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DOE OSTI2022

Role of copper in nitrous oxide accumulation in wetland soils from Illinois and South Carolina and stream sediments from Tennessee

Denitrification is microbially-mediated through enzymes containing metal cofactors. Laboratory studies of pure cultures have highlighted that the availability of copper (Cu), required for the multicopper enzyme nitrous oxide reductase, can limit nitrous oxide (N2O) reduction. However, in natural aquatic systems, such as wetlands and hyporheic zones in stream beds, the role of Cu in controlling denitrification remains incompletely understood. In this study, we collected soils and sediments from three natural environments -- riparian wetlands, marsh wetlands, and a stream -- to investigate their nitrogen species transformation activity at background Cu levels and different supplemented Cu loadings. All of the systems contained solid-phase associated Cu below or around geological levels (40–280 nmol g-1) and exhibited low dissolved Cu (3–50 nM), which made them appropriate sites for evaluating the effect of limited Cu availability on denitrification.The dataset contains the variation in the nutrient (nitrate (NO3-), nitrite (NO2-), and ammonium (NH4+)) and N2O concentrations during the incubation experiments to evaluate the effect of Cu. We have also reported the variation in metal concentrations (Cu, iron(Fe) and manganese (Mn)) and dissolved organic carbon (DOC) concentrations during the incubations. The parameters obtained using a kinetic model to quantitatively report the effect of Cu on nitrogen species conversion in natural aquatic systems are also added in the dataset. The dataset also contains the labile concentration of Cu estimated using a speciation model in MINTEQ. All data are provided in text-based CSV format with header sections indicating the data contained in each file and the corresponding units.Our study suggests that high concentrations of N2O accumulated in all microcosms lacking Cu amendment except for one stream sediment sample. With Cu added to provide dissolved concentrations at trace levels (10–300 nM), the reduction rate of N2O to N2 in the wetland soils and stream sediments was enhanced. A kinetic model could account for the trends in nitrogen species by combining the reactions for microbial reduction of NO3- to NO2-/N2O/N2 and abiotic reduction of NO2 to nitrogen (N2_. The model revealed that the rate of N2O to N2 conversion increased significantly in the presence of Cu. For riparian wetland soils and stream sediments, the kinetic model also suggested that overall denitrification is driven by abiotic reduction of NO2- in the presence of inorganic electron donors. This study demonstrated that natural aquatic systems containing Cu at concentrations less than or equal to crustal abundances may display incomplete reduction of N2O to N2 that would cause N2O accumulation and release to the atmosphere.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

An improved method for direct incident solar radiation calculation from hourly solar insolation data in building energy simulation

Solar radiation considerably influences the energy consumption of buildings and the power production of building integrated photovoltaic (BIPV) systems. Hourly solar insolation (Wh/m 2 ), represented as the amount of solar irradiance collected on the ground during a 1-h period, is the most common solar radiation data available and widely used in weather files applied in building energy modeling programs (BEMPs). Because the solar beam and position vary over time, the use of hourly insolation data as the input might result in errors in the estimation of the direct incident solar radiation on a particular surface. In this study, methods used in BEMPs for direct incident solar radiation calculations are first analyzed, and an improved method adopting a new algorithm for estimating the solar irradiance is proposed. Furthermore, the algorithm assumes that the solar irradiance changes linearly within a 1-h period and can be estimated based on the solar irradiance at the half clock and slope. The collected direct normal solar irradiance data of 2016 from eight solar radiation stations in China were used to demonstrate the proposed method and evaluate its performance by comparing the results with those from three conventional methods used in BEMPs along with the ground truth measurements. In addition, in this study, factors affecting the accuracy of the calculation results are explored. The results of the estimated direct incident solar radiation show that the proposed method achieves the best accuracy, followed by the methods used in DOE-2, EnergyPlus, and DeST. The proposed method guarantees that the hourly direct solar insolation will remain the same and reflects the variation in the direct solar irradiance across a 1-h time frame. The proposed method can be adopted in BEMPs to improve the accuracy of the solar radiation calculation, thereby improving the accuracy of the simulated building performance and the BIPV production.

