Phase Field System Design Description

This template follows Idaho National Laboratory (INL) template TEM-140, "IT System Design Description."

commentnote

This document serves as an addendum to Framework System Design Description and captures information for Software Design Description (SDD) specific to the Phase Field application.

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 object of creating a framework is to provide an interface to application developers that saves time and provides advanced capabilities not attainable otherwise. The Multiphysics Object Oriented Simulation Environment (MOOSE), mission is just that: provide a framework for engineers and scientists to build state-of-the-art, computationally scalable finite element 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 extensible

  • 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 framework 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 the framework, modules and derivative applications. More information about the design documentation 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 Finite Element Method (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 graphical user interface (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.

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]

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 Department of Energy, Nuclear Energy (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 his or her needs. The design of each of these systems is documented on the mooseframework.org wiki in the Tutorial section. Additionally, up-to-date documentation extracted from the source is maintained on the the mooseframework.org documentation site after every successful merge to MOOSE's stable branch. After these objects are created, the 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

AuxKernels

AuxKernels/MatVecRealGradAuxKernel

AuxKernels/MaterialVectorAuxKernel

AuxKernels/MaterialVectorGradAuxKernel

AuxScalarKernels

AuxVariables

AuxVariables/MultiAuxVariables

BCs

BCs/CavityPressure

BCs/CoupledPressure

BCs/InclinedNoDisplacementBC

BCs/Periodic

BCs/Pressure

Bounds

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

Executors

FVBCs

FVInterfaceKernels

FVKernels

FluidPropertiesInterrogator

Functions

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/DynamicTensorMechanics

Kernels/HHPFCRFFSplitKernel

Kernels/PFCRFFKernel

Kernels/PolycrystalElasticDrivingForce

Kernels/PolycrystalKernel

Kernels/PolycrystalStoredEnergy

Kernels/PoroMechanics

Kernels/RigidBodyMultiKernel

Kernels/TensorMechanics

Materials

Mesh

Mesh/Partitioner

Modules

Modules/CompressibleNavierStokes

Modules/FluidProperties

Modules/HeatConduction

Modules/HeatConduction/ThermalContact

Modules/HeatConduction/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/GrandPotential

Modules/PhaseField/Nonconserved

Modules/PorousFlow

Modules/PorousFlow/BCs

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

NodalKernels

NodalNormals

Outputs

PorousFlowBasicTHM

PorousFlowFullySaturated

PorousFlowUnsaturated

Postprocessors

Preconditioning

Problem

RayBCs

RayKernels

ReactionNetwork

ReactionNetwork/AqueousEquilibriumReactions

ReactionNetwork/SolidKineticReactions

Reporters

Samplers

ScalarKernels

SpatialReactionSolver

StochasticTools

Surrogates

ThermalContact

TimeDependentReactionSolver

TimeIndependentReactionSolver

Trainers

Transfers

UserObjects

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 it's 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 the mooseframework.org wiki. Each of these systems has 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 Github.org website.

Data Design and Control

At a high level, the system is designed to process Hierarchical Input Text (HIT) input files to construct several objects that will constitute an finite element (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

MOOSE is a command-line driven program. All interaction with MOOSE and MOOSE-based codes is ultimately done through the command line. This is typical for High Performance Computing (HPC) applications that use the Message Passing Interface (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 Input/Output (I/O) or through local Application Programming Interface (API) calls. Neither the framework, nor the 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 framework 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

  • phase_field: GBAnisotropy
  • 8.6.1A material shall be provided to compute anisotropic grain boundary energies and mobilities.

    Specification(s): test1

    Design: GBAnisotropy

    Issue(s): #4580

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.6.2A material shall be provided to compute anisotropic grain boundary energies and mobilities.

    Specification(s): test2

    Design: GBAnisotropy

    Issue(s): #4580

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.6.3A material shall be provided to compute anisotropic grain boundary energies and mobilities with an inclination dependence.

    Specification(s): test3

    Design: GBAnisotropy

    Issue(s): #4580

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: GBWidthAnisotropy
  • 8.6.4The anisotropic grain boundary system shall allow the user to specify grain boundary widths independently for each interface between grains.

