MOOSE Workshop

www.mooseframework.org

Idaho National Laboratory

www.inl.gov

Established in 2005, INL is the lead nuclear energy R&D laboratory for the Department of Energy

"Establish a world-class capability in the modeling and simulation of advanced energy systems..."

  • INL is the fifth-largest employer in Idaho with 3,900 employees and more than 350 interns

  • In 2018 the INL budget was $1,172,116,000

INL is the site where 52 nuclear reactors were designed and constructed, including the first reactor to generate usable amounts of electricity: Experimental Breeder Reactor I (ERB-1)

Advanced Test Reactor (ATR)

  • World's most powerful test reactor

  • Constructed in 1967

  • Volume of 1.4 cubic meters, with 43 kg of uranium, and operates at 60C

Transient Reactor Test Facility (TREAT)

TREAT is test facility specifically designed to evaluate the response of fuels and materials to accident conditions

High-intensity (20 GW), short-duration (80 ms) neutron pulses for severe accident testing

MOOSE Introduction

Multi-physics Object Oriented Simulation Environment

History and Purpose

  • Development started in 2008

  • Open-sourced in 2014

  • Designed to solve computational engineering problems and reduce the expense and time required to develop new applications by:

    • being easily extended and maintained

    • working efficiently on a few and many processors

    • providing an object-oriented, pluggable system for creating all aspects of a simulation tool

MOOSE Team

FEM Capabilities

  • User code agnostic of dimension

  • Continuous and Discontinuous Galerkin

  • Fully Coupled, Fully Implicit (and explicit)

  • automatic differentiation (AD)

  • Unstructured mesh with FEM shapes (Quads, Tris, Hexes, Tets, Pyramids, Wedges,...)

  • Higher order geometry (curvilinear, etc.)

  • Mesh Adaptivity (refinement and coarsening)

  • Massively Parallel (MPI+Threads)

  • User code agnostic of parallelism

  • User code agnostic of shape functions

Object-oriented, pluggable system

Example Code

Software Quality

  • MOOSE follows an Nuclear Quality Assurance Level 1 (NQA-1) development process

  • all commits undergo review using GitHub Pull Requests and must pass a set of application regression tests before they are available to our users

  • MOOSE includes a test suite and documentation system to allow for agile development while maintaining a NQA-1 process

  • Utilizes the Continuous Integration Environment for Verification, Enhancement, and Testing (CIVET)

Development Process

Community

moose-users@googlegroups.com

Total posts (top) and topics (bottom) from June 1, 2019 to May 25, 2020.

Creating a Multiphysics Code

  • Multiphysics is popular, but how is it achieved?

  • Scientists are adept at creating applications in their domain

  • What about collaborating across research groups and/or disciplines?

    • Head in the sand?

    • Development of "coupling" codes?

    • Is there something better?

Modularity is Key

  • Data should be accessed through strict interfaces with code having separation of responsibilities

    • Allows for "decoupling" of code

    • Leads to more reuse and less bugs

    • Challenging for FEM: Shape functions, DOFs, Elements, QPs, Material Properties, Analytic Functions, Global Integrals, Transferred Data and much more are needed in FEM assembly

      The complexity makes computational science codes brittle and hard to reuse

  • A consistent set of "systems" are needed to carry out common actions, these systems should be separated by interfaces

MOOSE Pluggable Systems

  • Systems break apart responsibility

  • No direct communication between systems

  • Everything flows through MOOSE interfaces

  • Objects can be mixed and matched to achieve simulation goals

  • Incoming data can be changed dynamically

  • Outputs can be manipulated (e.g. multiplication by radius for cylindrical coordinates)

  • An object, by itself, can be lifted from one application and used by another

MOOSE Pluggable Systems

Actions
AuxKernels
Base
BCs
Constraints
Controls
Dampers
DGKernels
DiracKernels
Distributions
Executioners

Functions
Geomsearch
ICs
Indicators
InterfaceKernels
Kernels
LineSearches
Markers
Materials
Mesh

MeshGenerators
MeshModifiers
Multiapps
NodalKernels
Outputs
Parser
Partitioner
Postprocessors
Preconditioners
Predictors

Problems
RelationshipManagers
Samplers
Splits
TimeIntegrators
TimeSteppers
Transfers
UserObject
Utils
Variables
VectorPostprocessors

Finite-Element Reactor Fuel Simulation

MOOSE Physics Modules

Chemical Reactions
Contact
External PETSc Solver
Fluid Properties
Function Expansion Tools
Heat Conduction
Level Set
Navier Stokes
Phase Field
Porous Flow
rDG
Stochastic Tools
Tensor (solid) Mechanics
XFEM
Shallow Water (work in progress)
Ray Tracing (work in progress)

Problem Statement

Consider a system containing two pressure vessels at differing temperatures. The vessels are connected via a pipe that contains a filter consisting of close-packed steel spheres. Predict the velocity and temperature of the fluid inside the filter. The pipe is 0.304 m in length and 0.0514 m in diameter.

Pamuk and Ozdemir, "Friction factor, permeability, and inertial coefficient of oscillating flow through porous media of packed balls", Experimental Thermal and Fluid Science, v. 38, pp. 134-139, 2012.

Governing Equations

Conservation of Mass:

(1)

Conservation of Energy:

(2)

Darcy's Law:

(3)

where is the fluid velocity, is porosity, is the permeability tensor, is fluid viscosity, is the pressure, is the density, is the gravity vector, and is the temperature.

Assuming that and imposing the divergence-free condition of Eq. (1) to Eq. (3) leads to the following system of two equations in the unknowns and :

The parameters , , and are the porosity-dependent density, heat capacity, and thermal conductivity of the combined fluid/solid medium, defined by:

where is the porosity, is the specific heat, and the subscripts and refer to fluid and solid, respectively.

Material Properties

PropertyValueUnits
Viscosity of water,
Density of water, 995.7
Density of steel, 8000
Thermal conductivity of water, 0.6
Thermal conductivity of steel, 18
Specific heat capacity of water, 4181.3
Specific heat capacity of steel, 466

Tutorial Steps

Step 1: Geometry and Diffusion
Step 2: Pressure Kernel
Step 3: Pressure Kernel with Material
Step 4: Velocity Auxiliary Variable
Step 5: Heat Conduction
Step 6: Equation Coupling
Step 7: Mesh Adaptivity
Step 8: Postprocessors
Step 9: Mechanics
Step 10: Multiscale Simulation
Step 11: Custom Syntax

Step 1: Geometry and Diffusion

The first step is to solve a simple "Diffusion" problem, which requires no code. This step will introduce the basic system of MOOSE.

Step 2: Pressure Kernel

In order to implement the Darcy pressure equation, a Kernel object is needed to represent:

Step 3: Pressure Kernel with Material

Instead of passing constant parameters to the pressure diffusion Kernel object, the Material system can be used to supply the values. This allows for properties that vary in space and time as well as be coupled to variables in the simulation.

Step 4: Velocity Auxiliary Variable

The velocity is computed from the pressure based on Darcy's law as:

This velocity can be computed using the Auxiliary system.

Step 5: Heat Conduction

Solve the transient heat equation using the "heat conduction" module.

Step 6: Equation Coupling

Solve the pressure and temperature in a coupled system of equations by adding the advection term to the heat equation.

Step 7: Mesh Adaptivity

In the transient simulation, a "traveling wave" profile moves through the porous medium. Instead of using a uniform mesh to resolve the wave profile, we can dynamically adapt the mesh to the solution.

Step 8: Postprocessors

Postprocessor and VectorPostprocessor objects can be used to compute aggregate value(s) for a simulation, such as the average temperature on the boundary or the temperatures along a line within the solution domain.

Step 9: Mechanics

Thermal expansion of the porous media can be added to the coupled set of equations using the "tensor mechanics" module, without adding additional code.

Step 10: Multiscale Simulation

MOOSE is capable of running multiple applications together and transfer data between the various applications.

This problem replaces the thermal conductivity calculated by the Material with a value computed by another application that runs a phase-based micro-structure simulation.

Step 11: Custom Syntax

MOOSE includes a system to create custom input syntax for common tasks, in this step the syntax for the two equations and velocity auxiliary calculation are simplified for end-users.

Step 1: Geometry and Diffusion

First, consider the steady-state diffusion equation on the domain : find such that

where on the left, on the right and with on the remaining boundaries.

The weak form of this equation, in inner-product notation, is given by:

where are the test functions and is the finite element solution.

Input File(s)

All capabilities of MOOSE, modules, and your application are compiled into a single executable. An input file is used define which capabilities are used to perform a simulation.

MOOSE uses the "hierarchical input text" (hit) format.

[Kernels]
  [diffusion]
    type = ADDiffusion # Laplacian operator using automatic differentiation
    variable = pressure # Operate on the "pressure" variable from above
  []
[]

A basic MOOSE input file requires six parts, each of which will be covered in greater detail later.

  • [Mesh]: Define the geometry of the domain

  • [Variables]: Define the unknown(s) of the problem

  • [Kernels]: Define the equation(s) to solve

  • [BCs]: Define the boundary condition(s) of the problem

  • [Executioner]: Define how the problem will solve

  • [Outputs]: Define how the solution will be written

Step 1: Input File

[Mesh]
  type = GeneratedMesh # Can generate simple lines, rectangles and rectangular prisms
  dim = 2              # Dimension of the mesh
  nx = 100             # Number of elements in the x direction
  ny = 10              # Number of elements in the y direction
  xmax = 0.304         # Length of test chamber
  ymax = 0.0257        # Test chamber radius
[]

[Variables]
  [pressure]
    # Adds a Linear Lagrange variable by default
  []
[]

[Kernels]
  [diffusion]
    type = ADDiffusion  # Laplacian operator using automatic differentiation
    variable = pressure # Operate on the "pressure" variable from above
  []
[]

[BCs]
  [inlet]
    type = DirichletBC  # Simple u=value BC
    variable = pressure # Variable to be set
    boundary = left     # Name of a sideset in the mesh
    value = 4000        # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0           # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
[]

[Problem]
  type = FEProblem  # This is the "normal" type of Finite Element Problem in MOOSE
  coord_type = RZ   # Axisymmetric RZ
  rz_coord_axis = X # Which axis the symmetry is around
[]

[Executioner]
  type = Steady       # Steady state problem
  solve_type = NEWTON # Perform a Newton solve, uses AD to compute Jacobian terms
  petsc_options_iname = '-pc_type -pc_hypre_type' # PETSc option pairs with values below
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true # Output Exodus format
[]

Step 1: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step01_diffusion
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step1.i

Step 1: Run via Command-line


cd ~/projects/moose/tutorials/darcy-thermo_mech/step01_diffusion
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step1.i

Step 1: Visualize Result


~/projects/moose/python/peacock/peacock -r step1_out.e

Finite Element Method (FEM)

Polynomial Fitting

To introduce the concept of FEM, consider a polynomial fitting exercise. When fitting a polynomial there is a known set of points as well as a set of coefficients that are unkown for a function that has the form:

where , and are scalar coefficients and , , are "basis functions". Thus, the problem is to find , , , etc. such that passes through the points given.

More generally,

where the are coefficients to be determined. is unique and interpolary if is the same as the number of points needed to fit. This defines a linear system that must be solved to find the coefficients.

Polynomial Example

Define a set of points:

Substitute data into the model:

This leads to the following linear system for , , and :

Solving for the coefficients results in:

These coefficients define the solution function:

The solution is the function, not the coefficients.

The coefficients are meaningless, they are just numbers used to define a function.

The solution is not the coefficients, but rather the function created when they are multiplied by their respective basis functions and summed.

The function does go through the points given, but it is also defined everywhere in between.

can be evaluated at the point , for example, by computing:

where the correspond to the coefficients in the solution vector, and the are the respective functions.

Simplified FEM

FEM is a method for numerically approximating the solution to partial differential equations (PDEs).

FEM finds a solution function that is made up of "shape functions" multiplied by coefficients and added together, just like in polynomial fitting, except the functions are not typically as simple (although they can be).

The Galerkin Finite Element method is different from finite difference and finite volume methods because it finds a piecewise continuous function which is an approximate solution to the governing PDEs.

Just as in polynomial fitting you can evaluate a finite element solution anywhere in the domain.

FEM is widely applicable for a large range of PDEs and domains.

It is supported by a rich mathematical theory with proofs about accuracy, stability, convergence and solution uniqueness.

Weak Form

Using FEM to find the solution to a PDE starts with forming a "weighted residual" or "variational statement" or "weak form", this processes if referred to here as generating a weak form.

The weak form provides flexibility, both mathematically and numerically and it is needed by MOOSE to solve a problem.

Generating a weak form generally involves these steps:

  1. Write down strong form of PDE.

  2. Rearrange terms so that zero is on the right of the equals sign.

  3. Multiply the whole equation by a "test" function .

  4. Integrate the whole equation over the domain .

  5. Integrate by parts and use the divergence theorem to get the desired derivative order on your functions and simultaneously generate boundary integrals.

Integration by Parts and Divergence Theorem

Suppose is a scalar function, is a vector function, and both are continuously differentialable functions, then the product rule states:

The function can be integrated over the volume and rearranged as:

(4)

The divergence theorem transforms a volume integral into a surface integral on surface :

(5)

where is the outward normal vector for surface . Combining Eq. (4) and Eq. (5) yield:

(6)

Example: Advection-Diffusion

(1) Write the strong form of the equation:

(2) Rearrange to get zero on the right-hand side:

(3) Multiply by the test function :

(4) Integrate over the domain :

(5) Integrate by parts and apply the divergence theorem, by using Eq. (6) on the left-most term of the PDE:

Write in inner product notation. Each term of the equation will inherit from an existing MOOSE type as shown below.

(7)

Finite Element Shape Functions

Basis Functions

While the weak form is essentially what is needed for adding physics to MOOSE, in traditional finite element software more work is necessary.

The weak form must be discretized using a set of "basis functions" amenable for manipulation by a computer.

Images copyright Becker et al. (1981)

Shape Functions

The discretized expansion of takes on the following form:

where are the "basis functions", which form the basis for the the "trial function", . is the total number of functions for the discretized domain.

The gradient of can be expanded similarly:

In the Galerkin finite element method, the same basis functions are used for both the trial and test functions:

Substituting these expansions back into the example weak form (Eq. (7)) yields:

(8)

The left-hand side of the equation above is referred to as the component of the "residual vector," .

Shape Functions are the functions that get multiplied by coefficients and summed to form the solution.

Individual shape functions are restrictions of the global basis functions to individual elements.

They are analogous to the functions from polynomial fitting (in fact, you can use those as shape functions).

Typical shape function families: Lagrange, Hermite, Hierarchic, Monomial, Clough-Toucher

Lagrange shape functions are the most common, which are interpolary at the nodes, i.e., the coefficients correspond to the values of the functions at the nodes.

Example 1D Shape Functions

2D Lagrange Shape Functions

Example bi-quadratic basis functions defined on the Quad9 element:

is associated to a "corner" node, it is zero on the opposite edges.
is associated to a "mid-edge" node, it is zero on all other edges.
is associated to the "center" node, it is symmetric and on the element.