14 SOLAR ENERGY↗

DOE OSTI2024

Vegetation Warming Experiment: Plant Physiology, Utqiagvik (Barrow), Alaska, 2021

Leaf gas exchange measurements on Carex aquatilis Wahlenb. following a single season warming treatment. Data were collected in 2021 from 5 treatment warming chambers and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Data include CO2 response (ACi) curves, light response (AQ) curves, and dark-adapted respiration (Rdark) logged data measured at controlled leaf temperatures from 5–25 °C. The data package includes 4 data files in .csv format, 10 metadata files and the complete instrument output for all measurements. These data were collected as part of an experiment using Zero Power Warming (ZPW) chambers that delivered a single season warming treatment of ~4 °C above ambient air temperature. Four different plant species were targeted over four experimental years from 2017–2021. See related data packages for processed gas exchange data, leaf trait data (leaf mass per area, leaf nitrogen concentration), ambient and chamber environmental conditions, phenocamera images, thaw depth and GPS locations of chambers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) 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).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

MBARI-WEC September and October 2022 Field Data

This data is needed to simulate a model of the MBARI-WEC (Monterey Bay Aquarium Research Institute, Wave Energy Converter device) in a simulation environment (e.g. Gazebo) for 56 observation dates in the time between September and October 2022, and to compare the simulation outputs to the corresponding field data of the physical MBARI-WEC. There were 50 observations chosen in Sept and 6 observations in Oct. To help understand terms below, a summary of the system can be found at the github link in the downloads section below. The Gazebo MBARI-WEC model is also provided, should users wish to simulate using this platform. There are 4 *mat files included. ................................................................................................................................................................................................................................... Spectrum and Simulation Inputs: September2022_spectrum_siminputs.mat and October2022_spectrum_siminputs.mat has data needed for simulation inputs in table format. These include the ocean spectrum for an observation and operating parameters of the MBARI-WEC during that observation. They are organized as rows representing an observation and columns representing data. For example, for the September *mat there are 50 rows. The first 7 columns are Datetime, sig_waveheight, peak_period, mean_period, heaveconedoor_status, pistonpos_mean, and scale_factor: - Datetime is the date and time the observation occurred in PST - sig_waveheight is the significant wave height of the ocean spectrum during that observation in meters - peak_period is the peak period of the ocean spectrum during that observation in seconds - mean_period is the mean period of the ocean spectrum during that observation in seconds - heaveconedoor_status is the status of the heave cone doors where 0 represents the doors are open and 1 represents they are closed - pistonpos_mean is the mean position of the PTO ram (piston) in meters - scale_factor is an additional factor of 0.5 --1.4 applied to a default damping relationship The next columns are data needed to represent the ocean spectrum. First are the frequencies [Hz] labeled as "f0-f38", then the variance density [m2/Hz] labeled as "vardens0-vardens38". October2022_spectrum_siminputs.mat follows as a similar format as above, but includes a larger amount of ocean spectrum frequencies and variance density elements. ................................................................................................................................................................................................................................... Field data: The field data is found in MBARIWEC_septdata.mat and MBARIWEC_octdata.mat for the observations of September and October, respectively. These contain data in a struct format. The struct contains the following fields for each observation: PC_BattCurr, PC_LoadCurr, PC_RPM, PC_Voltage, SC_Range, SC_Velocity, DateTime, where: - PC_BattCurr is the current flowing to or from the onboard batteries in Amps - PC_LoadCurr is the current flowing to the load dump in Amps - PC_RPM is the electric/hydraulic motor shaft speed (directly coupled) in RPM - PC_Voltage is the bus voltage at the power converter in Volts - SC_Range is the PTO ram (piston) position in meters where 0 is fully retracted and 2.03 is fully extended - SC_Velocity is the PTO ram (piston) velocity in meters/sec - DateTime is the date and time of the sampled field data in each observation in PST - Electric Power is equal to: PC_Voltage*(PC_BattCurr + PC_LoadCurr) in Watts For example, upon loading MBARIWEC_octdata.mat, the aforementioned fields would be loaded, each with {6x1} cells for the 6 observations chosen in October. Within the first cell of e.g. SC_Range would be sampled data representing the field data of the MBARIWEC PTO piston position for say, one hour, of the first October observation. The corresponding field DateTime would...

