MOOSE System Design Description

This template follows INL template TEM-140, "IT System Design Description."

Introduction

Frameworks are a software development construct aiming to simplify the creation of specific classes of applications through abstraction of low-level details. The main objective of creating a framework is to provide an interface to application developers that saves time and provides advanced capabilities not attainable otherwise. The MOOSE mission is just that: provide a framework for engineers and scientists to build state-of-the-art, computationally scalable finite element or finite volume based simulation tools.

MOOSE was conceived with one major objective: to be as easy and straightforward to use by scientists and engineers as possible. MOOSE is meant to be approachable by non-computational scientists who have systems of PDEs they need to solve. Every single aspect of MOOSE was driven by this singular principle from the build system to the API to the software development cycle. At every turn, decisions were made to enable this class of users to be successful with the framework. The pursuit of this goal has led to many of the unique features of MOOSE:

  • A streamlined build system

  • An API aimed at extensibility

  • Straightforward APIs providing sensible default information

  • Integrated, automatic, and rigorous testing

  • Rapid, continuous integration development cycle

  • Codified, rigorous path for contributing

  • Applications are modular and composable

Each of these characteristics is meant to build trust in the framework by those attempting to use it. For instance, the build system is the first thing potential framework users come into contact with when they download a new software framework. Onerous dependency issues, complicated, hard to follow instructions or build failure can all result in a user passing on the platform. Ultimately, the decision to utilize a framework comes down to whether or not you trust the code in the framework and those developing it to be able to support your desired use-case. No matter the technical capabilities of a framework, without trust users will look elsewhere. This is especially true of those not trained in software development or computational science.

Developing trust in a framework goes beyond utilizing "best practices" for the code developed, it is equally important that the framework itself is built upon tools that are trusted. For this reason, MOOSE relies on a well-established code base of libMesh and PETSc. The libMesh library provides foundational capability for the finite element method and provides interfaces to leading-edge numerical solution packages such as PETSc.

With these principles in mind, an open source, massively parallel, finite element, multiphysics framework has been conceived. MOOSE is an on-going project started in 2008 aimed toward a common platform for creation of new multiphysics tools. This document provides design details pertinent to application developers as well as framework developers.

Use Cases

The MOOSE Framework is targeted at two main groups of actors: Developers and Users. Developers are the main use case. These are typically students and professionals trained in science and engineering fields with some level of experience with coding but typically very little formal software development training. The other user group is Users. Those who intend to use an application built upon the framework without writing any computer code themselves. Instead they may modify or create input files for driving a simulation, run the application, and analyze the results. All interactions through MOOSE are primarily through the command-line interface and through a customizable block-based input file.

System Purpose

The Software Design Description provided here is description of each object in the system. The pluggable architecture of the underlying framework of MOOSE makes MOOSE and MOOSE-based applications straightforward to develop as each piece of end-user (developer) code that goes into the system follows a well-defined interface for the underlying systems that those object plug into. These descriptions are provided through developer-supplied "markdown" files that are required for all new objects that are developed as part of MOOSE. More information about the design documentation for MOOSE-based applications like MOOSE can be found in Documenting MOOSE.

System Scope

The purpose of this software is to provide several libraries that can be used to build an application based upon the framework. Additionally, several utilities are provided for assisting developers and users in end-to-end FEM analysis. A brief overview of the major components are listed here:

ComponentDescription
framework libraryThe base system from which all MOOSE-based applications are created
module librariesOptional "physics" libraries that may be used in an application to provide capability
build systemThe system responsible for creating applications for a series of libraries and applications
test harnessThe extendable testing system for finding, scheduling, running, and reporting regression tests
"peacock"The GUI for building input files, executing applications, and displaying results
MooseDocsThe extendable markdown system for MOOSE providing common documentation and requirements enforcement
"stork"The script and templates for generating a new MOOSE-based application ready for building and testing
examplesA set of complete applications demonstrating the use of MOOSE's pluggable systems
tutorialsStep by step guides to building up an application using MOOSE's pluggable systems
unitAn application for unit testing individual classes or methods of C++ code