Numerical Implementation

Numerical Integration

The only remaining non-discretized parts of the weak form are the integrals. First, split the domain integral into a sum of integrals over elements:

(9)

Through a change of variables, the element integrals are mapped to integrals over the "reference" elements .

where is the Jacobian of the map from the physical element to the reference element.

Reference Element (Quad9)

Quadrature

Quadrature, typically "Gaussian quadrature", is used to approximate the reference element integrals numerically.

where is the weight function at quadrature point .

Under certain common situations, the quadrature approximation is exact. For example, in 1 dimension, Gaussian Quadrature can exactly integrate polynomials of order with quadrature points.

Quadrature applied to Eq. (9) yields an equation that can be analyzed numerically:

where is the spatial location of the quadrature point and is its associated weight.

MOOSE handles multiplication by the Jacobian () and the weight () automatically, thus your Kernel object is only responsible for computing the part of the integrand.

Sampling at the quadrature points yields:

Thus, the weak form of Eq. (8) becomes:

(10)

The second sum is over boundary faces, . MOOSE Kernel or BoundaryCondition objects provide each of the terms in square brackets (evaluated at or as necessary), respectively.

Newton's Method

Newton's method is a "root finding" method with good convergence properties, in "update form", for finding roots of a scalar equation it is defined as: , is given by

Newton's Method in MOOSE

The residual, , as defined by Eq. (10) is a nonlinear system of equations,

that is used to solve for the coefficients .

For this system of nonlinear equations Newton's method is defined as:

(11)

where is the Jacobian matrix evaluated at the current iterate:

Jacobian Free Newton Krylov (JFNK)

is a linear system solved during each Newton step.

In MOOSE an iterative Krylov method is used to produce a sequence of iterates ,

  • and remain fixed during the iterative process.

The "linear residual" at step is defined as:

(12)

MOOSE prints the norm of this vector, , at each linear iteration and the "nonlinear residual" printed by MOOSE is .

Krylov methods construct a subspace () for the iterate :

where and .

Different Krylov methods produce the iterates in different ways:

  • Conjugate Gradients: orthogonal to .

  • GMRES/MINRES: has minimum norm for in .

  • Biconjugate Gradients: is orthogonal to

The important part is that is never explicitly needed to construct the subspace, only the action of on a vector is required.

This action can be approximated by:

(13)

This form has many advantages:

  • No need to do analytic derivatives to form

  • No time needed to compute (just residual computations)

  • No space needed to store

Preconditioned JFNK

Krylov methods need preconditioning to be efficient (or even effective!), see Knoll and Keyes (2004).

  • Reduces the total number of linear iterations

  • Krylov methods, in theory, converge in the number of linear iterations equal to the number of unknowns in the system

Even though the Jacobian is never formed, JFNK methods still require preconditioning.

When using right preconditioning:

symbolically represents the preconditioning matrix or process, and with GMRES only the action of on a vector is required.

When right-preconditioned, Eq. (12) becomes:

(14)

and Eq. (13) becomes:

(15)

MOOSE Solve Types

The solve type is specified in the [Executioner] block within the input file:


[Executioner]
  solve_type = PJFNK

Available options include:

  • PJFNK: Preconditioned Jacobian Free Newton Krylov (default)

  • JFNK: Jacobian Free Newton Krylov

  • NEWTON: Performs solve using exact Jacobian for preconditioning

  • FD: PETSc computes terms using a finite difference method (debug)

JFNK

The Kernel method computeQpResidual is called to compute during the nonlinear step (Eq. (11)).

During each linear step of Eq. (12) the computeQpResidual method is called to compute using Eq. (13).

PJFNK

The Kernel method computeQpResidual is called to compute during the nonlinear step (Eq. (11)).

During each linear step of Eq. (14) the computeQpResidual method is called to compute using Eq. (15). The computeQpJacobian and computeQpOffDiagJacobian methods are used to compute values for the preconditioning matrix .

NEWTON

The Kernel method computeQpResidual is called to compute during the nonlinear step (Eq. (11)).

The computeQpJacobian and computeQpOffDiagJacobian methods are used to compute the preconditioning matrix . It is assumed that , thus the approximation in Eq. (15) is not needed allowing for the residual and Jacobian calculations to remain constant during the linear iterations in Eq. (14).

Summary

The Finite Element Method is a way of numerically approximating the solution of PDEs.

Just like polynomial fitting, FEM finds coefficients for basis functions.

The solution is the combination of the coefficients and the basis functions, and the solution can be sampled anywhere in the domain.

Integrals are computed numerically using quadrature.

Newton's method provides a mechanism for solving a system of nonlinear equations.

The Preconditioned Jacobian Free Newton Krylov (JFNK) method allows us to avoid explicitly forming the Jacobian matrix while still computing its action.

Automatic Jacobian Calculation

MOOSE uses forward mode automatic differentiation from the MetaPhysicL package.

Moving forward, the idea is for application developers to be able to develop entire apps without writing a single Jacobian statement. This has the potential to decrease application development time.

In terms of computing performance, presently AD Jacobians are slower to compute than hand-coded Jacobians, but they parallelize extremely well and can benefit from using a NEWTON solve, which often results in decreased solve time overall.

Manual Jacobian Calculation

The remainder of the tutorial will focus on using AD for computing Jacobian terms, but it is possible to compute them manually.

It is recommended that all new Kernel objects use AD.

FEM Derivative Identities

The following relationships are useful when computing Jacobian terms.

(16)(17)

Newton for a Simple Equation

Again, consider the advection-diffusion equation with nonlinear , , and :

Thus, the component of the residual vector is:

Using the previously-defined rules in Eq. (16) and Eq. (17) for and , the entry of the Jacobian is then:

That even for this "simple" equation, the Jacobian entries are nontrivial: they depend on the partial derivatives of , , and , which may be difficult or time-consuming to compute analytically.

In a multiphysics setting with many coupled equations and complicated material properties, the Jacobian might be extremely difficult to determine.

C++
Fundamentals

C Preprocessor Commands

# Should be the first character on the line

  • #include <iostream>

  • #include "myheader.h"

  • #define SOMEWORD value

  • #ifdef, #ifndef, #endif


#pragma once
#pragma clang diagnostic push
#pragma clang diagnostic ignored "-Wunused-parameter"
#pragma clang diagnostic pop

Intrinsic Data Types

Basic TypeVariant(s)
|bool|
|charunsigned
intunsigned, long, short
float|
doublelong
void|

Note, void is the "anti-datatype", used in functions returning nothing

Operators

PurposeSymbols
Math+ - * / % += -= /= %= ++ --
Comparison< > <= >= != ==
Logical Comparison&& || !
Memory* & new delete sizeof
Assignment=
Member Access-> .
Name Resolution::

Curly Braces { }

Used to group statements together

Creates new layer of scope (we will get to this)

Expressions

Composite mathematical expressions:


a = b * (c - 4) / d++;

Composite boolean expressions:


if (a && b && f()) { e = a; }

Note, Operators && and || use "short-circuiting," so "b" and "f()" in the example above may not get evaluated.

Scope resolution operator:


t = std::pow(r, 2);
b = std::sqrt(d);

Dot and Pointer Operator:


t = my_obj.someFunction();
b = my_ptr->someFunction();

Type Casting


float pi = 3.14;

int approx_pi = static_cast<int>(pi);

Limits to Type Casting

Does not work to change to fundamentally different types


float f = (float) "3.14";   // won't compile

Be careful with your assumptions


unsigned int huge_value = 4294967295; // ok
int i = static_cast<int>(huge_value); // won't work!

Control Statements

For, While, and Do-While Loops:


for (int i=0; i<10; ++i) { }
while (boolean-expression)  { }
do { } while (boolean-expression);

If-Then-Else Tests:


if (boolean-expression) { }
else if (boolean-expression) { }
else { }

In the previous examples, boolean-expression is any valid C++ statement which results in true or false, such as:

  • if (0) // Always false

  • while (a > 5)

Switch Statement


switch (expression)
{
case constant1:
  // commands to execute if
  // expression==constant1 ...
  break;
case constant2:
case constant3:
  // commands to execute if
  // expression==constant2 OR expression==constant3...
  break;
default:
  // commands to execute if no previous case matched
}

Declarations and Definitions

In C++ we split our code into multiple files

  • headers (*.h)

  • bodies (*.C)

Headers generally contain declarations

  • Statement of the types we will use

  • Gives names to types

Bodies generally contain definitions

  • Our descriptions of those types, including what they do or how they are built

  • Memory consumed

  • The operations functions perform

Declaration Examples

Free functions:


returnType functionName(type1 name1, type2 name2);

Object member functions (methods):


class ClassName
{
  returnType methodName(type1 name1, type2 name2);
};

Definition Examples

Function definition:


returnType functionName(type1 name1, type2 name2)
{
  // statesments
}

Class method definition:


returnType ClassName::methodName(type1 name1, type2 name2)
{
   // statements
}

Function Example: Addition


#include <iostream>
int addition (int a, int b)
{
  return a + b;
}

int main ()
{
  int z = addition(5,3);
  std::cout << "The result is " << z << "\n";
  return 0;
}

Forward Declaration


#include <iostream>
int addition (int a, int b);

int main ()
{
  int z = addition (5,3);
  std::cout << "The result is " << z << "\n";
  return 0;
}

int addition (int a, int b)
{
  return a + b;
}

Make

A Makefile is a list of dependencies with rules to satisfy those dependencies All MOOSE-based applications are supplied with a complete Makefile To build a MOOSE-based application just type:


make

Compiling, Linking, Executing

Compile and Link


g++ -O3 -o myExample myExample.C

Compile only


g++ -O3 -o myExample.o -c myExample.C

Link only


g++ -O3 -o myExample myExample.o

Compiler/Linker Flags

Libraries (-L) and Include (-I) path Library Names (-l)

  • Remove the leading "lib" and trailing file extension when linking

  • libutils.so would link as -lutils


g++ -I/home/permcj/include -L/home/permcj/lib -lutils -Wall -o myExec myExec.o

Execution

Basic execution


./myExec

Finding shared libraries at runtime

  • Linux: ldd and $LD_LIBRARY_PATH

  • MacOS: otool

Addition Example (continued)

Header File (add.h)


#pragma once
int addition (int a, int b); // Function declaration

Headers typically contain declarations only

Source File (add.C)


#include "add.h"
int addition (int a, int b)
{
  return a + b;
}

Driver Program (main.C)


#include "add.h"
#include <iostream>
int main ()
{
  int z = addition(5,3);
  std::cout << "The result is " << z;
  return 0;
}

Compiling the Addition Example

  1. g++ -g -c -o add.o add.C

  2. g++ -g -c -o main.o main.C

  3. g++ -g -o main main.o add.o

    • The -c flag means compile only, do not link

    • These commands can be stored in a Makefile and executed automatically with the make command

C++
Scope, Memory, and Overloading

Scope

A scope is the extent of the program where a variable can be seen and used.

  • local variables have scope from the point of declaration to the end of the enclosing block { }

  • global variables are not enclosed within any scope and are available within the entire file

Variables have a limited lifetime

  • When a variable goes out of scope, its destructor is called

Dynamically-allocated (via new) memory is not automatically freed at the end of scope

"Named" Scopes

class scope


class MyObject
{
public:
  void myMethod();
};

namespace scope


namespace MyNamespace
{
  float a;
  void myMethod();
}

Scope Resolution Operator

"double colon" :: is used to refer to members inside of a named scope


// definition of the "myMethod" function of "MyObject"
void MyObject::myMethod()
{
  std::cout << "Hello, World!\n";
}
MyNamespace::a = 2.718;
MyNamespace::myMethod();

Namespaces permit data organization, but do not have all the features needed for full encapsulation

Assignment

(Prequel to Pointers and Refs)

Recall that assignment in C++ uses the "single equals" operator:


a = b; // Assignment

Assignments are one of the most common operations in programming

Two operands are required

  • An assignable location on the left hand side (memory location)

  • An expression on the right hand side

Pointers

Native type just like an int or long

Hold the location of another variable or object in memory

Useful in avoiding expensive copies of large objects

Facilitate shared memory

  • Example: One object "owns" the memory associated with some data, and allows others objects access through a pointer

Pointer Syntax

Declare a pointer


int *p;

Use the address-of operator to initialize a pointer


int a;
p = &a;

Use the dereference operator to get or set values pointed-to by the pointer


*p = 5;                  // set value of "a" through "p"
std::cout << *p << "\n"; // prints 5
std::cout <<  a << "\n"; // prints 5

Pointer Syntax (continued)


int a = 5;
int *p;       // declare a pointer
p = &a;       // set 'p' equal to address of 'a'
*p = *p + 2;  // get value pointed to by 'p', add 2,
              // store result in same location
std::cout <<  a << "\n";  // prints 7
std::cout << *p << "\n";  // prints 7
std::cout <<  p << "\n";  // prints an address (0x7fff5fbfe95c)

Pointers are Powerful but Unsafe

On the previous slide we had this:


p = &a;

But we can do almost anything we want with p!


p = p + 1000;

Now what happens when we do this?


*p;    // Access memory at &a + 1000

References to the Rescue

A reference is an alternative name for an object (Stroustrup), think of it as an alias for the original variable


int a = 5;
int &r = a;  // define and initialize a ref
r = r + 2;
std::cout <<  a << "\n";  // prints 7
std::cout <<  r << "\n";  // prints 7
std::cout << &r << "\n";  // prints address of a

References are Safe

References cannot be modified


&r = &r + 1;   // won't compile

References never start out un-initialized


int &r;     // won't compile
  • Note, that class declarations may contain references

  • If so, initialization must occur in the constructor!

Summary: Pointers and References

A pointer is a variable that holds a memory address to another variable


int *iPtr;  // Declaration
iPtr = &c;
int a = b + *iPtr;

A reference is an alternative name for an object (Stroustrup), so it must reference an existing object


int &iRef = c;    // Must initialize
int a = b + iRef;

Calling Conventions

What happens when you make a function call?


result = someFunction(a, b, my_shape);
  • If the function changes the values inside of a, b or myshape, are those changes reflected in my code?

  • Is this call expensive? (Are arguments copied around?)

  • C++ by default is "Pass by Value" (copy) but you can pass arguments by reference (alias) with additional syntax

Swap Example (Pass by Value)


void swap(int a, int b)
{
  int temp = a;
  a = b;
  b = temp;
}
int i = 1;
int j = 2;
swap (i, j);                  // i and j are arguments
std::cout << i << " " << j;   // prints 1 2
                              // i and j are not swapped

Swap Example (Pass by Reference)


void swap(int &a, int &b)
{
  int temp = a;
  a = b;
  b = temp;
}
int i = 1;
int j = 2;
swap (i, j);                  // i and j are arguments
std::cout << i << " " << j;   // prints 2 1
                              // i and j are properly swapped

Dynamic Memory Allocation

Why do we need dynamic memory allocation?

  • Data size specified at run time (rather than compile time)

  • Persistence without global variables (scopes)

  • Efficient use of space

  • Flexibility

Dynamic Memory in C++

"new" allocates memory

"delete" frees memory

Recall that variables typically have limited lifetimes (within the nearest enclosing scope)

Dynamic memory allocations do not have limited lifetimes

  • No automatic memory cleanup!