16 TIDAL AND WAVE POWER↗

DOE OSTI2015

TU-G-BRD-02: Automated Systematic Quality Assurance Program for Radiation Oncology Information System Upgrades

Purpose: To: (1) describe an independent, automated, systematic software-based protocol for verifying clinical data accuracy/integrity for mitigation of data corruption/loss risks following radiation oncology information system (ROIS) upgrades; and (2) report on application of this approach in an academic/community practice environment. Methods: We propose a robust approach to perform quality assurance on the ROIS after an upgrade, targeting four data sources: (1) ROIS relational database; (2) ROIS DICOM interface; (3) ROIS treatment machine data configuration; and (4) ROIS-generated clinical reports. We investigated the database schema for differences between pre-/post-upgrade states. Paired DICOM data streams for the same object (such as RT-Plan/Treatment Record) were compared between pre-/post-upgrade states for data corruption. We examined machine configuration and related commissioning data files for changes and corruption. ROIS-generated treatment appointment and treatment parameter reports were compared to ensure patient encounter and treatment plan accuracy. This protocol was supplemented by an end-to-end clinical workflow test to verify essential ROI functionality and integrity of components interfaced during patient care chain of activities. We describe the implementation of this protocol during a Varian ARIA system upgrade at our clinic. Results: We verified 1,638 data tables with 2.4 billion data records. For 222 under-treatment patients, 605 DICOM RT plans and 13,480 DICOM treatment records retrieved from the ROIS DICOM interface were compared, with no differences in fractions, doses delivered, or treatment parameters. We identified 82 new data tables and 78 amended/deleted tables consistent with the upgrade. Reports for 5,073 patient encounters over a 2-week horizon were compared and were identical to those before the upgrade. Content in 12,237 xml machine files was compared, with no differences identified. Conclusion: An independent QA/validation approach for ROIS upgrades was developed and implemented at our clinic. The success of this approach ensures a robust QA of ROIS upgrades without manual paper/electronic checks and associated intensive labor.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Leaf Nitrogen and Carbon Content, and Leaf Mass Per Area, Kougarok Road, Seward Peninsula, Alaska, 2018

Nitrogen and carbon content, leaf mass per area (LMA) and leaf water content (LWC) of leaves sampled from locations on the Kougarok mile marker 64 NGEE Arctic site, Seward Peninsula, Alaska. Samples were collected in July 2018 from Alnus viridis, Betula nana, Betula glandulosa, Arctostaphylos alpina and Salix pulchra. This data package includes leaf sample information and trait data (*.csv). Metadata files include data descriptions (_dd.csv) for tabular data and a key to species symbols used in data files. All included files are listed and described in NGA207_flmd.csv. See data package NGA208 "Full spectrum 350-2500 nm canopy spectral reflectance, Seward Peninsula, Alaska, 2018" for linked canopy spectral reflectance data, dGPS locations and sample photographs. 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).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

HERO WEC - Bills of Materials: WEC, RO System, and Submersible Pump

This submission includes detailed Bills of Materials for the NREL-designed and -built Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), as well as the reverse osmosis assembly and submersible pump that are used in the HERO WEC. The WEC file is specific to the components and sub-components that are included on the in-water buoy portion of the WEC. The RO file is specific to the components and sub-components that are included on the reverse osmosis module that is used for both the hydraulic and electric configuration. The submersible pumps file is specific to the components and sub-components that are included on the submersible pump module that is used feed the reverse osmosis module when the HERO WEC is in the electric configuration. In addition to this submission, an additional submission available for the WEC model itself, including the power electronics enclosure, and reverse osmosis assembly that is needed to supply water in the electric submission. A link is provided below. More details on this project including data, CAD drawings, etc. can be found in the HERO-WEC main page link below. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗

DOE OSTI2020

Processed data from the Building Management System for the System Engineering Building.