Dependencies and Limitations

The MOOSE platform has several dependencies on other software packages and has scope that is constantly evolving based upon funding, resources, priorities, and lab direction. However, the software is open-source and many features and even bugs can be offloaded to developers with appropriate levels of knowledge and direction from the main design team. The primary list of software dependencies is listed below. This list is not meant to be exhaustive. Individual operating systems may require specific packages to be installed prior to using MOOSE, which can be found on the Install MOOSE pages.

Software DependencyDescription
libMeshFinite Element Library and I/O routines
PETScSolver Package
hypreMultigrid Preconditioner
MPIA distributed parallel processing library (MPICH)

Figure 1: A diagram of the MOOSE code platform.

Definitions and Acronyms

This section defines, or provides the definition of, all terms and acronyms required to properly understand this specification.

Definitions

  • Pull (Merge) Request: A proposed change to the software (e.g. usually a code change, but may also include documentation, requirements, design, and/or testing).

  • Baseline: A specification or product (e.g., project plan, maintenance and operations (M&O) plan, requirements, or design) that has been formally reviewed and agreed upon, that thereafter serves as the basis for use and further development, and that can be changed only by using an approved change control process (NQA-1, 2009).

  • Validation: Confirmation, through the provision of objective evidence (e.g., acceptance test), that the requirements for a specific intended use or application have been fulfilled (24765:2010(E), 2010).

  • Verification: (1) The process of: evaluating a system or component to determine whether the products of a given development phase satisfy the conditions imposed at the start of that phase. (2) Formal proof of program correctness (e.g., requirements, design, implementation reviews, system tests) (24765:2010(E), 2010).

Acronyms

AcronymDescription
APIApplication Programming Interface
DOE-NEDepartment of Energy, Nuclear Energy
FEfinite element
FEMFinite Element Method
GUIgraphical user interface
HITHierarchical Input Text
HPCHigh Performance Computing
I/OInput/Output
INLIdaho National Laboratory
MOOSEMultiphysics Object Oriented Simulation Environment
MPIMessage Passing Interface
PDEspartial differential equations
SDDSoftware Design Description

Design Stakeholders and Concerns

Design Stakeholders

Stakeholders for MOOSE include several of the funding sources including DOE-NE and the INL. However, Since MOOSE is an open-source project, several universities, companies, and foreign governments have an interest in the development and maintenance of the MOOSE project.

Stakeholder Design Concerns

Concerns from many of the stakeholders are similar. These concerns include correctness, stability, and performance. The mitigation plan for each of these can be addressed. For correctness, MOOSE development requires either regression or unit testing for all new code added to the repository. The project contains several comparisons against analytical solutions where possible and also other verification methods such as MMS. For stability, MOOSE maintains multiple branches to incorporate several layers of testing both internally and for dependent applications. Finally, performance tests are also performed as part of the the normal testing suite to monitor code change impacts to performance.

System Design

The MOOSE framework itself is composed of a wide range of pluggable systems. Each system is generally composed of a single or small set of C++ objects intended to be specialized by a Developer to solve a specific problem. To accomplish this design goal, MOOSE uses several modern object-oriented design patterns. The primary overarching pattern is the "Factory Pattern". Users needing to extend MOOSE may inherit from one of MOOSE's systems to providing an implementation meeting their needs. The design of each of these systems is documented on the MOOSE homepage. Additionally, up-to-date documentation extracted from the source is maintained on the same documentation site after every successful merge to MOOSE's stable branch. After these objects are created, they can be registered with the framework and used immediately in a MOOSE input file.

System Structure

The MOOSE framework architecture consists of a core and several pluggable systems. The core of MOOSE consists of a number of key objects responsible for setting up and managing the user-defined objects of a finite element simulation. This core set of objects has limited extendability and exist for every simulation configuration that the framework is capable of running.