  • Watch out for memory leaks

  • Should have a "delete" for every "new".

During normal usage, dynamic memory allocation is unnecessary.

Example: Dynamic Memory


int a;
int *b;
b = new int; // dynamic allocation, what is b's value?
a = 4;
*b = 5;
int c = a + *b;
std::cout << c;  // prints 9
delete b;

Example: Dynamic Memory Using References


int a;
int *b = new int;    // dynamic allocation
int &r = *b;         // creating a reference to newly created variable
a = 4;
r = 5;
int c = a + r;
std::cout << c;  // prints 9
delete b;

Const

The const keyword is used to mark a variable, parameter, method or other argument as constant

Typically used with references and pointers to share objects but guarantee that they will not be modified


{
  std::string name("myObject");
  print(name);
  ...
}
void print(const std::string & name)
{
  // Attempting to modify name here will
  // cause a compile time error
  ...
}

Function Overloading

In C++ you may reuse function names as long as they have different parameter lists or types. A difference only in the return type is not enough to differentiate overloaded signatures.


int foo(int value);
int foo(float value);
int foo(float value, bool is_initialized);
...

This is very useful when we get to object "constructors".

C++
Types, Templates, and
Standard Template Library (STL)

Static vs Dynamic Type Systems

C++ is a "statically-typed" language

This means that "type checking" is performed during compile-time as opposed to run-time

Python and MATLAB are examples of "dynamically-typed" languages

Static Typing Pros and Cons

Pros:

  • Safety: compilers can detect many errors

  • Optimization: compilers can optimize for size and speed

  • Documentation: flow of types and their uses in expression is self documenting

Cons:

  • More explicit code is needed to convert ("cast") between types

  • Abstracting or creating generic algorithms is more difficult

Templates

C++ implements the generic programming paradigm with "templates".

Many of the finer details of C++ template usage are beyond the scope of this short tutorial.

Fortunately, only a small amount of syntactic knowledge is required to make effective basic use of templates.


template <class T>
T getMax (T a, T b)
{
  if (a > b)
    return a;
  else
    return b;
}

Templates (continued)


template <class T>
T getMax (T a, T b)
{
  return (a > b ? a : b); // "ternary" operator
}
int i = 5, j = 6, k;
float x = 3.142; y = 2.718, z;
k = getMax(i, j);       // uses int version
z = getMax(x, y);       // uses float version
k = getMax<int>(i, j);  // explicitly calls int version

Template Specialization


template<class T>
void print(T value)
{
  std::cout << value << std::endl;
}

template<>
void print<bool>(bool value)
{
  if (value)
    std::cout << "true\n";
  else
    std::cout << "false\n";
}

Template Specialization (continued)


int main()
{
  int a = 5;
  bool b = true;
  print(a); // prints 5
  print(b); // prints true
}

C++ Standard Template Library (STL)

Using the C++ Vector Container


#include <vector>
int main()
{
  // start with 10 elements
  std::vector<int> v(10);
  for (unsigned int i=0; i<v.size(); ++i)
    v[i] = i;
}

#include <vector>
int main()
{
  // start with 0 elements
  std::vector<int> v;
  for (unsigned int i=0; i<10; ++i)
    v.push_back(i);
}

#include <vector>
int main()
{
  // start with 0 elements
  std::vector<int> v;
  v.resize(10);  // creates 10 elements
  for (unsigned int i=0; i<10; ++i)
    v[i] = i;
}

C++
Classes and Object Oriented Programming

Object Oriented Definitions

A "class" is a new data type that contains data and methods for operating on that data

  • Think of it as a "blue print" for building an object

An "interface" is defined as a class's publicly available "methods" and "members"

An "instance" is a variable of one of these new data types.

  • Also known as an "object"

  • Analogy: You can use one "blue-print" to build many buildings. You can use one "class" to build many "objects".

Object Oriented Design

Instead of manipulating data, one manipulates objects that have defined interfaces

Data encapsulation is the idea that objects or new types should be black boxes. Implementation details are unimportant as long as an object works as advertised without side effects.

Inheritance gives us the ability to abstract or "factor out" common data and functions out of related types into a single location for consistency (avoids code duplication) and enables code re-use.

Polymorphism gives us the ability to write generic algorithms that automatically work with derived types.

Encapsulation (Point.h)


class Point
{
public:
  Point(float x, float y);   // Constructor

  // Accessors
  float getX();
  float getY();
  void setX(float x);
  void setY(float y);
private:
  float _x, _y;
};

Constructors

The method that is called explicitly or implicitly to build an object

Always has the same name as the class with no return type

May have many overloaded versions with different parameters

The constructor body uses a special syntax for initialization called an initialization list

Every member that can be initialized in the initialized list - should be

  • References have to be initialized here

Point Class Definitions (Point.C)


#include "Point.h"

Point::Point(float x, float y): _x(x), _y(y) { }
float Point::getX() { return _x; }
float Point::getY() { return _y; }
void Point::setX(float x) { _x = x; }
void Point::setY(float y) { _y = y; }

The data is safely encapsulated so we can change the implementation without affecting users of this type

Changing the Implementation (Point.h)


class Point
{
public:
  Point(float x, float y);
  float getX();
  float getY();
  void setX(float x);
  void setY(float y);
private:
  // Store a vector of values rather than separate scalars
  std::vector<float> _coords;
};

New Point Class Body (Point.C)


#include "Point.h"
Point::Point(float x, float y)
{
  _coords.push_back(x);
  _coords.push_back(y);
}

float Point::getX() { return _coords[0]; }
float Point::getY() { return _coords[1]; }
void Point::setX(float x) { _coords[0] = x; }
void Point::setY(float y) { _coords[1] = y; }

Using the Point Class (main.C)


#include "Point.h"
int main()
{
  Point p1(1, 2);
  Point p2 = Point(3, 4);
  Point p3; // compile error, no default constructor
  std::cout << p1.getX() << "," << p1.getY() << "\n"
            << p2.getX() << "," << p2.getY() << "\n";
}

Operator Overloading

For some user-defined types (objects) it makes sense to use built-in operators to perform functions with those types

For example, without operator overloading, adding the coordinates of two points and assigning the result to a third object might be performed like this:


Point a(1,2), b(3,4), c(5,6);
// Assign c = a + b using accessors
c.setX(a.getX() + b.getX());
c.setY(a.getY() + b.getY());

However the ability to reuse existing operators on new types makes the following possible:


c = a + b;

Operator Overloading (continued)

Inside our Point class, we define new member functions with the special operator keyword:


Point Point::operator+(const Point & p)
{
  return Point(_x + p._x, _y + p._y);
}

Point & Point::operator=(const Point & p)
{
  _x = p._x;
  _y = p._y;
  return *this;
}

Using "Point" with Operators


#include "Point.h"

int main()
{
  Point p1(0, 0), p2(1, 2), p3(3, 4);
  p1 = p2 + p3;
  std::cout << p1.getX() << "," << p1.getY() << "\n";
}

A More Advanced Example (Shape.h)


class Shape {
public:
  Shape(int x=0, int y=0): _x(x), _y(y) {}  // Constructor
  virtual ~Shape() {} // Destructor
  virtual float area()=0;  // Pure Virtual Function
  void printPosition();    // Body appears elsewhere

protected:
  // Coordinates at the centroid of the shape
  int _x;
  int _y;
};

The Derived Class: Rectangle.h


#include "Shape.h"
class Rectangle: public Shape
{
public:
  Rectangle(int width, int height, int x=0, int y=0) :
    Shape(x,y),
    _width(width),
    _height(height)
  {}

  virtual ~Rectangle() {}

  virtual float area() { return _width * _height; }

protected:
  int _width;
  int _height;
};

A Derived Class: Circle.h


#include "Shape.h"
class Circle: public Shape
{
public:
  Circle(int radius, int x=0, int y=0) :
    Shape(x,y),
    _radius(radius)
  {}

  virtual ~Circle() {}

  virtual float area() { return PI * _radius * _radius; }
protected:
  int _radius;
  const double PI = 3.14159265359;
};

Inheritance (Is a...)

When using inheritance, the derived class can be described in terms of the base class

  • A Rectangle "is a" Shape

Derived classes are "type" compatible with the base class (or any of its ancestors)

  • We can use a base class variable to point to or refer to an instance of a derived class


Rectangle rectangle(3, 4);
Shape & s_ref = rectangle;
Shape * s_ptr = &rectangle;

Deciphering Long Declarations

Read the declaration from right to left


// mesh is a pointer to a Mesh object
Mesh * mesh;

// params is a reference to an InputParameters object
InputParameters & params;

// the following are identical
// value is a reference to a constant Real object
const Real & value;
Real const & value;

Writing a Generic Algorithm


// create a couple of shapes
Rectangle r(3, 4);
Circle c(3, 10, 10);
printInformation(r);   // pass a Rectangle into a Shape reference
printInformation(c);   // pass a Circle into a Shape reference
...
void printInformation(const Shape & shape)
{
  shape.printPosition();
  std::cout << shape.area() << '\n';
}
// (0, 0)
// 12
// (10, 10)
// 28.274

Homework Ideas

  1. Implement a new Shape called Square. Try deriving from Rectangle directly instead of Shape. What advantages/disadvantages do the two designs have?

  2. Implement a Triangle shape. What interesting subclasses of Triangle can you imagine?

  3. Add another constructor to the Rectangle class that accepts coordinates instead of height and width.

MOOSE C++ Standard

Clang Format

MOOSE uses "clang-format" to automatically format code:


git clang-format branch_name_here
  • Single spacing around all binary operators

  • No spacing around unary operators

  • No spacing on the inside of brackets or parenthesis in expressions

  • Avoid braces for single statement control statements (i.e for, if, while, etc.)

  • C++ constructor spacing is demonstrated in the bottom of the example below

File Layout

  • Header files should have a ".h" extension

  • Header files always go either into "include" or a sub-directory of "include"

  • C++ source files should have a ".C" extension

  • Source files go into "src" or a subdirectory of "src".

Files

Header and source file names must match the name of the class that the files define. Hence, each set of .h and .C files should contain code for a single class.

  • src/ClassName.C

  • include/ClassName.h

Naming

  • ClassName Class names utilize camel case, note the .h and .C filenames must match the class name.

  • methodName() Method and function names utilize camel case with the leading letter lower case.

  • _member_variable Member variables begin with underscore and are all lower case and use underscore between words.

  • local_variable Local variables are lowercase, begin with a letter, and use underscore between words

Example Code

Below is a sample that covers many (not all) of our code style conventions.


namespace moose // lower case namespace names
{
// don't add indentation level for namespaces

int // return type should go on separate line
junkFunction()
{
  // indent two spaces!
  if (name == "moose") // space after the control keyword "if"
  {
    // Spaces on both sides of '&' and '*'
    SomeClass & a_ref;
    SomeClass * a_pointer;
  }

  // Omit curly braces for single statements following an if the statement must be on its own line
  if (name == "squirrel")
    doStuff();
  else
    doOtherStuff();

  // No curly braces for single statement branches and loops
  for (unsigned int i = 0; i < some_number; ++i) // space after control keyword "for"
    doSomething();

  // space around assignment operator
  Real foo = 5.0;

  switch (stuff) // space after the control keyword "switch"
  {
    // Indent case statements
    case 2:
      junk = 4;
      break;
    case 3:
    { // Only use curly braces if you have a declaration in your case statement
      int bar = 9;
      junk = bar;
      break;
    }
    default:
      junk = 8;
  }

  while (--foo) // space after the control keyword "while"
    std::cout << "Count down " << foo;
}

// (short) function definitions on a single line
SomeClass::SomeFunc() {}

// Constructor initialization lists can all be on the same line.
SomeClass::SomeClass() : member_a(2), member_b(3) { }

// Four-space indent and one item per line for long (i.e. won't fit on one line) initialization list.
SomeOtherClass::SomeOtherClass()
  : member_a(2),
    member_b(3),
    member_c(4),
    member_d(5),
    member_e(6),
    member_f(7),
    member_g(8),
    member_h(9)
{ // braces on separate lines since func def is already longer than 1 line
}

} // namespace moose

Using auto

Use auto for most new code unless it complicates readability. Make sure your variables have good names when using auto!


auto dof = elem->dof_number(0, 0, 0);
auto & obj = getSomeObject();
auto & elem_it = mesh.active_local_elements_begin();
auto & item_pair = map.find(some_item);

// Cannot use reference here
for (auto it = obj.begin(); it != obj.end(); ++it)
  doSomething();

// Use reference here
for (auto & obj : container)
  doSomething();

Do not use auto in any kind of function or method declaration

Lambdas


// List captured variables (by value or reference) in the capture list explicitly where possible.
std::for_each(container.begin(), container.end(), [= local_var](Foo & foo) {
  foo.item = local_var;
  foo.item2 = local_var2;
});

C++11

  • Use the override keyword on overridden virtual methods

  • Use std::make_shared<T>() when allocating new memory for shared pointers

  • Use libmesh_make_unique<T>() when allocating new memory for unique pointers

  • Make use of std::move() for efficiency when possible

Variable Initialization

When creating a new variable use these patterns:


unsigned int i = 4;  // Built-in types
SomeObject junk(17); // Objects
SomeObject * stuff = new SomeObject(18); // Pointers

Trailing Whitespace and Tabs

MOOSE does not allow any trailing whitespace or tabs in the repository. Try running the following one-liner from the appropriate directory:


find . -name '*.[Chi]' -or -name '*.py' | xargs perl -pli -e 's/\s+$//'

Includes

Firstly, only include things that are absolutely necessary in header files. Please use forward declarations when you can:


// Forward declarations
class Something;

All non-system includes should use quotes and there is a space between include and the filename.


#include "LocalInclude.h"
#include "libmesh/libmesh_include.h"

#include <system_library>

In-Code Documentation

Try to document as much as possible, using Doxygen style comments


/**
 * The Kernel class is responsible for calculating the residuals for various physics.
 */
class Kernel
{
public:
  /**
   * This constructor should be used most often.  It initializes all internal
   * references needed for residual computation.
   *
   * @param system The system this variable is in
   * @param var_name The variable this Kernel is going to compute a residual for.
   */
  Kernel(System * system, std::string var_name);

  /**
   * This function is used to get stuff based on junk.
   *
   * @param junk The index of the stuff you want to get
   * @return The stuff associated with the junk you passed in
   */
  int returnStuff(int junk);

protected:
  /// This is the stuff this class holds on to.
  std::vector<int> stuff;
};

Python

Where possible, follow the above rules for Python. The only modifications are:

  1. Four spaces are used for indenting and

  2. Member variables should be named as follows:


class MyClass:
    def __init__(self):
        self.public_member
        self._protected_member
        self.__private_member

Code Recommendations

  1. Use references whenever possible

  2. Methods should return pointers to objects if returned objects are stored as pointers and references if returned objects are stored as references

  3. When creating a new class include dependent header files in the *.C file whenever possible

  4. Avoid using a global variables

  5. Every destructor must be virtual

  6. All function definitions should be in *.C files, if possible

Step 2: Pressure Kernel

Kernel Object

To implement the Darcy pressure equation, a Kernel object is needed to add the coefficient to diffusion equation.

where is the permeability tensor and is the fluid viscosity.