The dataset spans November 2018 to May 2020 and includes time-series measurements corresponding to supply and return temperatures of air and water, air, hot water and cold water flow rates, energy and power consumption, set-points etc. as a single CSV file. In addition to the measurements, a metadata .json file, and a .ttl file to visualize the data as per BRICK schema are also included.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

FLASSH 1.0: Thermal Scattering Law Evaluation and Cross Section Generation

The Full Law Analysis Scattering System Hub ( FLASSH ) is an advanced code which evaluates the thermal scattering law (i.e. TSL, S(α,β)) for thermal scattering cross sections and resonance Doppler broadening. The ability to accurately capture these two key cross section features is dependent on accurate, high fidelity TSL evaluations. FLASSH 1.0 provides advanced physics capabilities resulting in an improved, generalized TSL to most accurately represent the lattice dynamics within any material. This improved TSL will allow for consistent analysis in both the thermal and epithermal energy ranges. The features for TSL analysis are packaged within the FLASSH GUI for easy user interface along with data output in many file formats including ENDF File 7 and ACE files.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

AutoLabs: cognitive multi-agent systems with self-correction for autonomous chemical experimentation

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs approaches expert-authored reference procedures on the benchmark (F1-score > 0.89) on challenging multi-plate syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Deep Learning on Operational Facility Data Related to Large-Scale Distributed Area Scientific Workflows

Abstract—Distributed computing platforms provide a robust mechanism to perform large-scale computations by splitting the task and data among multiple locations, possibly located thousands of miles apart geographically. This distribution of resources can lead to benefits such as redundancy of data, engagement with scientific teams that involve a diverse group of domain experts distributed spatially around the globe. It allows scientists to share their expertise and data with everyone and achieve insights by deploying collective intelligence of entire team. However, this distributed computing comes with its associated problems such as rampant duplication of file transfers increasing congestion, long job completion times, unexpected site crashing, suboptimal data transfer rates, unpredictable reliability in a time range, overshooting congestion, suboptimal usage of storage elements. In addition, each sub-system becomes a potential failure node that can trigger system wide disruptions.

Machine Learning, Provenance, Time Series, Semanti↗

DOE OSTI2019

Applying Machine Learning to Understand Write Performance of Large-scale Parallel Filesystems

In high-performance computing (HPC), I/O performance prediction offers the potential to improve the efficiency of scientific computing. In particular, accurate prediction can make runtime estimates more precise, guide users toward optimal checkpoint strategies, and better inform facility provisioning and scheduling policies. HPC I/O performance is notoriously difficult to predict and model, however, in large part because of inherent variability and a lack of transparency in the behaviors of constituent storage system components. In this work we seek to advance the state of the art in HPC I/O performance prediction by (1) modeling the mean performance to address high variability, (2) deriving model features from write patterns, system architecture and system configurations, and (3) employing Lasso regression model to improve model accuracy. We demonstrate the efficacy of our approach by applying it to a crucial subset of common HPC I/O motifs, namely, file-per-process checkpoint write workloads. We conduct experiments on two distinct production HPC platforms—Titan at the Oak Ridge Leadership Computing Facility and Cetus at the Argonne Leadership Computing Facility—to train and evaluate our models. We find that we can attain ≤ 30% relative error for 92.79% and 99.64% of the samples in our test set on these platforms, respectively.