    Specification(s): testwidth1

    Design: GBWidthAnisotropy

    Issue(s): #8079

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: KKSCHBulk
  • 8.9.2A non-split version of the Kim-Kim-Suzuki shall be provided

    Specification(s): kks_example

    Design: KKSCHBulk

    Issue(s): #4835

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: ACMultiInterface
  • 8.11.10The system shall provide an Allen-Cahn gradient energy kernel with cross term contributions

    Specification(s): acmultiinterface

    Design: ACMultiInterface

    Issue(s): #4545

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.11.11The system shall provide an Allen-Cahn gradient energy kernel with cross term contributions, and some order parameters may be aux variables

    Specification(s): acmultiinterface_aux

    Design: ACMultiInterface

    Issue(s): #4545

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: MultiSmoothCircleIC
  • 8.12.1We shall be able to generate multiple smooth circle initial conditions with uniform radius variation type

    Specification(s): multi_test

    Design: MultiSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.12.2We shall be able to generate multiple smooth circle initial conditions with normal radius variation type

    Specification(s): multi_normal_test

    Design: MultiSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: LatticeSmoothCircleIC
  • 8.12.3We shall be able to produce a lattice of smooth circle initial conditions, allowing the circles to exist on the simulation cell boundaries and using a uniform radius variation type

    Specification(s): lattice_bounds

    Design: LatticeSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.12.4We shall be able to produce a lattice of smooth circle initial conditions, using a uniform radius variation type

    Specification(s): lattice_test

    Design: LatticeSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.12.5We shall be able to produce a lattice of smooth circle initial conditions using a normal radius variation type

    Specification(s): lattice_normal_test

    Design: LatticeSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.12.6We shall be able to create multiple SpecifiedSmoothCircleICs with a small invalue

    Specification(s): lattice_small_invalue_test

    Design: LatticeSmoothCircleIC

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: DiscreteNucleationData
  • 8.13.10The nucleation data porocessor shall return the number of currently active nuclei or whether a change to the nucleus list has occurred

    Specification(s): data

    Design: DiscreteNucleationData

    Issue(s): #12114

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • phase_field: DiscreteNucleationFromFile
  • 8.13.13The discrete nucleation system shall provide a deterministic nucleus inserter that uses tabulated time and location data from a file. This test assigns fixed radius

    Specification(s): file

    Design: DiscreteNucleationFromFile

    Issue(s): #12262

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.13.14The discrete nucleation system shall provide a deterministic nucleus inserter that uses tabulated time and location data from a file. This test assigns variable radius

    Specification(s): file2

    Design: DiscreteNucleationFromFile

    Issue(s): #14544

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: SoretDiffusion
  • 8.16.1A temperature gradient driving force for diffusion shall be added to the split form of the Cahn-Hilliard equation.

    Specification(s): split

    Design: SoretDiffusion

    Issue(s): #5324

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.16.2A temperature gradient driving force for diffusion shall be added to the split form of the Cahn-Hilliard equation, where temperature is a coupled non-linear variable

    Specification(s): split_temp

    Design: SoretDiffusion

    Issue(s): #5324

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.16.3A temperature gradient driving force for diffusion shall be added to the non-split form of the Cahn-Hilliard equation.

    Specification(s): direct

    Design: SoretDiffusion

    Issue(s): #5324

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.16.4A temperature gradient driving force for diffusion shall be added to the non-split form of the Cahn-Hilliard equation, where temperature is a coupled non-linear variable

    Specification(s): direct_temp

    Design: SoretDiffusion

    Issue(s): #5324

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: TotalFreeEnergy
  • 8.18.1We shall be able to calculate the free energy (with one variable) using an AuxKernel

    Specification(s): TotalFreeEnergy

    Design: TotalFreeEnergy

    Issue(s): #4413

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.18.2We shall be able to calculate the free energy (with two variables) using an AuxKernel

    Specification(s): 2var

    Design: TotalFreeEnergy

    Issue(s): #4413

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: GrainGrowthAction
  • 8.19.13The phase field module shall provide an action to set up grain growth problems

    Specification(s): grain_growth

    Design: GrainGrowthAction

    Issue(s): #9485

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.19.14The action to set up grain growth problems shall be able to set up an AD version of the problem which yields the same results as the non-AD version

    Specification(s): ad_grain_growth

    Design: GrainGrowthAction

    Issue(s): #13539

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.19.15The action to set up grain growth problems shall be able to set up an AD version of the problem which yields the same results as the non-AD version