A Kernel is C++ class, which inherits from MooseObject that is used by MOOSE for coding volume integrals of a partial differential equation (PDE).

MooseObject

All user-facing objects in MOOSE derive from MooseObject, this allows for a common structure for all applications and is the basis for the modular design of MOOSE.

Basic Header: CustomObject.h


#pragma once

#include "BaseObject.h"

class CustomObject : public BaseObject
{
public:
  static InputParameters validParams();

  CustomObject(const InputParameters & parameters);

protected:

  virtual Real doSomething() override;

  const Real & _scale;
};

Basic Source: CustomObject.C


#include "CustomObject.h"

registerMooseObject("CustomApp", CustomObject);

InputParameters
CustomObject::validParams()
{
  InputParameters params = BaseObject::validParams();
  params.addClassDescription("The CustomObject does something with a scale parameter.");
  params.addParam<Real>("scale", 1, "A scale factor for use when doing something.");
  return params;
}

CustomObject::CustomObject(const InputParameters & parameters) :
    BaseObject(parameters),
    _scale(getParam<Real>("scale"))
{
}

double
CustomObject::doSomething()
{
  // Do some sort of import calculation here that needs a scale factor
  return _scale;
}

Input Parameters

Every MooseObject includes a set of custom parameters within the InputParameters object that is used to construct the object.

The InputParameters object for each object is created using the static validParams method, which every class contains.

validParams Declaration


static InputParameters Convection::validParams();

validParams Definition


InputParameters
Convection::validParams()
{
  InputParameters params = Kernel::validParams();  // Start with parent
  params.addRequiredParam<RealVectorValue>("velocity", "Velocity Vector");
  params.addParam<Real>("coefficient", "Diffusion coefficient");
  return params;
}

InputParameters Object

Class Description

Class level documentation may be included within the source code using the addClassDescription method.


params.addClassDescription("Use this method to provide a summary of the class being created...");

Optional Parameter(s)

Adds an input file parameter, of type int, that includes a default value of 1980.


params.addParam<int>("year", 1980, "Provide the year you were born.");

[UserObjects]
  [date_object]
    type = Date
    year = 1990
  []
[]

Required Parameter(s)

Adds an input file parameter, of type int, must be supplied in the input file.


params.addRequiredParam<int>("month", "Provide the month you were born.");

[UserObjects]
  [date_object]
    type = Date
    month = 6
  []
[]

Coupled Variable

Various types of objects in MOOSE support variable coupling, this is done using the addCoupledVar method.


params.addCoupledVar("temperature", "The temperature (C) of interest.");
params.addCoupledVar("pressure", 101.325, "The pressure (kPa) of the atomsphere.");

[Variables]
  [P][]
  [T][]
[]

[UserObjects]
  [temp_pressure_check]
    type = CheckTemperatureAndPressue
    temperature = T
    pressure = P # if not provided a value of 101.325 would be used
  []
[]

Within the input file it is possible to used a variable name, a constant value, a function, or a postprocessor name as a the right-hand side.


pressure = P
pressure = 42
pressure = 3*x     # more about this later
pressure = pp_name # more about this later

Range Checked Parameters

Input variables may be restricted to a range of values directly in the validParams function.

  params.addRangeCheckedParam<Real>(
      "growth_factor",
      2,
      "growth_factor>=1",
      "Maximum ratio of new to previous timestep sizes following a step that required the time"
      " step to be cut due to a failed solve.");

Syntax: warp.povusers.org/FunctionParser/fparser.html

Documentation

Each application is capable of generating documentation from the validParams functions.

Option 1: All parameter documentation and class description is displayed in MOOSE GUI "peacock"
Option 2: Command line --dump

  • --dump [optional search string]

  • the search string may contain wildcard characters

  • searches both block names and parameters

Option 3: Command line --show-input generates a tree based on your input file\\

Option 4: mooseframework.org/syntax

C++ Types

Built-in types and std::vector are supported via template methods:

  • addParam<Real>("year", 1980, "The year you were born.");

  • `addParam<int>("count", 1, "doc");

  • addParam<unsigned int>("another_num", "doc");

  • addParam<std::vector<int> >("vec", "doc");

Other supported parameter types include:

  • Point

  • RealVectorValue

  • RealTensorValue

  • SubdomainID

  • BoundaryID

MOOSE uses a large number of string types to make Peacock more context-aware. All of these types can be treated just like strings, but will cause compile errors if mixed improperly in the template functions.

  • SubdomainName

  • BoundaryName

  • FileName

  • VariableName

  • FunctionName

  • UserObjectName

  • PostprocessorName

  • MeshFileName

  • OutFileName

  • NonlinearVariableName

  • AuxVariableName

A complete list, see the instantiations at the bottom of framework/include/utils/MooseTypes.h.

MooseEnum

MOOSE includes a "smart" enum utility to overcome many of the deficiencies in the standard C++ enum type. It works in both integer and string contexts and is self-checked for consistency.


#include "MooseEnum.h"

// The valid options are specified in a space separated list.
// You can optionally supply the default value as a second argument.
// MooseEnums are case preserving but case-insensitive.
MooseEnum option_enum("first=1 second fourth=4", "second");

// Use in a string context
if (option_enum == "first")
  doSomething();

// Use in an integer context
switch (option_enum)
{
  case 1: ... break;
  case 2: ... break;
  case 4: ... break;
  default: ... ;
}

MooseEnum with InputParameters

Objects that have a specific set of named options should use a MooseEnum so that parsing and error checking code can be omitted.


InputParameters MyObject::validParams()
{
  InputParameters params = ParentObject::validParams();
  MooseEnum component("X Y Z");  // No default supplied
  params.addRequiredParam<MooseEnum>("component", component,
                                     "The X, Y, or Z component");
  return params;
}

Peacock will create a drop box when using MooseEnum and if an invalid value is supplied, an error message is provided.

Multiple Value MooseEnums (MultiMooseEnum)

Operates the same way as MooseEnum but supports multiple ordered options.


InputParameters MyObject::validParams()
{
  InputParameters params = ParentObject::validParams();
  MultiMooseEnum transforms("scale rotate translate");
  params.addRequiredParam<MultiMooseEnum>("transforms", transforms,
                                          "The transforms to perform");
  return params;
}

Kernel System

A system for computing the residual contribution from a volumetric term within a PDE using the Galerkin finite element method.

Kernel Object

A Kernel objects represents one or more terms in a PDE.

A Kernel object is required to compute a residual at a quadrature point, which is done by calling the computeQpResidual method.

Kernel Object Members

_u, _grad_u
Value and gradient of the variable this Kernel is operating on

_test, _grad_test
Value () and gradient () of the test functions at the quadrature points

_phi, _grad_phi
Value () and gradient () of the trial functions at the quadrature points

_q_point
Coordinates of the current quadrature point

_i, _j
Current index for test and trial functions, respectively

_qp
Current quadrature point index

Kernel Base Classes

BaseOverrideUse
Kernel
ADKernel
computeQpResidualUse when the term in the PDE is multiplied by both the test function and the gradient of the test function (_test and _grad_test must be applied)
KernelValue
ADKernelValue
precomputeQpResidualUse when the term computed in the PDE is only multiplied by the test function (do not use _test in the override, it is applied automatically)
KernelGrad
ADKernelGrad
precomputeQpResidualUse when the term computed in the PDE is only multiplied by the gradient of the test function (do not use _grad_test in the override, it is applied automatically)

Diffusion

Recall the steady-state diffusion equation on the 3D domain :

The weak form of this equation includes a volume integral, which in inner-product notation, is given by:

where are the test functions and is the finite element solution.

ADDiffusion.h


#pragma once

#include "ADKernelGrad.h"

class ADDiffusion : public ADKernelGrad
{
public:
  static InputParameters validParams();

  ADDiffusion(const InputParameters & parameters);

protected:
  virtual ADRealVectorValue precomputeQpResidual() override;
};

ADDiffusion.C


#include "ADDiffusion.h"

registerMooseObject("MooseApp", ADDiffusion);

InputParameters
ADDiffusion::validParams()
{
  auto params = ADKernelGrad::validParams();
  params.addClassDescription("Same as `Diffusion` in terms of physics/residual, but the Jacobian "
                             "is computed using forward automatic differentiation");
  return params;
}

ADDiffusion::ADDiffusion(const InputParameters & parameters) : ADKernelGrad(parameters) {}

ADRealVectorValue
ADDiffusion::precomputeQpResidual()
{
  return _grad_u[_qp];
}

Step 2: Pressure Kernel

(continued)

DarcyPressure Kernel

To implement the coefficient a new Kernel object must be created: DarcyPressure.

This object will inherit from ADDiffusion and will use input parameters for specifying the permeability and viscosity.

DarcyPressure.h


#pragma once

// Including the "ADKernel" Kernel here so we can extend it
#include "ADKernel.h"

/**
 * Computes the residual contribution: K / mu * grad_u * grad_phi.
 */
class DarcyPressure : public ADKernel
{
public:
  static InputParameters validParams();

  DarcyPressure(const InputParameters & parameters);

protected:
  /// ADKernel objects must override precomputeQpResidual
  virtual ADReal computeQpResidual() override;

  /// References to be set from input file
  const Real & _permeability;
  const Real & _viscosity;
};

DarcyPressure.C


#include "DarcyPressure.h"

registerMooseObject("DarcyThermoMechApp", DarcyPressure);

InputParameters
DarcyPressure::validParams()
{
  InputParameters params = ADKernel::validParams();
  params.addClassDescription("Compute the diffusion term for Darcy pressure ($p$) equation: "
                             "$-\\nabla \\cdot \\frac{\\mathbf{K}}{\\mu} \\nabla p = 0$");

  // Add a required parameter.  If this isn't provided in the input file MOOSE will error.
  params.addRequiredParam<Real>("permeability", "The permeability ($\\mathrm{K}$) of the fluid.");

  // Add a parameter with a default value; this value can be overridden in the input file.
  params.addParam<Real>(
      "viscosity",
      7.98e-4,
      "The viscosity ($\\mu$) of the fluid in Pa, the default is for water at 30 degrees C.");
  return params;
}

DarcyPressure::DarcyPressure(const InputParameters & parameters)
  : ADKernel(parameters),

    // Get the parameters from the input file
    _permeability(getParam<Real>("permeability")),
    _viscosity(getParam<Real>("viscosity"))
{
}

ADReal
DarcyPressure::computeQpResidual()
{
  return (_permeability / _viscosity) * _grad_test[_i][_qp] * _grad_u[_qp];
}

Step 2: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables/pressure]
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
    permeability = 0.8451e-9 # (m^2) 1mm spheres.
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Steady
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 2: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step02_darcy_pressure
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step2.i

Step 2: Run via Command-line


cd ~/projects/moose/tutorials/darcy-thermo_mech/step02_darcy_pressure
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step2.i

Step 2: Visualize Result


~/projects/moose/python/peacock/peacock -r step2_out.e

Hands-on: Laplace Young

Problem Statement

Given a domain , find such that:

and

where

Laplace-Young Solution

Mesh System

A system for defining a finite element mesh.

Creating a Mesh

For complicated geometries, we generally use CUBIT from Sandia National Laboratories cubit.sandia.gov.

Other mesh generators can work as long as they output a file format that libMesh reads.

FileMesh

FileMesh is the default type:

[Mesh]
  file = sample.msh
  dim = 3
[]

MOOSE supports reading and writing a large number of formats and could be extended to read more.

ExtensionDescription
.datTecplot ASCII file
.e, .exdSandia's ExodusII format
.froACDL's surface triangulation file
.gmvLANL's GMV (General Mesh Viewer) format
.matMatlab triangular ASCII file (read only)
.mshGMSH ASCII file
.n, .nemSandia's Nemesis format
.pltTecplot binary file (write only)
.node, .ele; .polyTetGen ASCII file (read; write)
.inpAbaqus .inp format (read only)
.ucdAVS's ASCII UCD format
.unvI-deas Universal format
.xda, .xdrlibMesh formats
.vtk, .pvtuVisualization Toolkit

GeneratedMesh

Built-in mesh generation is implemented for lines, rectangles, and rectangular prisms

[Mesh]
  type = GeneratedMesh
  dim = 2
  xmin = -1
  xmax = 1
  ymin = -1
  ymax = 1
  nx = 2
  ny = 2
  elem_type = QUAD9
[]

The sides are named in a logical way and are numbered:

  • 1D: left = 0, right = 1

  • 2D: bottom = 0, right = 1, top = 2, left = 3

  • 3D: back = 0, bottom = 1, right = 2, top = 3, left = 4, front = 5

Named Entity Support

Human-readable names can be assigned to blocks, sidesets, and nodesets that can be used throughout an input file.

A parameter that requires an ID will accept either numbers or "names".

Names can be assigned to IDs for existing meshes to ease input file maintenance.

[Mesh]
  file = three_block.e

  # These names will be applied on the fly to the
  # mesh so that they can be used in the input file
  # In addition they will show up in the output file
  block_id = '1 2 3'
  block_name = 'wood steel copper'

  boundary_id = '1 2'
  boundary_name = 'left right'
[]

[BCs]
  active = 'left right'

  [./left]
    type = DirichletBC
    variable = u
    boundary = 'left'
    value = 0
  [../]

  [./right]
    type = DirichletBC
    variable = u
    boundary = 'right'
    value = 1
  [../]
[]

[Materials]
  active = empty

  [./empty]
    type = MTMaterial
    block = 'wood steel copper'
  [../]
[]

Replicated Mesh

When running in parallel the default mode for operation is to use a replicated mesh, which creates a complete copy of the mesh for each processor.


parallel_type = replicated

Distributed Mesh

Changing the type to distributed when running in parallel operates such that only the portion of the mesh owned by a processor is stored on that processor.


parallel_type = distributed

If the mesh is too large to read in on a single processor, it can be split prior to the simulation.

  1. Copy the mesh to a large memory machine

  2. Use the --split-mesh option to split the mesh into pieces

  3. Run the executable with --use-split

Displaced Mesh

Calculations can take place in either the initial mesh configuration or, when requested, the "displaced" configuration.

To enable displacements, provide a vector of displacement variable names for each spatial dimension in the Mesh block.

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
  displacements = 'disp_x disp_y'
[]

Objects can enforce the use of the displaced mesh within the validParams function.

  params.set<bool>("use_displaced_mesh") = true;

Output System

A system for producing outputting simulation data to the screen or files.

The output system is designed to be just like any other system in MOOSE: modular and expandable.

It is possible to create multiple output objects for outputting:

  • at specific time or timestep intervals,

  • custom subsets of variables, and

  • to various file types.

There exists a short-cut syntax for common output types as well as common parameters.

Short-cut Syntax

The following two methods for creating an Output object are equivalent within the internals of MOOSE.