Xie, Bing↗

DOE OSTI2014

SU-E-J-129: A Strategy to Consolidate the Image Database of a VERO Unit Into a Radiotherapy Management System

Purpose: To present a strategy to integrate the imaging database of a VERO unit with a treatment management system (TMS) to improve clinical workflow and consolidate image data to facilitate clinical quality control and documentation. Methods: A VERO unit is equipped with both kV and MV imaging capabilities for IGRT treatments. It has its own imaging database behind a firewall. It has been a challenge to transfer images on this unit to a TMS in a radiation therapy clinic so that registered images can be reviewed remotely with an approval or rejection record. In this study, a software system, iPump-VERO, was developed to connect VERO and a TMS in our clinic. The patient database folder on the VERO unit was mapped to a read-only folder on a file server outside VERO firewall. The application runs on a regular computer with the read access to the patient database folder. It finds the latest registered images and fuses them in one of six predefined patterns before sends them via DICOM connection to the TMS. The residual image registration errors will be overlaid on the fused image to facilitate image review. Results: The fused images of either registered kV planar images or CBCT images are fully DICOM compatible. A sentinel module is built to sense new registered images with negligible computing resources from the VERO ExacTrac imaging computer. It takes a few seconds to fuse registered images and send them to the TMS. The whole process is automated without any human intervention. Conclusion: Transferring images in DICOM connection is the easiest way to consolidate images of various sources in your TMS. Technically the attending does not have to go to the VERO treatment console to review image registration prior delivery. It is a useful tool for a busy clinic with a VERO unit.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-E-T-50: Automatic Validation of Megavoltage Beams Modeled for Clinical Use in Radiation Therapy

Purpose: To automatically validate megavoltage beams modeled in XiO™ 4.50 (Elekta, Stockholm, Sweden) and Varian Eclipse™ Treatment Planning Systems (TPS) (Varian Associates, Palo Alto, CA, USA), reducing validation time before beam-on for clinical use. Methods: A software application that can automatically read and analyze DICOM RT Dose and W2CAD files was developed using MatLab integrated development environment.TPS calculated dose distributions, in DICOM RT Dose format, and dose values measured in different Varian Clinac beams, in W2CAD format, were compared. Experimental beam data used were those acquired for beam commissioning, collected on a water phantom with a 2D automatic beam scanning system.Two methods were chosen to evaluate dose distributions fitting: gamma analysis and point tests described in Appendix E of IAEA TECDOC-1583. Depth dose curves and beam profiles were evaluated for both open and wedged beams. Tolerance parameters chosen for gamma analysis are 3% and 3 mm dose and distance, respectively.Absolute dose was measured independently at points proposed in Appendix E of TECDOC-1583 to validate software results. Results: TPS calculated depth dose distributions agree with measured beam data under fixed precision values at all depths analyzed. Measured beam dose profiles match TPS calculated doses with high accuracy in both open and wedged beams. Depth and profile dose distributions fitting analysis show gamma values < 1. Relative errors at points proposed in Appendix E of TECDOC-1583 meet therein recommended tolerances.Independent absolute dose measurements at points proposed in Appendix E of TECDOC-1583 confirm software results. Conclusion: Automatic validation of megavoltage beams modeled for their use in the clinic was accomplished. The software tool developed proved efficient, giving users a convenient and reliable environment to decide whether to accept or not a beam model for clinical use. Validation time before beam-on for clinical use was reduced to a few hours.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

TH-E-BRE-09: TrueBeam Monte Carlo Absolute Dose Calculations Using Monitor Chamber Backscatter Simulations and Linac-Logged Target Current