Adaptivity

Adaptivity/Indicators

Adaptivity/Markers

Application

AuxKernels

AuxKernels/MatVecRealGradAuxKernel

AuxKernels/MaterialVectorAuxKernel

AuxKernels/MaterialVectorGradAuxKernel

AuxScalarKernels

AuxVariables

AuxVariables/MultiAuxVariables

BCs

BCs/CavityPressure

BCs/CoupledPressure

BCs/InclinedNoDisplacementBC

BCs/Periodic

BCs/Pressure

Bounds

ChemicalComposition

Closures

Components

Constraints

Contact

ControlLogic

Controls

CoupledHeatTransfers

Covariance

DGKernels

Dampers

Debug

Debug/MaterialDerivativeTest

DeprecatedBlock

DiracKernels

Distributions

DomainIntegral

Executioner

Executioner/Adaptivity

Executioner/Predictor

Executioner/Quadrature

Executioner/TimeIntegrator

Executioner/TimeStepper

Executioner/TimeSteppers

Executors

ExplicitDynamicsContact

FVBCs

FVICs

FVInterfaceKernels

FVKernels

FluidProperties

FluidPropertiesInterrogator

Functions

FunctorMaterials

GeochemicalModelInterrogator

GlobalParams

GrayDiffuseRadiation

HeatStructureMaterials

ICs

ICs/PolycrystalICs

ICs/PolycrystalICs/BicrystalBoundingBoxIC

ICs/PolycrystalICs/BicrystalCircleGrainIC

ICs/PolycrystalICs/PolycrystalColoringIC

ICs/PolycrystalICs/PolycrystalRandomIC

ICs/PolycrystalICs/PolycrystalVoronoiVoidIC

ICs/PolycrystalICs/Tricrystal2CircleGrainsIC

InterfaceKernels

Kernels

Kernels/CHPFCRFFSplitKernel

Kernels/DynamicSolidMechanics

Kernels/DynamicTensorMechanics

Kernels/HHPFCRFFSplitKernel

Kernels/PFCRFFKernel

Kernels/PolycrystalElasticDrivingForce

Kernels/PolycrystalKernel

Kernels/PolycrystalStoredEnergy

Kernels/PoroMechanics

Kernels/RigidBodyMultiKernel

Kernels/SolidMechanics

Kernels/TensorMechanics

Likelihood

Materials

Mesh

Mesh/Partitioner

MeshDivisions

Modules

Modules/CompressibleNavierStokes

Modules/FluidProperties

Modules/HeatTransfer

Modules/HeatTransfer/ThermalContact

Modules/HeatTransfer/ThermalContact/BC

Modules/IncompressibleNavierStokes

Modules/NavierStokesFV

Modules/Peridynamics

Modules/Peridynamics/Mechanics

Modules/Peridynamics/Mechanics/GeneralizedPlaneStrain
Modules/Peridynamics/Mechanics/Master