[Outputs]
  exodus = true
[]

[Outputs]
  [out]
    type = Exodus
  []
[]

Common Parameters


[Outputs]
  interval = 10
  exodus = true
  [all]
    type = Exodus
    interval = 1 # overrides interval from top-level
  []
[]

Output Names

The default naming scheme for output files utilizes the input file name (e.g., input.i) with a suffix that differs depending on how the output is defined: An "_out" suffix is used for Outputs created using the short-cut syntax. sub-blocks use the actual sub-block name as the suffix.


[Outputs]
  exodus = true    # creates input_out.e
  [other]          # creates input_other.e
     type = Exodus
     interval = 2
  []
  [base]
    type = Exodus
    file_base = out # creates out.e
  []
[]

The use of 'file_base' anywhere in the [Outputs] block disables all default naming behavior.

Short-cutSub-block ("type=")Description
consoleConsoleWrites to the screen and optionally a file
exodusExodusThe most common,well supported, and controllable output type
vtkVTKVisualization Toolkit format, requires --enable-vtk when building libMesh
gmvGMVGeneral Mesh Viewer format
nemesisNemesisParallel ExodusII format
tecplotTecplotRequires --enable-tecplot when building libMesh
xdaXDAlibMesh internal format (ascii)
xdrXDRlibMesh internal format (binary)
csvCSVComma separated scalar values
gnuplotGNUPlotOnly support scalar outputs
checkpointCheckpointMOOSE internal format used for restart and recovery

Step 3: Pressure Kernel with Material

Instead of passing constant parameters to the DarcyPressure object use the Material system to supply the values.

where is the permeability tensor and is the fluid viscosity.

This system allows for properties that vary in space and time, that can be coupled to variables in the simulation.

Material System

A system for defining material properties to be used by multiple systems and allow for variable coupling.

The material system operates by creating a producer/consumer relationship among objects

  • Material objects produce properties.

  • Other MOOSE objects (including materials) consume these properties.

Producing Properties

  1. Each property to be produced must be declared to be available for use, the declareProperty<TYPE>() method does this and returns a writable reference.

  2. Override computeQpProperties() to compute all of the declared properties at one quadrature point. Within this method, the references obtained from declaring the property are updated.

Consuming Properties

To consume a material property, call the correct get method in an object and store the constant reference as a member variable.

getMaterialProperty<TYPE>()
Use within non-AD objects to retrieve non-AD material properties.

getADMaterialProperty<TYPE>()
Use within AD objects to retrieve AD material properties.

Material Property Evaluation

Quantities are recomputed at quadrature points, as needed.

Multiple Material objects may define the same "property" for different parts of the subdomain or boundaries.

Stateful Material Properties

The values are not stored between timesteps unless "stateful" properties are enabled, which is accomplished by calling getMaterialPropertyOld<TYPE>() or getMaterialPropertyOlder<TYPE>()

It can be useful to have "old" values of Material properties available in a simulation, such as in solid mechanics plasticity constitutive models.

Traditionally, this type of value is called a "state variable"; in MOOSE, they are called "stateful material properties".

Stateful Material properties require more memory.

Default Material Properties

Default values for material properties may be assigned within the validParams function.


addParam<MaterialPropertyName>("combination_property_name", 12345,
 "The name of the property providing the luggage combination");

Only scalar (Real) values may have defaults.

When getMaterialProperty<Real>("combination_property_name") is called, the default will be returned if the value has not been computed via a delcareProperty call within a Material object.

Material Property Output

Output of Material properties is enabled by setting the "outputs" parameter.

The following example creates two additional variables called "mat1" and "mat2" that will show up in the output file.

[Materials]
  [block_1]
    type = OutputTestMaterial
    block = 1
    output_properties = 'real_property tensor_property'
    outputs = exodus
    variable = u
  []
  [block_2]
    type = OutputTestMaterial
    block = 2
    output_properties = 'vector_property tensor_property'
    outputs = exodus
    variable = u
  []
[]

[Outputs]
  exodus = true
[]

Supported Property Types for Output

Material properties can be of arbitrary (C++) type, but not all types can be output.

TypeAuxKernelVariable Name(s)
RealMaterialRealAuxprop
RealVectorValueMaterialRealVectorValueAuxprop_1, prop_2, and prop_3
RealTensorValueMaterialRealTensorValueAuxprop_11, prop_12, prop_13, prop_21, etc.

Function System

A system for defining analytic expressions based on the spatial location (, , ) and time, .

A Function object is created by inheriting from Function and overriding the virtual value() (and optionally other methods as well) functions.

Functions can be accessed in most MOOSE objects by calling getFunction("name"), where "name" matches a name from the input file.

Function Use

Many objects exist in MOOSE that utilize a function, such as:

  • FunctionDirichletBC

  • FunctionNeumannBC

  • FunctionIC

  • BodyForce

Each of these objects has a "function" parameter which is set in the input file, and controls which Function object is used.

Parsed Function

A ParsedFunction allow functions to be defined by strings directly in the input file, e.g.:

[Functions]
  [sin_fn]
    type = ParsedFunction
    value = sin(x)
  []
  [cos_fn]
    type = ParsedFunction
    value = cos(x)
  []
  [fn]
    type = ParsedFunction
    value = 's/c'
    vars = 's c'
    vals = 'sin_fn cos_fn'
  []
[]

It is possible to include other functions, as shown above, as well as scalar variables and postprocessor values with the function definition.

Default Functions

Whenever a Function object is added via addParam(), a default can be provided.

Both constant values and parsed function strings can be used as the default.


// Adding a Function with a default constant
params.addParam<FunctionName>("pressure_grad", "0.5", "The gradient of ...");

// Adding a Function with a default parsed function
params.addParam<FunctionName>("power_history", "t+100*sin(y)", "The power history of ...");

A ParsedFunction or ConstantFunction object is automatically constructed based on the default value if a function name is not supplied in the input file.

Step 3: Pressure Kernel with Material

(continued)

PackedColumn Material

Two material properties must be produced for consumption by DarcyPressure object: permeability and viscosity.

Both shall be computed with a single Material object: PackedColumn.

As in the reference article, permeability varies with the size of the steel spheres, so linear interpolation will be used for defining this property.

PackedColumn.h


#pragma once

#include "Material.h"

// A helper class from MOOSE that linear interpolates x,y data
#include "LinearInterpolation.h"

/**
 * Material objects inherit from Material and override computeQpProperties.
 *
 * Their job is to declare properties for use by other objects in the
 * calculation such as Kernels and BoundaryConditions.
 */
class PackedColumn : public Material
{
public:
  static InputParameters validParams();

  PackedColumn(const InputParameters & parameters);

protected:
  /// Necessary override. This is where the values of the properties are computed.
  virtual void computeQpProperties() override;

  /// The radius of the spheres in the column
  const Function & _radius;

  /// Value of viscosity from the input file
  const Real & _input_viscosity;

  /// Compute permeability based on the radius (mm)
  LinearInterpolation _permeability_interpolation;

  /// The permeability (K)
  ADMaterialProperty<Real> & _permeability;

  /// The viscosity of the fluid (mu)
  ADMaterialProperty<Real> & _viscosity;
};

PackedColumn.C


#include "PackedColumn.h"
#include "Function.h"

registerMooseObject("DarcyThermoMechApp", PackedColumn);

InputParameters
PackedColumn::validParams()
{
  InputParameters params = Material::validParams();

  // Parameter for radius of the spheres used to interpolate permeability.
  params.addParam<FunctionName>("radius",
                                "1.0",
                                "The radius of the steel spheres (mm) that are packed in the "
                                "column for computing permeability.");
  params.addParam<Real>(
      "viscosity",
      7.98e-4,
      "The viscosity ($\\mu$) of the fluid in Pa, the default is for water at 30 degrees C.");

  return params;
}

PackedColumn::PackedColumn(const InputParameters & parameters)
  : Material(parameters),

    // Get the parameters from the input file
    _radius(getFunction("radius")),
    _input_viscosity(getParam<Real>("viscosity")),

    // Declare two material properties by getting a reference from the MOOSE Material system
    _permeability(declareADProperty<Real>("permeability")),
    _viscosity(declareADProperty<Real>("viscosity"))
{
  // From the paper: Table 1
  std::vector<Real> sphere_sizes = {1, 3};
  std::vector<Real> permeability = {0.8451e-9, 8.968e-9};

  // Set the x,y data on the LinearInterpolation object.
  _permeability_interpolation.setData(sphere_sizes, permeability);
}

void
PackedColumn::computeQpProperties()
{
  Real value = _radius.value(_t, _q_point[_qp]);
  mooseAssert(value >= 1 && value <= 3,
              "The radius range must be in the range [1, 3], but " << value << " provided.");

  _viscosity[_qp] = _input_viscosity;
  _permeability[_qp] = _permeability_interpolation.sample(value);
}

DarcyPressure Kernel

The existing Kernel object uses input parameters for defining permeability and viscosity, it must be updated to consume the newly created material properties.

DarcyPressure.h


#pragma once

// Including the "ADKernel" Kernel here so we can extend it
#include "ADKernel.h"

/**
 * Computes the residual contribution: K / mu * grad_u * grad_phi.
 */
class DarcyPressure : public ADKernel
{
public:
  static InputParameters validParams();

  DarcyPressure(const InputParameters & parameters);

protected:
  /// ADKernel objects must override precomputeQpResidual
  virtual ADReal computeQpResidual() override;

  // References to be set from Material system

  /// The permeability. Note that this is declared as a \p MaterialProperty. This means that if
  /// calculation of this property in the producing \p Material depends on non-linear variables, the
  /// derivative information will be lost here in the consumer and the non-linear solve will suffer
  const ADMaterialProperty<Real> & _permeability;

  /// The viscosity. This is declared as an \p ADMaterialProperty, meaning any derivative
  /// information coming from the producing \p Material will be preserved and the integrity of the
  /// non-linear solve will be likewise preserved
  const ADMaterialProperty<Real> & _viscosity;
};

DarcyPressure.C


#include "DarcyPressure.h"

registerMooseObject("DarcyThermoMechApp", DarcyPressure);

InputParameters
DarcyPressure::validParams()
{
  InputParameters params = ADKernel::validParams();
  params.addClassDescription("Compute the diffusion term for Darcy pressure ($p$) equation: "
                             "$-\\nabla \\cdot \\frac{\\mathbf{K}}{\\mu} \\nabla p = 0$");
  return params;
}

DarcyPressure::DarcyPressure(const InputParameters & parameters)
  : ADKernel(parameters),
    _permeability(getADMaterialProperty<Real>("permeability")),
    _viscosity(getADMaterialProperty<Real>("viscosity"))
{
}

ADReal
DarcyPressure::computeQpResidual()
{
  return (_permeability[_qp] / _viscosity[_qp]) * _grad_test[_i][_qp] * _grad_u[_qp];
}

Step 3: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables/pressure]
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
[]

[Materials]
  [column]
    type = PackedColumn
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Steady
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 3: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step03_darcy_material
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step3.i

Step 3: Run via Command-line


cd ~/projects/moose/tutorials/darcy-thermo_mech/step03_darcy_material
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step3.i

Step 3: Visualize Result


~/projects/moose/python/peacock/peacock -r step3_out.e

Step 3b: Variable Spheres

Update the input file to vary the sphere size from 1 to 3 along the length of the pipe.

Step 3b: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables/pressure]
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = '1 + 2/3.04*x'
    outputs = exodus
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Steady
  solve_type = PJFNK
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 3b: Visualize Result

Test System

Overview

MOOSE includes an extendable test system (python) for executing code with different input files.

Each kernel (or logical set of kernels) should have test(s) for verification.

The test system is flexible, it performs many different operations such as testing for expected error conditions.

Additionally, custom "Tester" objects can be created.

Test Setup

Related tests should be grouped into an individual directory and have a consistent naming convention.

It is recommended to organize tests in a hierarchy similar to the application source (i.e., kernels, BCs, materials, etc).

Tests are found dynamically by matching patterns (highlighted below)


tests/
  kernels/
    my_kernel_test/
      my_kernel_test.e   [input mesh]
      my_kernel_test.i   [input file]
      tests              [test specification file]
      gold/              [gold standard folder for validated solution]
      out.e              [solution]

Test Specification

Test specifications use the hit format, the same format as the standard MOOSE input file.


[Tests]
   [my_kernel_test]
     type    = Exodiff
     input   = my_kernel_test.i
     exodiff = my_kernel_test_out.e
   []

   [kernel_check_exception]
     type       = RunException
     input      = my_kernel_exception.i
     expect_err = 'Bad stuff happened with variable \w+'
   []
 []

Test Objects

RunApp: Runs a MOOSE-based application with specified options
Exodiff: Checks Exodus files for differences within specified tolerances
CSVDiff: Checks CSV files for differences within specified tolerances
VTKDiff: Checks VTK files for differences within specified tolerances
RunException: Tests for error conditions
CheckFiles: Checks for the existence of specific files after a completed run
ImageDiff: Compares images (e.g., *.png) for differences within specified tolerances
PythonUnitTest: Runs python "unittest" based tests
AnalyzeJacobian: Compares computed Jacobian with finite difference version
PetscJacobianTester: Compares computed Jacobian using PETSc

Running Tests


./run_tests -j 12

For more information view the help:


./run_tests -h

Test Object Options


./run_tests --dump

input: The name of the input file
exodiff: The list of output filenames to compare
abs_zero: Absolute zero tolerance for exodiff
rel_err: Relative error tolerance for exodiff
prereq: Name of the test that needs to complete before running this test
min_parallel: Minimum number of processors to use for a test (default: 1)
max_parallel: Maximum number of processors to use for a test

Notes on Tests

Individual tests should run relatively quickly (2 second rule)

Outputs or other generated files should not be checked into the repository

MOOSE developers rely on application tests when refactoring to verify correctness

  • poor test coverage = higher code failure rate

Step 4: Velocity Auxiliary Variable

The velocity is the primary variable of interest, it is computed base on the pressure as:

Auxiliary System

A system for direct calculation of field variables ("AuxVariables") that is designed for postprocessing, coupling, and proxy calculations.

The term "nonlinear variable" is defined, in MOOSE language, as a variable that is being solved for using a nonlinear system of PDEs using Kernel and BoundaryCondition objects.

The term "auxiliary variable" is defined, in MOOSE language, as a variable that is directly calculated using an AuxKernel object.

AuxVariables

Auxiliary variables are declared in the [AuxVariables] input file block

Auxiliary variables are field variables that are associated with finite element shape functions and can serve as a proxy for nonlinear variables

Auxiliary variables currently come in two flavors:

  • Element (constant or higher order monomials)

  • Nodal (linear Lagrange)

Auxiliary variables have "old" and "older" states just like nonlinear variables

Elemental Auxiliary Variables

Element auxiliary variables compute average values per element (constant)

AuxKernel objects computing elemental values can couple to nonlinear variables and both element and nodal auxiliary variables


[AuxVariables]
  [aux]
    order = CONSTANT
    family = MONOMIAL
  []
[]

Nodal Auxiliary Variables

Element auxiliary variables are computed at each node and are stored as linear Lagrange variables

AuxKernel objects computing nodal values can only couple to nonlinear variables and other nodal auxiliary variables


[AuxVariables]
  [aux]
    order = LAGRANGE
    family = FIRST
  []
[]

AuxKernel Objects

Directly compute AuxVariable values by overriding computeValue() and they can operate on both elemental and nodal auxiliary variable.