    Specification(s): ad_grain_growth-jac

    Design: GrainGrowthAction

    Issue(s): #13539

    Collection(s): FUNCTIONAL

    Type(s): PetscJacobianTester

  • 8.19.16The grain growth action shall have the ability to set up problems with a pinning particle

    Specification(s): grain_growth_with_c

    Design: GrainGrowthAction

    Issue(s): #9485

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.19.17The grain growth action shall have the ability to set up problems with a temperature gradient

    Specification(s): grain_growth_with_T_grad

    Design: GrainGrowthAction

    Issue(s): #9485

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.39.4A capability to initialize polycrystal phase field variables from a file mesh shall be provided through the GrainGrowth action

    Specification(s): GrainGrowth_initial_from_file

    Design: GrainGrowthAction

    Issue(s): #13624

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: Coupleable
  • 8.20.1The phase field module shall be able to compute the gradient of the rate of the variable using automatic differentiation.

    Specification(s): diffusionrate

    Design: Coupleable

    Issue(s): #16167

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • phase_field: ADMatReaction
  • 8.23.1The system shall provide an automatic differentiation mat reaction kernel

    Specification(s): admatreaction

    Design: ADMatReaction

    Issue(s): #13484

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.23.2The Jacobian for the automatic differentiation mat reaction kernel shall be perfect

    Specification(s): admatreaction-jac

    Design: ADMatReaction

    Issue(s): #13484

    Collection(s): FUNCTIONAL

    Type(s): PetscJacobianTester

  • phase_field: Langevin Noise
  • 8.25.1A system to supply a noise field with a domain integral of zero shall be provided

    Specification(s): integral

    Design: Langevin Noise

    Issue(s): #4763

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.25.2A system to supply a normal distributed noise field with a domain integral of zero shall be provided

    Specification(s): normal

    Design: Langevin Noise

    Issue(s): #4763

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.25.3A system to supply a uniformly distributed noise field with a domain integral of zero shall be provided

    Specification(s): uniform

    Design: Langevin Noise

    Issue(s): #4763

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.25.4A system to supply a normal distributed noise field with an amplitude mask and a domain integral of zero shall be provided

    Specification(s): integral_normal_masked

    Design: Langevin Noise

    Issue(s): #4763

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.25.5The conserved noise kernel shall error out with a helpful message if a 'seed' parameter is supplied

    Specification(s): seed_error

    Design: Langevin Noise

    Issue(s): #4763

    Collection(s): FAILURE_ANALYSISFUNCTIONAL

    Type(s): RunException

  • phase_field: FourierNoise
  • 8.32.1A function that returns a new periodic random field with a lower wavelength cut-off shall be provided.

    Specification(s): fourier_noise

    Design: FourierNoise

    Issue(s): #13316

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: PolycrystalHex
  • 8.34.4A hexagonal grain structure IC shall be provided

    Specification(s): hex

    Design: PolycrystalHex

    Issue(s): #8810

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.34.5A hexagonal grain structure IC shall be provided using KDTree

    Specification(s): hex_kdtree

    Design: PolycrystalHex

    Issue(s): #8810

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: FauxPolycrystalVoronoi
  • 8.34.12The system shall support a faux voronoi tesselation grain structure IC without using FeatureFloodCount when the number of grains equal to the number of order parameters

    Specification(s): faux_voronoi

    Design: FauxPolycrystalVoronoi

    Issue(s): #14697

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: GrainTracker
  • 8.35.1The system shall properly create and track grains when using the Nodal mode of the GrainTracker algorithm.

    Specification(s): test_nodal

    Design: GrainTracker

    Issue(s): #4765

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.2The system shall properly create and track grains when using the Elemental mode of the GrainTracker algorithm.

    Specification(s): test_elemental

    Design: GrainTracker

    Issue(s): #4881

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.3The PolycrystalVoronoi object shall create a valid coloring for a given number of grains and order parameters.

    Specification(s): test_advanced_op_assignment

    Design: GrainTracker

    Issue(s): #7005#9018

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.6The GrainTracker/PolycrystalUserObject base class shall support having only a grain halo bleeding over a periodic edge.

    Specification(s): test_halo_periodic_bc

    Design: GrainTracker

    Issue(s): #6713#8926

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.7The GrainTracker object shall support remapping order parameter values.

    Specification(s): test_remapping_serial

    Design: GrainTracker

    Issue(s): #1298

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.8The FeatureFloodCount object shall distribute the merging of features when the processor count exceeds number of order parameters for efficiency.

