribution data for broadband photometric measurements, thus removing aspect angle dependencies that can affect target size estimates using the optical size estimation model. Narrow-band surface material characterization using spectroscopic instrumentation gives insight into how the albedo parameter – also important in the optical size estimation model – may vary depending on the state of the material. The OMC also performs simulations of photometric measurements using optical ray-tracing software to model the OMC optical throughput. In addition to the OMC, the ODPO houses a start-of-the-art Fragment Analysis Facility that uses multiple microscopic inspection instruments to support in situ measurements and material characterization. An overview of both facilities will be highlighted in this paper.
In recent years, there has been considerable effort to modernize existing and new nuclear power plants with digital instrumentation and control systems (DI&C). However, there has also been considerable concern both by industry and regulatory bodies for the risk and consequence analysis of these systems. Of particular concern are digital common cause failures (CCFs) specifically related to software defects. These “misbehaviors” by the software can occur in both the control and monitoring of a system. While many new methods have been proposed to identify potential software failure modes, such as Systems-theoretic Process Analysis (STPA), Hazard and Consequence Analysis for Digital Systems (HAZCADS), etc., these methods are focused primarily on the control action pathway of a system. In contrast, the information feedback pathway lacks unsafe control actions (UCAs), which are typically related to software basic events; thus, assessment of software basic events in such systems is unclear. In this work, we present the idea of intermediate processors and unsafe information flow (UIF) to help safety analysts trace failure mechanisms in the feedback pathway and how they can be integrated into a fault tree for improved assessment capability. The concepts presented are demonstrated in two comprehensive case studies, a smart sensor integrated platform for unmanned autonomous vehicles and another on a representative advanced human system interface (HSI) for safety critical plant monitoring. The qualitative software basic events are identified, and a fault tree analysis is conducted based on a modified Redundancy-guided Systems-theoretic Hazard Analysis (RESHA) methodology. The case studies demonstrate the use of UIF and intermediate processors in the fault tree to improve traceability of software failures in highly complex digital instrumentation feedback. The improved method can also clarify fault tree construction when multiple component dependencies are present in the system.
In recent years, there has been considerable effort to modernize existing and new nuclear power plants with digital instrumentation and control systems (DI&C). However, there has also been considerable concern both by industry and regulatory bodies for the risk and consequence analysis of these systems. Of particular concern are digital common cause failures (CCFs) specifically related to software defects. These “misbehaviors” by the software can occur in both the control and monitoring of a system. While many new methods have been proposed to identify potential software failure modes, such as Systems-theoretic Process Analysis (STPA), Hazard and Consequence Analysis for Digital Systems (HAZCADS), etc., these methods are focused primarily on the control action pathway of a system. In contrast, the information feedback pathway lacks unsafe control actions (UCAs), which are typically related to software basic events; thus, assessment of software basic events in such systems is unclear. In this work, we present the idea of intermediate processors and unsafe information flow (UIF) to help safety analysts trace failure mechanisms in the feedback pathway and how they can be integrated into a fault tree for improved assessment capability. The concepts presented are demonstrated in two comprehensive case studies, a smart sensor integrated platform for unmanned autonomous vehicles and another on a representative advanced human system interface (HSI) for safety critical plant monitoring. The qualitative software basic events are identified, and a fault tree analysis is conducted based on a modified Redundancy-guided Systems-theoretic Hazard Analysis (RESHA) methodology. The case studies demonstrate the use of UIF and intermediate processors in the fault tree to improve traceability of software failures in highly complex digital instrumentation feedback. The improved method can also clarify fault tree construction when multiple component dependencies are present in the system.