When operating on a nodal variable computeValue() operates on each node; when operating on a elemental variable it operates on each element.

AuxKernel Object Members

_u, _grad_u
Value and gradient of variable this AuxKernel is operating on

_q_point
Coordinates of the current q-point that is only valid for elemental AuxKernels, _current_node should be used for nodal variables

_qp
Current quadrature point, this is used for both nodal and elemental variables for consistency

_current_elem
Pointer to the current element that is being operated on (elemental only)

_current_node
Pointer to the current node that is being operated on (nodal only)

VectorAuxKernel Objects

Directly compute a vector AuxVariable values by overriding computeValue(), with the difference being the return value of a RealVectorValue instead of Real.


[AuxVariables]
  [aux]
    order = FIRST
    family = LAGRANGE_VEC
  []
[]

Step 4: Velocity Auxiliary Variable

(continued)

DarcyVelocity AuxKernel

The primary unknown ("nonlinear variable") is the pressure

Once the pressure is computed, the AuxiliarySystem can compute and output the velocity field using the coupled pressure variable and the permeability and viscosity properties.

Auxiliary variables come in two flavors: Nodal and Elemental.

Nodal auxiliary variables cannot couple to gradients of nonlinear variables since gradients of continuous variables are not well-defined at the nodes.

Elemental auxiliary variables can couple to gradients of nonlinear variables since evaluation occurs in the element interiors.

DarcyVelocity.h


#pragma once

#include "AuxKernel.h"

/**
 * Auxiliary kernel responsible for computing the Darcy velocity given
 * several fluid properties and the pressure gradient.
 */
class DarcyVelocity : public VectorAuxKernel
{
public:
  static InputParameters validParams();

  DarcyVelocity(const InputParameters & parameters);

protected:
  /**
   * AuxKernels MUST override computeValue.  computeValue() is called on
   * every quadrature point.  For Nodal Auxiliary variables those quadrature
   * points coincide with the nodes.
   */
  virtual RealVectorValue computeValue() override;

  /// The gradient of a coupled variable
  const VariableGradient & _pressure_gradient;

  /// Holds the permeability and viscosity from the material system
  const ADMaterialProperty<Real> & _permeability;
  const ADMaterialProperty<Real> & _viscosity;
};

DarcyVelocity.C


#include "DarcyVelocity.h"

#include "metaphysicl/raw_type.h"

registerMooseObject("DarcyThermoMechApp", DarcyVelocity);

InputParameters
DarcyVelocity::validParams()
{
  InputParameters params = VectorAuxKernel::validParams();

  // Add a "coupling paramater" to get a variable from the input file.
  params.addRequiredCoupledVar("pressure", "The pressure field.");

  return params;
}

DarcyVelocity::DarcyVelocity(const InputParameters & parameters)
  : VectorAuxKernel(parameters),

    // Get the gradient of the variable
    _pressure_gradient(coupledGradient("pressure")),

    // Set reference to the permeability MaterialProperty.
    // Only AuxKernels operating on Elemental Auxiliary Variables can do this
    _permeability(getADMaterialProperty<Real>("permeability")),

    // Set reference to the viscosity MaterialProperty.
    // Only AuxKernels operating on Elemental Auxiliary Variables can do this
    _viscosity(getADMaterialProperty<Real>("viscosity"))
{
}

RealVectorValue
DarcyVelocity::computeValue()
{
  // Access the gradient of the pressure at this quadrature point, then pull out the "component" of
  // it requested (x, y or z). Note, that getting a particular component of a gradient is done using
  // the parenthesis operator.
  return -MetaPhysicL::raw_value(_permeability[_qp] / _viscosity[_qp]) * _pressure_gradient[_qp];
}

Step 4: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables/pressure]
[]

[AuxVariables]
  [velocity_x]
    order = CONSTANT
    family = MONOMIAL
  []
  [velocity_y]
    order = CONSTANT
    family = MONOMIAL
  []
  [velocity_z]
    order = CONSTANT
    family = MONOMIAL
  []
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
  [velocity_x]
    type = VectorVariableComponentAux
    variable = velocity_x
    component = x
    execute_on = timestep_end
    vector_variable = velocity
  []
  [velocity_y]
    type = VectorVariableComponentAux
    variable = velocity_y
    component = y
    execute_on = timestep_end
    vector_variable = velocity
  []
  [velocity_z]
    type = VectorVariableComponentAux
    variable = velocity_z
    component = z
    execute_on = timestep_end
    vector_variable = velocity
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Steady
  solve_type = PJFNK
  #nl_rel_tol = 1e-12
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 4: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step04_velocity_aux
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step4.i

Step 4: Run via Command-line


cd ~/projects/moose/tutorials/darcy-thermo_mech/step04_velocity_aux
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step3.i

Step 4: Visualize Result


~/projects/moose/python/peacock/peacock -r step4_out.e

Tighter Solve Tolerance


cd ~/projects/moose/tutorials/darcy-thermo_mech/step04_velocity_aux
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step4.i Executioner/nl_rel_tol=1e-12

Step 5: Heat Conduction

With the pressure equation handled, the heat conduction equation is next.

Initially, only the steady heat conduction equation is considered:

This is another diffusion-type term that depends on the thermal conductivity, . This term is implemented in the MOOSE heat conduction module as ADHeatConduction.

ADHeatConduction.h


#pragma once

#include "ADDiffusion.h"

class ADHeatConduction : public ADDiffusion
{
public:
  static InputParameters validParams();

  ADHeatConduction(const InputParameters & parameters);

protected:
  virtual ADRealVectorValue precomputeQpResidual() override;

  const ADMaterialProperty<Real> & _thermal_conductivity;
};

ADHeatConduction.C


#include "ADHeatConduction.h"

registerMooseObject("HeatConductionApp", ADHeatConduction);

InputParameters
ADHeatConduction::validParams()
{
  InputParameters params = ADDiffusion::validParams();
  params.addParam<MaterialPropertyName>("thermal_conductivity",
                                        "thermal_conductivity",
                                        "the name of the thermal conductivity material property");
  params.set<bool>("use_displaced_mesh") = true;
  return params;
}

ADHeatConduction::ADHeatConduction(const InputParameters & parameters)
  : ADDiffusion(parameters),
    _thermal_conductivity(getADMaterialProperty<Real>("thermal_conductivity"))
{
}

ADRealVectorValue
ADHeatConduction::precomputeQpResidual()
{
  return _thermal_conductivity[_qp] * ADDiffusion::precomputeQpResidual();
}

The ADHeatCondution Kernel in conjunction with a GenericConstantMaterial is all that is needed to perform a steady state heat conduction solve (with at the inlet and at the outlet).

GenericConstantMaterial

GenericConstantMaterial is a simple way to define constant material properties.

Two input parameters are provided using "list" syntax common to MOOSE:


prop_names  = 'conductivity density'
prop_values = '0.01         200'

Step 5a: Steady-State Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [temperature]
  []
[]

[Kernels]
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
[]

[BCs]
  [inlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = left
    value = 350 # (K)
  []
  [outlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = right
    value = 300 # (K)
  []
[]

[Materials]
  [steel]
    type = ADGenericConstantMaterial
    prop_names = thermal_conductivity
    prop_values = 18 # K: (W/m*K) from wikipedia @296K
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Steady
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 5b: Running Input File


cd ~/projects/moose/tutorials/darcy-thermo_mech/step5_heat_conduction
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step5a_steady.i

Transient Heat Conduction (5b)

To create a time-dependent problem add in the time derivative:

The time term exists in the heat conduction module as ADHeatConductionTimeDerivative, thus only an update to the input file is required to run the transient case.

Executioner System

A system for dictating the simulation solving strategy.

Steady-state Executioner

Steady-state executioners generally solve the nonlinear system just once.

[Executioner]
  type = Steady
[]

The Steady executioner can solve the nonlinear system multiple times while adaptively refining the mesh to improve the solution.

Transient Executioners

Transient executioners solve the nonlinear system at least once per time step.

OptionDefinition
dtStarting time step size
num_stepsNumber of time steps
start_timeThe start time of the simulation
end_timeThe end time of the simulation
schemeTime integration scheme (discussed next)
[Executioner]
  type = Transient
  scheme = 'implicit-euler'
  solve_type = 'PJFNK'
  start_time = 0.0
  num_steps = 5
  dt = 0.1
[]

Steady-State Detection

OptionDefinition
steady_state_detectionWhether to try and detect achievement of steady-state (Default = false)
steady_state_toleranceUsed for determining a steady-state; Compared against the difference in solution vectors between current and old time steps (Default = 1e-8)

Common Executioner Options

There are a number of options that appear in the executioner block and are used to control the solver. Here are a few common options:

OptionDefinition
l_tolLinear Tolerance (default: 1e-5)
l_max_itsMax Linear Iterations (default: 10000)
nl_rel_tolNonlinear Relative Tolerance (default: 1e-8)
nl_abs_tolNonlinear Absolute Tolerance (default: 1e-50)
nl_max_itsMax Nonlinear Iterations (default: 50)

TimeKernel Object

The TimeKernel object adds two member variables to a Kernel object:

_u_dot
Time derivative of the associated nonlinear variable

_du_dot_du
The derivative of _u_dot with respect to _u

TimeKernel Base Classes

BaseOverrideUse
TimeKernel
ADTimeKernel
computeQpResidualUse when the time term in the PDE is multiplied by both the test function and the gradient of the test function (_test and _grad_test must be applied)
TimeKernelValue
ADTimeKernelValue
precomputeQpResidualUse when the time term computed in the PDE is only multiplied by the test function (do not use _test in the override, it is applied automatically)
TimeKernelGrad
ADTimeKernelGrad
precomputeQpResidualUse when the time term computed in the PDE is only multiplied by the gradient of the test function (do not use _grad_test in the override, it is applied automatically)

Time Integrator System

A system for defining schemes for numerical integration in time.

The TimeIntegrator can be set using "scheme" parameter within the [Executioner] block, if the "type = Transient", the following options exist:

  • implicit-euler: Backward Euler (default)

  • bdf2: Second order backward difference formula

  • crank-nicolson: Second order Crank-Nicolson method

  • dirk: Second order Diagonally-Implicit Runge-Kutta (DIRK)

  • newmark-beta: Second order Newmark-beta method (structural dynamics)

TimeIntegrator Block

It is also possible to specify a time integrator as a separate sub-block within the input file. This allows for additional types and parameters to be defined, including custom TimeIntegrator objects.

[Executioner]
  type = Transient
  start_time = 0.0
  num_steps = 6
  dt = 0.1
  [TimeIntegrator]
    type = NewmarkBeta
    beta = 0.4225
    gamma = 0.8
  []
[]

Convergence Rates

Consider the test problem:

for , and , is chosen so the exact solution is given by and and are the initial and Dirichlet boundary conditions corresponding to this exact solution.

Time Stepper System

A system for suggesting time steps for transient executioners.

[Executioner]
  type = Transient
  solve_type = NEWTON
  start_time = 0.0
  end_time = 5.0
  [TimeStepper]
    type = IterationAdaptiveDT
    dt = 1.0
    optimal_iterations = 10
    time_t = '0.0 5.0'
    time_dt = '1.0 5.0'
  []
[]

Custom objects are created by inheriting from TimeStepper overriding computeDT().

Built-in TimeSteppers

MOOSE includes many built-in TimeStepper objects:

  • ConstantDT

  • SolutionTimeAdaptiveDT

  • IterationAdaptiveDT

  • FunctionDT

  • PostprocessorDT

  • DT2

  • TimeSequenceStepper

IterationAdaptiveDT

IterationAdaptiveDT grows or shrinks the time step based on the number of iterations taken to obtain a converged solution in the last converged step.

[Executioner]
  type = Transient
  solve_type = NEWTON
  start_time = 0.0
  dtmin = 1.0
  end_time = 10.0
  [TimeStepper]
    type = IterationAdaptiveDT
    optimal_iterations = 1
    linear_iteration_ratio = 1
    dt = 5.0
  []
[]

DT2 Adaptive TimeStepper

  1. Take one time step of size to get from

  2. Take two time steps of size to get from

  3. Calculate local relative time discretization error estimate

  4. Obtain global relative time discretization error estimate

  5. Adaptivity is based on target error tolerance and a maximum acceptable error tolerance .

    • If , continue with a new time step size

      where is the global convergence rate of the time stepping scheme.

    • If , or if the solver fails, shrink .

Parameters and can be specified in the input file as e_tol and e_max (in the Executioner block).

TimeSequenceStepper

Provide a vector of time points using parameter time_sequence, the object simply moves through these time points.

The and parameters are automatically added to the sequence.

Only time points satisfying are considered.

If a solve fails at step an additional time point is inserted and the step is resolved.

Step 5: Heat Conduction

(continued)

Transient Heat Conduction (5b)

To create a time-dependent problem add in the time derivative:

The time term exists in the heat conduction module as ADHeatConductionTimeDerivative, thus only an update to the input file is required to run the transient case.

ADHeatConductionTimeDerivative.h


#pragma once

#include "ADTimeDerivative.h"

class ADHeatConductionTimeDerivative : public ADTimeDerivative
{
public:
  static InputParameters validParams();

  ADHeatConductionTimeDerivative(const InputParameters & parameters);

protected:
  virtual ADReal precomputeQpResidual() override;

  /// Specific heat material property
  const ADMaterialProperty<Real> & _specific_heat;

  /// Density material property
  const ADMaterialProperty<Real> & _density;
};

ADHeatConductionTimeDerivative.C


#include "ADHeatConductionTimeDerivative.h"

registerMooseObject("HeatConductionApp", ADHeatConductionTimeDerivative);

InputParameters
ADHeatConductionTimeDerivative::validParams()
{
  InputParameters params = ADTimeDerivative::validParams();
  params.addClassDescription(
      "AD Time derivative term $\\rho c_p \\frac{\\partial T}{\\partial t}$ of "
      "the heat equation for quasi-constant specific heat $c_p$ and the density $\\rho$.");
  params.set<bool>("use_displaced_mesh") = true;
  params.addParam<MaterialPropertyName>(
      "specific_heat", "specific_heat", "Property name of the specific heat material property");
  params.addParam<MaterialPropertyName>(
      "density_name", "density", "Property name of the density material property");
  return params;
}

ADHeatConductionTimeDerivative::ADHeatConductionTimeDerivative(const InputParameters & parameters)
  : ADTimeDerivative(parameters),
    _specific_heat(getADMaterialProperty<Real>("specific_heat")),
    _density(getADMaterialProperty<Real>("density_name"))
{
}

ADReal
ADHeatConductionTimeDerivative::precomputeQpResidual()
{
  return _specific_heat[_qp] * _density[_qp] * ADTimeDerivative::precomputeQpResidual();
}

Step 5b: Time-dependent Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[Kernels]
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
[]

[BCs]
  [inlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = left
    value = 350 # (K)
  []
  [outlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = right
    value = 300 # (K)
  []
[]

[Materials]
  [steel]
    type = ADGenericConstantMaterial
    prop_names = 'thermal_conductivity specific_heat density'
    prop_values = '18 0.466 8000' # W/m*K, J/kg-K, kg/m^3 @ 296K
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  num_steps = 10
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 5b: Running Input File


cd ~/projects/moose/tutorials/darcy-thermo_mech/step5_heat_conduction
make -j 12 # use number of processors for you system
cd problems
../darcy_thermo_mech-opt -i step5b_transient.i

Outflow Boundary Condition (5c)

The flow is assumed to exit the pipe into a large tank, which is modeled with the "No BC" boundary condition of Griffiths (1997).