Purpose: To simulate and measure radiation backscattered into the monitor chamber of a TrueBeam linac; establish a rigorous framework for absolute dose calculations for TrueBeam Monte Carlo (MC) simulations through a novel approach, taking into account the backscattered radiation and the actual machine output during beam delivery; improve agreement between measured and simulated relative output factors. Methods: The ‘monitor backscatter factor’ is an essential ingredient of a well-established MC absolute dose formalism (the MC equivalent of the TG-51 protocol). This quantity was determined for the 6 MV, 6X FFF, and 10X FFF beams by two independent Methods: (1) MC simulations in the monitor chamber of the TrueBeam linac; (2) linac-generated beam record data for target current, logged for each beam delivery. Upper head MC simulations used a freelyavailable manufacturer-provided interface to a cloud-based platform, allowing use of the same head model as that used to generate the publicly-available TrueBeam phase spaces, without revealing the upper head design. The MC absolute dose formalism was expanded to allow direct use of target current data. Results: The relation between backscatter, number of electrons incident on the target for one monitor unit, and MC absolute dose was analyzed for open fields, as well as a jaw-tracking VMAT plan. The agreement between the two methods was better than 0.15%. It was demonstrated that the agreement between measured and simulated relative output factors improves across all field sizes when backscatter is taken into account. Conclusion: For the first time, simulated monitor chamber dose and measured target current for an actual TrueBeam linac were incorporated in the MC absolute dose formalism. In conjunction with the use of MC inputs generated from post-delivery trajectory-log files, the present method allows accurate MC dose calculations, without resorting to any of the simplifying assumptions previously made in the TrueBeam MC literature. This work has been partially funded by Varian Medical Systems.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2014

Poster — Thur Eve — 30: 4D VMAT dose calculation methodology to investigate the interplay effect: experimental validation using TrueBeam Developer Mode and Gafchromic film

The interplay effect between the tumor motion and the radiation beam modulation during a VMAT treatment delivery alters the delivered dose distribution from the planned one. This work present and validate a method to accurately calculate the dose distribution in 4D taking into account the tumor motion, the field modulation and the treatment starting phase. A QUASAR™ respiratory motion phantom was 4D scanned with motion amplitude of 3 cm and with a 3 second period. A static scan was also acquired with the lung insert and the tumor contained in it centered. A VMAT plan with a 6XFFF beam was created on the averaged CT and delivered on a Varian TrueBeam and the trajectory log file was saved. From the trajectory log file 10 VMAT plans (one for each breathing phase) and a developer mode XML file were created. For the 10 VMAT plans, the tumor motion was modeled by moving the isocentre on the static scan, the plans were re-calculated and summed in the treatment planning system. In the developer mode, the tumor motion was simulated by moving the couch dynamically during the treatment. Gafchromic films were placed in the QUASAR phantom static and irradiated using the developer mode. Different treatment starting phase were investigated (no phase shift, maximum inhalation and maximum exhalation). Calculated and measured isodose lines and profiles are in very good agreement. For each starting phase, the dose distribution exhibit significant differences but are accurately calculated with the methodology presented in this work.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Cantera and Cantera Electrolyte Thermodynamics Objects

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the numbers out" utility for Cantera, and as such it is very useful as a verification tool. These add-on utilities are encapsulated into a directory structure named cantera_apps, whose installation uses autoconf and also utilizes Cantera's application environment (i.e., they utilize Cantera as a library).

John Hewson, HarryMoffat↗

DOE OSTI2018

Generate reveal.js slfdeshow from reStructuredText

Rst2slldes Is a python extension package for the standard docuti!s documentation generation system. Docutlls translates a simple text markup language called reStructuredText Into a variety of formals, Including HTML and PDF. The reveal.Js presentation framework is a popular syslem klr displaying a specially prepared HTML file as a slldeshow. Because reStructuredText is far simpler to compose end read than HTML, rst2slldes is a useful tool for creating and maintaining technical presentations, which can be delivered to the audience using any web browser. Most of the functionality of rst2slldes, Including lhe ability to display equations written In LaTeX and to embed Images, Is Inherited from docutlls. Besides slightly modifying Ule HTML output to work with reveal.js, the features added by rst2slldes are the ability to embed video, and to set reveal.js configuration options.

Munro, DavidH.↗