    Specification(s): test_remapping_parallel

    Design: GrainTracker

    Issue(s): #11805

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.9The GrainTracker object shall properly checkpoint unique grain information in serial.

    Specification(s): test_recovery_serial_part1

    Design: GrainTracker

    Issue(s): #6713#12427

    Collection(s): FUNCTIONAL

    Type(s): RunApp

  • 8.35.10The GrainTracker object shall properly recover unique grain information in serial.

    Specification(s): test_recovery_serial_part2

    Design: GrainTracker

    Issue(s): #6713#12427

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.11The GrainTracker object shall properly checkpoint unique grain information in parallel.

    Specification(s): test_recovery_parallel_part1

    Design: GrainTracker

    Issue(s): #6713#12427

    Collection(s): FUNCTIONAL

    Type(s): RunApp

  • 8.35.12The GrainTracker object shall properly recover unique grain information in parallel.

    Specification(s): test_recovery_parallel_part2

    Design: GrainTracker

    Issue(s): #6713#12427

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.14The GrainTracker shall support maintaining reserve order parameters for simulations where new grains can form.

    Specification(s): remapping_with_reserve

    Design: GrainTracker

    Issue(s): #7605

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.15The GrainTracker shall support beginning a simulation with no active grain structure.

    Specification(s): start_with_zero_grains

    Design: GrainTracker

    Issue(s): #12200

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.18The GrainTracker shall support handling the splitting of a grain during a simulation.

    Specification(s): split_grain

    Design: GrainTracker

    Issue(s): #7875

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.19The AverageFeatureVolume Postprocessor shall calculate the average volume of each active grain in a simulation.

    Specification(s): changing_avg_volume

    Design: GrainTracker

    Issue(s): #11822

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.20The GrainTracker shall support a mode where it can continue even when it fails to remap for post-modern analysis and debugging.

    Specification(s): tolerate_remap_failure

    Design: GrainTracker

    Issue(s): #11843

    Collection(s): FUNCTIONAL

    Type(s): RunApp

  • 8.35.22The system shall properly handle a single feature or grain taking up the entire domain.

    Specification(s): one_grain

    Design: GrainTracker

    Issue(s): #12216

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.23The system shall grain tracking behavior even when the number of grains equals the number of order parameters when using mode Nodal.

    Specification(s): test_faux_nodal

    Design: GrainTracker

    Issue(s): #5453

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.24The system shall grain tracking behavior even when the number of grains equals the number of order parameters when using mode Elemental.

    Specification(s): test_faux_element

    Design: GrainTracker

    Issue(s): #5453

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.35.25The system shall output individual grain tracker volumes.

    Specification(s): grain_tracker_volume

    Design: GrainTracker

    Issue(s): #7769

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.26The system shall output individual grain tracker volumes assigning each element to only one grain (conservative).

    Specification(s): grain_tracker_volume_single

    Design: GrainTracker

    Issue(s): #7769

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • 8.35.27The system shall output individual grain tracker volumes when the number of order parameters equals the number of grains.

    Specification(s): feature_flood_volume

    Design: GrainTracker

    Issue(s): #5453

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • phase_field: CHPFCRFF
  • 8.40.2The system shall support a tolerance approach to handing the natural log when using the Cahn-Hilliard RFF kernel

    Specification(s): tolerance_test

    Design: CHPFCRFF

    Issue(s): #5338

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.40.3The system shall support a cancelation approach to handing the natural log when using the Cahn-Hilliard RFF kernel

    Specification(s): cancelation_test

    Design: CHPFCRFF

    Issue(s): #5338

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.40.4The system shall support an expansion approach to handing the natural log when using the Cahn-Hilliard RFF kernel

    Specification(s): expansion_test

    Design: CHPFCRFF

    Issue(s): #5338

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: SplitCHWRes
  • 8.41.5The system shall provide a kernel option to implement transport terms for the off-diagonal Onsager matrix components

    Specification(s): SplitCHWRes

    Design: SplitCHWRes

    Issue(s): #14140

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: AllenCahn
  • 8.41.6The system shall provide a Allen-Cahn phase field formulation.

    Specification(s): AllenCahn

    Design: AllenCahn

    Issue(s): #3816

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.41.7The system shall provide perfect Jacobian contributions for the Allen-Cahn phase field formulation.