The boundary term, , is computed implicitly rather than being replaced with a known flux, as is done in a NeumannBC.

Boundary Condition System

System for computing residual contributions from boundary terms of a PDE.

A BoundaryCondition (BC) object computes a residual on a boundary (or internal side) of a domain.

There are two flavors of BC objects: Nodal and Integrated.

Integrated BC

Integrated BCs are integrated over a boundary or internal side and should inherit from ADIntegratedBC.

The structure is very similar to Kernels: objects must override computeQpResidual

ADIntegrtedBC Object Members

_u, _grad_u
Value and gradient of the variable this Kernel is operating on

_test, _grad_test
Value () and gradient () of the test functions at the quadrature points

_phi, _grad_phi
Value () and gradient () of the trial functions at the quadrature points

_i, _j, _qp
Current index for test function, trial functions, and quadrature point, respectively

_normals:
Outward normal vector for boundary element

_boundary_id
The boundary ID

_current_elem, _current_side
A pointer to the element and index to the current boundary side

Non-Integrated BC

Non-integrated BCs set values of the residual directly on a boundary or internal side and should inherit from ADNodalBC.

The structure is very similar to Kernels: objects must override computeQpResidual.

NodalBC Object Members

_u
Value of the variable this Kernel is operating on

_qp
Current index, used for interface consistency

_boundary_id
The boundary ID

_current_node
A pointer to the current node that is being operated on.

Dirichlet BCs

Set a condition on the value of a variable on a boundary:

becomes

DirichletBC.h


#pragma once

#include "DirichletBCBase.h"

class DirichletBC;

template <>
InputParameters validParams<DirichletBC>();

/**
 * Boundary condition of a Dirichlet type
 *
 * Sets the value in the node
 */
class DirichletBC : public DirichletBCBase
{
public:
  static InputParameters validParams();

  DirichletBC(const InputParameters & parameters);

protected:
  virtual Real computeQpValue() override;

  /// The value for this BC
  const Real & _value;
};

DirichletBC.C


#include "DirichletBC.h"

registerMooseObject("MooseApp", DirichletBC);

defineLegacyParams(DirichletBC);

InputParameters
DirichletBC::validParams()
{
  InputParameters params = DirichletBCBase::validParams();
  params.addRequiredParam<Real>("value", "Value of the BC");
  params.declareControllable("value");
  params.addClassDescription("Imposes the essential boundary condition $u=g$, where $g$ "
                             "is a constant, controllable value.");
  return params;
}

DirichletBC::DirichletBC(const InputParameters & parameters)
  : DirichletBCBase(parameters), _value(getParam<Real>("value"))
{
}

Real
DirichletBC::computeQpValue()
{
  return _value;
}

Integrated BCs

Integrated BCs (including Neumann BCs) are actually integrated over the external face of an element.

becomes:

If , then the boundary integral is zero ("natural boundary condition").

NeumannBC.h


#pragma once

#include "IntegratedBC.h"

class NeumannBC;

template <>
InputParameters validParams<NeumannBC>();

/**
 * Implements a simple constant Neumann BC where grad(u)=value on the boundary.
 * Uses the term produced from integrating the diffusion operator by parts.
 */
class NeumannBC : public IntegratedBC
{
public:
  /**
   * Factory constructor, takes parameters so that all derived classes can be built using the same
   * constructor.
   */
  static InputParameters validParams();

  NeumannBC(const InputParameters & parameters);

protected:
  virtual Real computeQpResidual() override;

  /// Value of grad(u) on the boundary.
  const Real & _value;
};

NeumannBC.C


#include "NeumannBC.h"

registerMooseObject("MooseApp", NeumannBC);

defineLegacyParams(NeumannBC);

InputParameters
NeumannBC::validParams()
{
  InputParameters params = IntegratedBC::validParams();
  params.addParam<Real>("value", 0.0, "The value of the gradient on the boundary.");
  params.declareControllable("value");
  params.addClassDescription("Imposes the integrated boundary condition "
                             "$\\frac{\\partial u}{\\partial n}=h$, "
                             "where $h$ is a constant, controllable value.");
  return params;
}

NeumannBC::NeumannBC(const InputParameters & parameters)
  : IntegratedBC(parameters), _value(getParam<Real>("value"))
{
}

Real
NeumannBC::computeQpResidual()
{
  return -_test[_i][_qp] * _value;
}

Periodic BCs

Periodic boundary conditions are useful for modeling quasi-infinite domains and systems with conserved quantities.

  • 1D, 2D, and 3D

  • With mesh adaptivity

  • Can be restricted to specific variables

  • Supports arbitrary translation vectors for defining periodicity

Step 5: Heat Conduction

(continued)

Outflow Boundary Condition (5c)

The flow is assumed to exit the pipe into a large tank, which is modeled with the "No BC" boundary condition of Griffiths (1997).

The boundary term, , is computed implicitly rather than being replaced with a known flux, as is done in a NeumannBC.

HeatConductionOutflow.h


#pragma once

// Include the base class so it can be extended
#include "ADIntegratedBC.h"

/**
 * An IntegratedBC representing the "No BC" boundary condition for
 * heat conduction.
 *
 * The residual is simply -test*k*grad_u*normal... the term you get
 * from integration by parts.  This is a standard technique for
 * truncating longer domains when solving the convection/diffusion
 * equation.
 *
 * See also: Griffiths, David F. "The 'no boundary condition' outflow
 * boundary condition.", International Journal for Numerical Methods
 * in Fluids, vol. 24, no. 4, 1997, pp. 393-411.
 */
class HeatConductionOutflow : public ADIntegratedBC
{
public:
  static InputParameters validParams();

  HeatConductionOutflow(const InputParameters & parameters);

protected:
  /**
   * This is called to integrate the residual across the boundary.
   */
  virtual ADReal computeQpResidual() override;

  /// Thermal conductivity of the material
  const ADMaterialProperty<Real> & _thermal_conductivity;
};

HeatConductionOutflow.C


#include "HeatConductionOutflow.h"

registerMooseObject("DarcyThermoMechApp", HeatConductionOutflow);

InputParameters
HeatConductionOutflow::validParams()
{
  InputParameters params = ADIntegratedBC::validParams();
  params.addClassDescription("Compute the outflow boundary condition.");
  return params;
}

HeatConductionOutflow::HeatConductionOutflow(const InputParameters & parameters)
  : ADIntegratedBC(parameters),
    _thermal_conductivity(getADMaterialProperty<Real>("thermal_conductivity"))
{
}

ADReal
HeatConductionOutflow::computeQpResidual()
{
  return -_test[_i][_qp] * _thermal_conductivity[_qp] * _grad_u[_qp] * _normals[_qp];
}

Step5c: Outflow Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 100
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[Kernels]
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
[]

[BCs]
  [inlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = left
    value = 350 # (K)
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [steel]
    type = ADGenericConstantMaterial
    prop_names = 'thermal_conductivity specific_heat density'
    prop_values = '18 466 8000' # W/m*K, J/kg-K, kg/m^3 @ 296K
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  num_steps = 10
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 5c: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step05_heat_conduction
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step5b_transient.i

Step 5c: Results

Step 6: Equation Coupling

The pressure and heat equations have been developed independently up to this point, in this step, they are coupled together.

  • Objects have been created for everything except the term; a Kernel, DarcyAdvection, will be developed for this term.

  • A more sophisticated Material object will be created that includes temperature dependence

DarcyAdvection.h


#pragma once

#include "ADKernelValue.h"

/**
 * Kernel which implements the convective term in the transient heat
 * conduction equation, and provides coupling with the Darcy pressure
 * equation.
 */
class DarcyAdvection : public ADKernelValue
{
public:
  static InputParameters validParams();

  DarcyAdvection(const InputParameters & parameters);

protected:
  /// ADKernelValue objects must override precomputeQpResidual
  virtual ADReal precomputeQpResidual() override;

  /// The gradient of pressure
  const ADVariableGradient & _pressure_grad;

  /// These references will be set by the initialization list so that
  /// values can be pulled from the Material system.
  const ADMaterialProperty<Real> & _permeability;
  const ADMaterialProperty<Real> & _porosity;
  const ADMaterialProperty<Real> & _viscosity;
  const ADMaterialProperty<Real> & _density;
  const ADMaterialProperty<Real> & _specific_heat;
};

DarcyAdvection.C


#include "DarcyAdvection.h"

registerMooseObject("DarcyThermoMechApp", DarcyAdvection);

InputParameters
DarcyAdvection::validParams()
{
  InputParameters params = ADKernelValue::validParams();
  params.addRequiredCoupledVar("pressure", "The variable representing the pressure.");
  return params;
}

DarcyAdvection::DarcyAdvection(const InputParameters & parameters)
  : ADKernelValue(parameters),
    // Couple to the gradient of the pressure
    _pressure_grad(adCoupledGradient("pressure")),
    // Grab necessary material properties
    _permeability(getADMaterialProperty<Real>("permeability")),
    _porosity(getADMaterialProperty<Real>("porosity")),
    _viscosity(getADMaterialProperty<Real>("viscosity")),
    _density(getADMaterialProperty<Real>("density")),
    _specific_heat(getADMaterialProperty<Real>("specific_heat"))
{
}

ADReal
DarcyAdvection::precomputeQpResidual()
{
  // See also: E. Majchrzak and L. Turchan, "The Finite Difference
  // Method For Transient Convection Diffusion", Scientific Research
  // of the Institute of Mathematics and Computer Science, vol. 1,
  // no. 11, 2012, pp. 63-72.
  // http://srimcs.im.pcz.pl/2012_1/art_07.pdf

  // http://en.wikipedia.org/wiki/Superficial_velocity
  ADRealVectorValue superficial_velocity =
      _porosity[_qp] * -(_permeability[_qp] / _viscosity[_qp]) * _pressure_grad[_qp];

  return _density[_qp] * _specific_heat[_qp] * superficial_velocity * _grad_u[_qp];
}

PackedColumn.h


#pragma once

#include "ADMaterial.h"

// A helper class from MOOSE that linear interpolates x,y data
#include "LinearInterpolation.h"

/**
 * Material-derived objects override the computeQpProperties()
 * function.  They must declare and compute material properties for
 * use by other objects in the calculation such as Kernels and
 * BoundaryConditions.
 */
class PackedColumn : public ADMaterial
{
public:
  static InputParameters validParams();

  PackedColumn(const InputParameters & parameters);

protected:
  /**
   * Necessary override.  This is where the values of the properties
   * are computed.
   */
  virtual void computeQpProperties() override;

  /**
   * Helper function for reading CSV data for use in an interpolator object.
   */
  bool initInputData(const std::string & param_name, ADLinearInterpolation & interp);

  /// The radius of the spheres in the column
  const Function & _input_radius;

  /// The input porosity
  const Function & _input_porosity;

  /// Temperature
  const ADVariableValue & _temperature;

  /// Compute permeability based on the radius (mm)
  LinearInterpolation _permeability_interpolation;

  /// Fluid viscosity
  bool _use_fluid_mu_interp;
  const Real & _fluid_mu;
  ADLinearInterpolation _fluid_mu_interpolation;

  /// Fluid thermal conductivity
  bool _use_fluid_k_interp = false;
  const Real & _fluid_k;
  ADLinearInterpolation _fluid_k_interpolation;

  /// Fluid density
  bool _use_fluid_rho_interp = false;
  const Real & _fluid_rho;
  ADLinearInterpolation _fluid_rho_interpolation;

  /// Fluid specific heat
  bool _use_fluid_cp_interp;
  const Real & _fluid_cp;
  ADLinearInterpolation _fluid_cp_interpolation;

  /// Solid thermal conductivity
  bool _use_solid_k_interp = false;
  const Real & _solid_k;
  ADLinearInterpolation _solid_k_interpolation;

  /// Solid density
  bool _use_solid_rho_interp = false;
  const Real & _solid_rho;
  ADLinearInterpolation _solid_rho_interpolation;

  /// Fluid specific heat
  bool _use_solid_cp_interp;
  const Real & _solid_cp;
  ADLinearInterpolation _solid_cp_interpolation;

  /// The permeability (K)
  ADMaterialProperty<Real> & _permeability;

  /// The porosity (eps)
  ADMaterialProperty<Real> & _porosity;

  /// The viscosity of the fluid (mu)
  ADMaterialProperty<Real> & _viscosity;

  /// The bulk thermal conductivity
  ADMaterialProperty<Real> & _thermal_conductivity;

  /// The bulk heat capacity
  ADMaterialProperty<Real> & _specific_heat;

  /// The bulk density
  ADMaterialProperty<Real> & _density;
};

PackedColumn.C


#include "PackedColumn.h"
#include "Function.h"
#include "DelimitedFileReader.h"

registerMooseObject("DarcyThermoMechApp", PackedColumn);

InputParameters
PackedColumn::validParams()
{
  InputParameters params = ADMaterial::validParams();
  params.addRequiredCoupledVar("temperature", "The temperature (C) of the fluid.");

  // Add a parameter to get the radius of the spheres in the column
  // (used later to interpolate permeability).
  params.addParam<FunctionName>("radius",
                                "1.0",
                                "The radius of the steel spheres (mm) that are packed in the "
                                "column for computing permeability.");

  // http://en.wikipedia.org/wiki/Close-packing_of_equal_spheres
  params.addParam<FunctionName>(
      "porosity", 0.25952, "Porosity of porous media, default is for closed packed spheres.");

  // Fluid properties
  params.addParam<Real>(
      "fluid_viscosity", 1.002e-3, "Fluid viscosity (Pa s); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_viscosity_file",
      "The name of a file containing the fluid viscosity (Pa-s) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("fluid_thermal_conductivity",
                        0.59803,
                        "Fluid thermal conductivity (W/(mK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_thermal_conductivity_file",
      "The name of a file containing fluid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_density", 998.21, "Fluid density (kg/m^3); default is for water at 20C).");
  params.addParam<FileName>("fluid_density_file",
                            "The name of a file containing fluid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_specific_heat", 4157.0, "Fluid specific heat (J/(kgK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_specific_heat_file",
      "The name of a file containing fluid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  // Solid properties
  // https://en.wikipedia.org/wiki/Stainless_steel#Properties
  params.addParam<Real>("solid_thermal_conductivity",
                        15.0,
                        "Solid thermal conductivity (W/(mK); default is for AISI/ASTIM 304 "
                        "stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_thermal_conductivity_file",
      "The name of a file containing solid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_density",
      7900,
      "Solid density (kg/m^3); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>("solid_density_file",
                            "The name of a file containing solid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_specific_heat",
      500,
      "Solid specific heat (J/(kgK); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_specific_heat_file",
      "The name of a file containing solid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");
  return params;
}