Modules/PhaseField

Modules/PhaseField/Conserved

Modules/PhaseField/DisplacementGradients

Modules/PhaseField/EulerAngles2RGB

Modules/PhaseField/GrainGrowth

Modules/PhaseField/GrainGrowthLinearizedInterface

Modules/PhaseField/GrandPotential

Modules/PhaseField/Nonconserved

Modules/PorousFlow

Modules/PorousFlow/BCs

Modules/SolidProperties

Modules/TensorMechanics

Modules/TensorMechanics/CohesiveZoneMaster

Modules/TensorMechanics/DynamicMaster

Modules/TensorMechanics/GeneralizedPlaneStrain

Modules/TensorMechanics/GlobalStrain

Modules/TensorMechanics/LineElementMaster

Modules/TensorMechanics/Master

Modules/TensorMechanics/MaterialVectorBodyForce

MortarGapHeatTransfer

MultiApps

NEML2

NodalKernels

NodalNormals

Optimization

OptimizationReporter

Outputs

ParameterStudy

Physics

Physics/Diffusion

Physics/Diffusion/ContinuousGalerkin

Physics/Diffusion/FiniteVolume

Physics/HeatConduction

Physics/HeatConduction/FiniteElement

Physics/SolidMechanics

Physics/SolidMechanics/CohesiveZone

Physics/SolidMechanics/Dynamic

Physics/SolidMechanics/GeneralizedPlaneStrain

Physics/SolidMechanics/GlobalStrain

Physics/SolidMechanics/LineElement

Physics/SolidMechanics/LineElement/QuasiStatic

Physics/SolidMechanics/MaterialVectorBodyForce

Physics/SolidMechanics/QuasiStatic

PorousFlowBasicTHM

PorousFlowFullySaturated

PorousFlowUnsaturated

Positions

Postprocessors

Preconditioning

Problem

ProjectedStatefulMaterialStorage

RayBCs

RayKernels

ReactionNetwork

ReactionNetwork/AqueousEquilibriumReactions

ReactionNetwork/SolidKineticReactions

Reporters

Samplers

ScalarKernels

SolidProperties

SpatialReactionSolver

StochasticTools

Surrogates

ThermalContact

TimeDependentReactionSolver

TimeIndependentReactionSolver

Times

Trainers

Transfers

UserObjects

VariableMappings

Variables

Variables/CHPFCRFFSplitVariables

Variables/HHPFCRFFSplitVariables

Variables/PFCRFFVariables

Variables/PolycrystalVariables

VectorPostprocessors

XFEM

The MooseApp is the top-level object used to hold all of the other objects in a simulation. In a normal simulation a single MooseApp object is created and "run()". This object uses its Factory objects to build user defined objects which are stored in a series of Warehouse objects and executed. The Finite Element data is stored in the Systems and Assembly object while the domain information (the Mesh) is stored in the Mesh object. A series of threaded loops are used to run parallel calculations on the objects created and stored within the warehouses.

MOOSE's pluggable systems are documented on https://mooseframework.inl.gov. Each of these systems has a set of defined polymorphic interfaces and are designed to accomplish a specific task within the simulation. The design of these systems is fluid and is managed through agile methods and ticket request system on the MOOSE repository website.

Data Design and Control

At a high level, the system is designed to process HIT input files to construct several objects that will constitute an FE simulation. Some of the objects in the simulation may in turn load other file-based resources to complete the simulation. Examples include meshes or data files. The system will then assemble systems of equations and solve them using the libraries of the Code Platform. The system can then output the solution in one or more supported output formats commonly used for visualization.

Human-Machine Interface Design

The MOOSE application is a command-line driven program. All interaction with MOOSE is ultimately done through the command line. This is typical for HPC applications that use the MPI interface for running on super computing clusters. Optional GUIs may be used to assist in creating input files and launching executables on the command line.

System Design Interface

All external system interaction is performed either through file I/O or through local API calls. Neither MOOSE, nor the MOOSE framework, nor the MOOSE modules are designed to interact with any external system directly through remote procedure calls. Any code to code coupling performed using the framework are done directly through API calls either in a static binary or after loading shared libraries.

Security Structure

The MOOSE application does not require any elevated privileges to operate and does not run any stateful services, daemons or other network programs. Distributed runs rely on the MPI library.

Requirements Cross-Reference

All of the design documents for MOOSE are provided in the dependent SDD documents, please refer to the documents listed below.

References

  1. ISO/IEC/IEEE 24765:2010(E). Systems and software engineering—Vocabulary. first edition, December 15 2010.[BibTeX]
  2. ASME NQA-1. ASME NQA-1-2008 with the NQA-1a-2009 addenda: Quality Assurance Requirements for Nuclear Facility Applications. first edition, August 31 2009.[BibTeX]