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PDQ Users Manual Version 1 for PDQ Code Version 1.12

PDQ is a tool for the management of the input and execution of batch jobs for simulation codes that use a text based input system. It accomplishes this goal by operating at two levels. First, it takes input file templates (commonly known at LANL as input deck templates) and creates multiple instantiations by performing substitutions of data from table files into symbols (variables) found in the template. Second, it provides commands to submit the created files to the SLURM batch system for execution. These two activities taken together produce a whole that is greater than the sum of its parts and provides an elegant way of executing studies across multiple similar simulations while minimizing the risk of typographical errors in the input files.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero User Manual - Version 4.58

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

SIERRA Code Coupling Module: Arpeggio User Manual - Version 4.58

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SIERRA Low Mach Module: Fuego User Manual - Version 4.58

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

97 MATHEMATICS AND COMPUTING↗

SIERRA Multimechanics Module: Aria User Manual - Version 4.58

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( %3C 1 ) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic -adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

SIERRA Multimechanics Module: Aria User Manual - Version 4.52

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Aria's more advanced capabilities.

42 ENGINEERING↗

SIERRA Low Mach Module: Fuego User Manual - Version 4.52

The SIERRA Low Mach Module: Fuego along with the SIERRA Participating Media Radiation Module: Syrinx, henceforth referred to as Fuego and Syrinx, respectively, are the key elements of the ASCI fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Syrinx represents the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

42 ENGINEERING↗

SIERRA Code Coupling Module: Arpeggio User Manual - Version 4.52

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

42 ENGINEERING↗

SIERRA/Aero User Manual - Version 4.52

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

42 ENGINEERING↗

Charon User Manual (V.2.1) (Rev.01)

This manual gives usage information for the Charon semiconductor device simulator. Charon was developed to meet the modeling needs of Sandia National Laboratories and to improve on the capabilities of the commercial TCAD simulators; in particular, the additional capabilities are running very large simulations on parallel computers and modeling displacement damage and other radiation effects in significant detail. The parallel capabilities are based around the MPI interface which allows the code to be ported to a large number of parallel systems, including linux clusters and proprietary "big iron" systems found at the national laboratories and in large industrial settings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Refinery Products Volatile Organic Compounds Emissions Estimator (RP-VOC): User Manual and Technical Documentation

The estimation of well-to-distributor volatile organic compound (VOC) emissions resulting from the extraction of crude oil in an oilfield, transportation to a crude oil terminal upstream of the refinery, operation of the refinery, and subsequent pipeline and product distribution has previously been approached as a top-down industry-wide average; RP-VOC performs its core calculations using a “from-the-ground-up” approach. By taking this approach, the tool results can be used for the supply network of a single refinery, or to generalize the average performance of all refineries.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

ADETS User Manual

ADETS (Automated DEpletion Transport System) calculates coupled neutronic/isotopic results for nuclear systems and produces a large number of criticality and burnup results based on various material feed/removal specifications, power(s), and time intervals. ADETS is a fully automated tool that links the LANL MCNP Monte Carlo transport code with the SCALE system, specifically ORIGEN-ARP (radioactive decay and burnup code). Additionally, ADETS can compute the dose at various distances of the reactor using a point gamma source, whose characteristics are computed by ORIGEN-ARP. In addition, ADETS is fully coupled with the Uncertanty Quantification, Probabilistic Risk Assessment, Parameter Optimization and Data Analysis code RAVEN (developed at the Idaho National Laboratory as well). RAVEN is released with ADETS but MCNP and SCALE (ORIGEN-ARP) are not included.

42 ENGINEERING↗

SIERRA Multimechanics Module: Aria User Manual (V.5.0)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process %1Cows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

SIERRA Code Coupling Module: Arpeggio User Manual (V.5.0)

The SNL Sierra Mechanics code suite is designed to enable simulation of complex multiphysics scenarios. The code suite is composed of several specialized applications which can operate either in standalone mode or coupled with each other. Arpeggio is a supported utility that enables loose coupling of the various Sierra Mechanics applications by providing access to Framework services that facilitate the coupling. More importantly Arpeggio orchestrates the execution of applications that participate in the coupling. This document describes the various components of Arpeggio and their operability. The intent of the document is to provide a fast path for analysts interested in coupled applications via simple examples of its usage.

97 MATHEMATICS AND COMPUTING↗

SIERRA/Aero User Manual (V.5.0)

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment.

97 MATHEMATICS AND COMPUTING↗

SIERRA Low Mach Module: Fuego User Manual (V.5.0)

The SIERRA Low Mach Module: Fuego, henceforth referred to as Fuego, is the key element of the ASC fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Using MPMD coupling, Scefire and Nalu handle the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

97 MATHEMATICS AND COMPUTING↗

UQTk Version 3.1.1 User Manual

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Version 3.1.1 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sensitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

97 MATHEMATICS AND COMPUTING↗

RAVEN User Manual

RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncertainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by inputs files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused to- ward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN has started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is interested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for an important process such as peak pressure in a pipe) is exceeded under certain conditions. The initial development of RAVEN has been focused on providing dynamic risk assessment capability to RELAP-7, currently under development at the INL and, likely, future replacement of the RELAP5-3D code. Most the capabilities that have been implemented having RELAP-7 as principal focus are easily deployable for other system codes. For this reason, several side activates are currently ongoing for coupling RAVEN with soft- ware such as RELAP5-3D, etc. The aim of this document is the explanation of the input requirements, focalizing on the input structure.

97 MATHEMATICS AND COMPUTING↗