    Specification(s): analyzejacobian_AllenCahn

    Design: AllenCahn

    Issue(s): #3816

    Collection(s): FUNCTIONAL

    Type(s): AnalyzeJacobian

  • 8.41.8The system shall provide a Allen-Cahn phase field formulation with a variable dependent mobility.

    Specification(s): AllenCahnVariableL

    Design: AllenCahn

    Issue(s): #3816

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • phase_field: ADAllenCahn
  • 8.41.9The system shall provide an AD version of the Allen-Cahn phase field formulation.

    Specification(s): ADAllenCahn

    Design: ADAllenCahn

    Issue(s): #13197

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.41.10The system shall calculate a perfect Jacobian for the AD Allen-Cahn problem.

    Specification(s): ADAllenCahn-jac

    Design: ADAllenCahn

    Issue(s): #13197

    Collection(s): FUNCTIONAL

    Type(s): PetscJacobianTester

  • 8.41.11The system shall provide an AD version of the Allen-Cahn phase field formulation with a variable dependent mobility.

    Specification(s): ADAllenCahnVariableL

    Design: ADAllenCahn

    Issue(s): #13197

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.41.12The system shall calculate a perfect Jacobian for the AD Allen-Cahn problem with a variable dependent mobility.

    Specification(s): ADAllenCahnVariableL-jac

    Design: ADAllenCahn

    Issue(s): #13197

    Collection(s): FUNCTIONAL

    Type(s): PetscJacobianTester

  • phase_field: Reading EBSD Data
  • 8.43.2The system shall support reading EBSD data and initializing a Polycrystal grain structure with that data.

    Specification(s): 1phase_reconstruction

    Design: Reading EBSD Data

    Issue(s): #9110

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.3The system shall support reading EBSD data to initalized Polycrystal grain structures while supporting reduced order parameter IC assignment.

    Specification(s): 1phase_reconstruction_40x40

    Design: Reading EBSD Data

    Issue(s): #9110

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.4The system shall support reading EBSD data to initalized Polycrystal grain structures while supporting reduced order parameter IC assignment on a distributed mesh.

    Specification(s): 1phase_reconstruction_40x40_distributed

    Design: Reading EBSD Data

    Issue(s): #19150

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.5The system shall support reading EBSD data to initalized Polycrystal grain structures while supporting reduced order parameter IC assignment on a distributed mesh with pre-refinement to allow for adaptive coarsening.

    Specification(s): 1phase_reconstruction_40x40_distributed_pre_refine

    Design: Reading EBSD Data

    Issue(s): #19150

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.6The system shall support grain evolution when beginning from EBSD ICs.

    Specification(s): 1phase_evolution

    Design: Reading EBSD Data

    Issue(s): #9110

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.7The system shall support reading a single phase of EBSD data at a time to initialize PolycrystalICs.

    Specification(s): 2phase_reconstruction

    Design: Reading EBSD Data

    Issue(s): #9110#5920

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.8The system shall support reading a single phase of EBSD data at a time to initialize PolycrystalICs while supporting reduced order parameter IC assignment.

    Specification(s): 2phase_reconstruction2

    Design: Reading EBSD Data

    Issue(s): #9110#5920

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.9The system shall support reading EBSD data to initialize PolycrystalICs with discontinuous numbering.

    Specification(s): 2phase_reconstruction3

    Design: Reading EBSD Data

    Issue(s): #9110#5920

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.10The system shall support reading a single phase of EBSD data at a time to initialize PolycrystalICs while supporting reduced order parameter IC assignment and display the coloring.

    Specification(s): 2phase_reconstruction4

    Design: Reading EBSD Data

    Issue(s): #9110#5920

    Collection(s): FUNCTIONAL

    Type(s): Exodiff

  • 8.43.11The system shall support reading a single phase of EBSD data at a time to initialize PolycrystalICs and support regions within the domain that contain no grains at all.

    Specification(s): regions_without_grains

    Design: Reading EBSD Data

    Issue(s): #9110#5920

    Collection(s): FUNCTIONAL

    Type(s): CSVDiff

  • phase_field: EBSDReader
  • 8.43.12The system shall support grain evolution when beginning from EBSD ICs and compute average orientation of non-uniformly oriented grains.

    Specification(s): average_orientation

    Design: EBSDReader

    Issue(s): #13869

    Collection(s): FUNCTIONAL

    Type(s): Exodiff