PackedColumn::PackedColumn(const InputParameters & parameters)
  : ADMaterial(parameters),
    // Get the one parameter from the input file
    _input_radius(getFunction("radius")),
    _input_porosity(getFunction("porosity")),
    _temperature(adCoupledValue("temperature")),

    // Fluid
    _fluid_mu(getParam<Real>("fluid_viscosity")),
    _fluid_k(getParam<Real>("fluid_thermal_conductivity")),
    _fluid_rho(getParam<Real>("fluid_density")),
    _fluid_cp(getParam<Real>("fluid_specific_heat")),

    // Solid
    _solid_k(getParam<Real>("solid_thermal_conductivity")),
    _solid_rho(getParam<Real>("solid_density")),
    _solid_cp(getParam<Real>("solid_specific_heat")),

    // Material Properties being produced by this object
    _permeability(declareADProperty<Real>("permeability")),
    _porosity(declareADProperty<Real>("porosity")),
    _viscosity(declareADProperty<Real>("viscosity")),
    _thermal_conductivity(declareADProperty<Real>("thermal_conductivity")),
    _specific_heat(declareADProperty<Real>("specific_heat")),
    _density(declareADProperty<Real>("density"))
{
  // Set data for permeability interpolation
  std::vector<Real> sphere_sizes = {1, 3};
  std::vector<Real> permeability = {0.8451e-9, 8.968e-9};
  _permeability_interpolation.setData(sphere_sizes, permeability);

  // Fluid viscosity, thermal conductivity, density, and specific heat
  _use_fluid_mu_interp = initInputData("fluid_viscosity_file", _fluid_mu_interpolation);
  _use_fluid_k_interp = initInputData("fluid_thermal_conductivity_file", _fluid_k_interpolation);
  _use_fluid_rho_interp = initInputData("fluid_density_file", _fluid_rho_interpolation);
  _use_fluid_cp_interp = initInputData("fluid_specific_heat_file", _fluid_cp_interpolation);

  // Solid thermal conductivity, density, and specific heat
  _use_solid_k_interp = initInputData("solid_thermal_conductivity_file", _solid_k_interpolation);
  _use_solid_rho_interp = initInputData("solid_density_file", _solid_rho_interpolation);
  _use_solid_cp_interp = initInputData("solid_specific_heat_file", _solid_cp_interpolation);
}

void
PackedColumn::computeQpProperties()
{
  // Current temperature
  ADReal temp = _temperature[_qp] - 273.15;

  // Permeability
  Real radius_value = _input_radius.value(_t, _q_point[_qp]);
  mooseAssert(radius_value >= 1 && radius_value <= 3,
              "The radius range must be in the range [1, 3], but " << radius_value << " provided.");
  _permeability[_qp] = _permeability_interpolation.sample(radius_value);

  // Porosity
  Real porosity_value = _input_porosity.value(_t, _q_point[_qp]);
  mooseAssert(porosity_value > 0 && porosity_value <= 1,
              "The porosity range must be in the range (0, 1], but " << porosity_value
                                                                     << " provided.");
  _porosity[_qp] = porosity_value;

  // Fluid properties
  _viscosity[_qp] = _use_fluid_mu_interp ? _fluid_mu_interpolation.sample(temp) : _fluid_mu;
  ADReal fluid_k = _use_fluid_k_interp ? _fluid_k_interpolation.sample(temp) : _fluid_k;
  ADReal fluid_rho = _use_fluid_rho_interp ? _fluid_rho_interpolation.sample(temp) : _fluid_rho;
  ADReal fluid_cp = _use_fluid_cp_interp ? _fluid_cp_interpolation.sample(temp) : _fluid_cp;

  // Solid properties
  ADReal solid_k = _use_solid_k_interp ? _solid_k_interpolation.sample(temp) : _solid_k;
  ADReal solid_rho = _use_solid_rho_interp ? _solid_rho_interpolation.sample(temp) : _solid_rho;
  ADReal solid_cp = _use_solid_cp_interp ? _solid_cp_interpolation.sample(temp) : _solid_cp;

  // Compute the heat conduction material properties as a linear combination of
  // the material properties for fluid and steel.
  _thermal_conductivity[_qp] = _porosity[_qp] * fluid_k + (1.0 - _porosity[_qp]) * solid_k;
  _density[_qp] = _porosity[_qp] * fluid_rho + (1.0 - _porosity[_qp]) * solid_rho;
  _specific_heat[_qp] = _porosity[_qp] * fluid_cp + (1.0 - _porosity[_qp]) * solid_cp;
}

bool
PackedColumn::initInputData(const std::string & param_name, ADLinearInterpolation & interp)
{
  if (isParamValid(param_name))
  {
    const std::string & filename = getParam<FileName>(param_name);
    MooseUtils::DelimitedFileReader reader(filename, &_communicator);
    reader.setComment("#");
    reader.read();
    interp.setData(reader.getData(0), reader.getData(1));
    return true;
  }
  return false;
}

HeatConductionOutflow.h


#pragma once

// Include the base class so it can be extended
#include "ADIntegratedBC.h"

/**
 * An IntegratedBC representing the "No BC" boundary condition for
 * heat conduction.
 *
 * The residual is simply -test*k*grad_u*normal... the term you get
 * from integration by parts.  This is a standard technique for
 * truncating longer domains when solving the convection/diffusion
 * equation.
 *
 * See also: Griffiths, David F. "The 'no boundary condition' outflow
 * boundary condition.", International Journal for Numerical Methods
 * in Fluids, vol. 24, no. 4, 1997, pp. 393-411.
 */
class HeatConductionOutflow : public ADIntegratedBC
{
public:
  static InputParameters validParams();

  HeatConductionOutflow(const InputParameters & parameters);

protected:
  /**
   * This is called to integrate the residual across the boundary.
   */
  virtual ADReal computeQpResidual() override;

  /// Thermal conductivity of the material
  const ADMaterialProperty<Real> & _thermal_conductivity;
};

HeatConductionOutflow.C


#include "HeatConductionOutflow.h"

registerMooseObject("DarcyThermoMechApp", HeatConductionOutflow);

InputParameters
HeatConductionOutflow::validParams()
{
  InputParameters params = ADIntegratedBC::validParams();
  params.addClassDescription("Compute the outflow boundary condition.");
  return params;
}

HeatConductionOutflow::HeatConductionOutflow(const InputParameters & parameters)
  : ADIntegratedBC(parameters),
    _thermal_conductivity(getADMaterialProperty<Real>("thermal_conductivity"))
{
}

ADReal
HeatConductionOutflow::computeQpResidual()
{
  return -_test[_i][_qp] * _thermal_conductivity[_qp] * _grad_u[_qp] * _normals[_qp];
}

Step 6a: Coupled Pressure and Heat Equations

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 200
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    temperature = temperature
    radius = 1
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  exodus = true
[]

Auto Variable Scaling

To obtain an optimum numerical solution, the non-linear variables should be on the same scale.

MOOSE includes the ability to automatically scale non-linear variables

Condition Number without Scaling

The condition number can be used to determine if variable scaling is required.


cd ~/projects/moose/tutorials/darcy-thermo_mech/step06_coupled_darcy_heat_conduction
make -j 12
../darcy_thermo_mech-opt -i step6a_coupled.i Mesh/nx=50 Mesh/ny=3 Executioner/num_steps=1 Executioner/automatic_scaling=0 -pc_type svd -pc_svd_monitor -ksp_view_pmat

Time Step 1, time = 0.1, dt = 0.1

 0 Nonlinear |R| = 8.000625e+03
      SVD: condition number 2.835686200265e+15, 2 of 408 singular values are (nearly) zero
      SVD: smallest singular values: 1.434461194336e-13 5.583840793234e-13 1.222432395761e-12 2.076808734751e-12 3.047037450013e-12
      SVD: largest singular values : 4.006299266699e+02 4.029206639889e+02 4.047115548038e+02 4.059957077255e+02 4.067681813595e+02
      0 Linear |R| = 8.000625e+03
      1 Linear |R| = 8.101613e-09
Mat Object: () 1 MPI processes
  type: seqaij
row 0: (0, 1.)  (1, 0.)  (2, 0.)  (3, 0.)  (4, 0.)  (5, 0.)  (6, 0.)  (7, 0.)
row 1: (0, 0.)  (1, 1.)  (2, 0.)  (3, 0.)  (4, 0.)  (5, 0.)  (6, 0.)  (7, 0.)
row 2: (0, 1.32667e-12)  (1, 0.)  (2, -1.07325e-11)  (3, 0.)  (4, 3.97056e-14)  (5, 0.)  (6, 4.01973e-12)  (7, 0.)  (8, 1.32667e-12)  (9, 0.)  (10, 4.01973e-12)  (11, 0.)
row 3: (0, -2.81185e-20)  (1, 3.41152)  (2, -1.12474e-19)  (3, 14.0732)  (4, 1.12474e-19)  (5, 13.7863)  (6, 2.81185e-20)  (7, 3.33981)  (8, -2.81185e-20)  (9, 3.41152)  (10, 2.81185e-20)  (11, 3.33981)
row 4: (0, 4.01973e-12)  (1, 0.)  (2, 3.97056e-14)  (3, 0.)  (4, -6.43156e-11)  (5, 0.)  (6, 1.59995e-11)  (7, 0.)  (8, 4.01973e-12)  (9, 0.)  (10, 1.59995e-11)  (11, 0.)  (204, 1.19117e-13)  (205, 0.)  (206, 1.20592e-11)  (207, 0.)  (208, 1.20592e-11)  (209, 0.)

Condition Number with Scaling


cd ~/projects/moose/tutorials/darcy-thermo_mech/step06_coupled_darcy_heat_conduction
make -j 12
../darcy_thermo_mech-opt -i step6a_coupled.i Mesh/nx=50 Mesh/ny=3 Executioner/num_steps=1 -pc_type svd -pc_svd_monitor -ksp_view_pmat

Time Step 1, time = 0.1, dt = 0.1

 0 Nonlinear |R| = 8.000625e+03
      SVD: condition number 2.877175736279e+04, 0 of 408 singular values are (nearly) zero
      SVD: smallest singular values: 1.413775933915e-02 5.524422458767e-02 1.194077235260e-01 2.001521770346e-01 2.889664356969e-01
      SVD: largest singular values : 4.006299266699e+02 4.029206639889e+02 4.047115548038e+02 4.059957077255e+02 4.067681813595e+02
      0 Linear |R| = 8.000625e+03
      1 Linear |R| = 3.858046e-09
Mat Object: () 1 MPI processes
  type: seqaij
row 0: (0, 1.)  (1, 0.)  (2, 0.)  (3, 0.)  (4, 0.)  (5, 0.)  (6, 0.)  (7, 0.)
row 1: (0, 0.)  (1, 1.)  (2, 0.)  (3, 0.)  (4, 0.)  (5, 0.)  (6, 0.)  (7, 0.)
row 2: (0, 0.132667)  (1, 0.)  (2, -1.07325)  (3, 0.)  (4, 0.00397056)  (5, 0.)  (6, 0.401973)  (7, 0.)  (8, 0.132667)  (9, 0.)  (10, 0.401973)  (11, 0.)
row 3: (0, -2.81185e-20)  (1, 3.41152)  (2, -1.12474e-19)  (3, 14.0732)  (4, 1.12474e-19)  (5, 13.7863)  (6, 2.81185e-20)  (7, 3.33981)  (8, -2.81185e-20)  (9, 3.41152)  (10, 2.81185e-20)  (11, 3.33981)
row 4: (0, 0.401973)  (1, 0.)  (2, 0.00397056)  (3, 0.)  (4, -6.43156)  (5, 0.)  (6, 1.59995)  (7, 0.)  (8, 0.401973)  (9, 0.)  (10, 1.59995)  (11, 0.)  (204, 0.0119117)  (205, 0.)  (206, 1.20592)  (207, 0.)  (208, 1.20592)  (209, 0.)

Step 6a: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step06_coupled_darcy_heat_conduction
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step6a_coupled.i

Step 6a: Results

Step 6b:
Oscillating Pressure and Temperature Dependence

Vary the inlet and output pressure:

  • Inlet (left):

  • Outlet (right):

Viscosity, density, thermal conductivity, and specific heat capacity of the fluid are setup to vary as a function of temperature.

Step 6b: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 200
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[Functions]
  [inlet_function]
    type = ParsedFunction
    value = 2000*sin(0.466*pi*t) # Inlet signal from Fig. 3
  []
  [outlet_function]
    type = ParsedFunction
    value = 2000*cos(0.466*pi*t) # Outlet signal from Fig. 3
  []
[]

[BCs]
  [inlet]
    type = FunctionDirichletBC
    variable = pressure
    boundary = left
    function = inlet_function
  []
  [outlet]
    type = FunctionDirichletBC
    variable = pressure
    boundary = right
    function = outlet_function
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = temperature
    fluid_viscosity_file = data/water_viscosity.csv
    fluid_density_file = data/water_density.csv
    fluid_thermal_conductivity_file = data/water_thermal_conductivity.csv
    fluid_specific_heat_file = data/water_specific_heat.csv
    outputs = exodus
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,(2*pi/(0.466*pi))/16)' # dt to always hit the peaks of sine/cosine BC
  []
[]

[Outputs]
  exodus = true
[]

Step 6b: Run and Visualize with Peacock


cd ~/projects/moose/tutorials/darcy-thermo_mech/step06_coupled_darcy_heat_conduction
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step6b_transient_inflow.i

Step 6b: Results

Decoupling Heat Equation

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 200
  ny = 10
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [pressure]
  []
[]

[AuxKernels]
  [pressure]
    type = FunctionAux
    variable = pressure
    function = 't*x*x*y'
    execute_on = timestep_end
  []
[]

[Kernels]
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[BCs]
  [inlet_temperature]
    type = DirichletBC
    variable = temperature
    boundary = left
    value = 350
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = 293.15 # 20C
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  num_steps = 300
  dt = 0.1
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Outputs]
  exodus = true
[]

Step 7: Mesh Adaptivity

Adaptivity System

h-Adaptivity

-adaptivity is a method of automatically refining/coarsening the mesh in regions of high/low estimated solution error.

Concentrate degrees of freedom (DOFs) where the error is highest, while reducing DOFs where the solution is already well-captured.

  1. Compute a measure of error using an Indicator object

  2. Mark an element for refinement or coarsening based on the error using a Marker object

Mesh adaptivity can be employed in both Steady and Transient executioners.

Refinement Patterns

MOOSE employs "self-similar", isotropic refinement patterns: when refining an element is split into elements of the same type.

  • For example, when using Quad4 elements, four "child" elements are created when the element is refined.

  • Coarsening happens in reverse, children are deleted and the "parent" element is reactivated.

  • The original mesh starts at refinement level 0.

Indicator Objects

Indicators report an amount of "error" for each element, built-in Indicators include:

GradientJumpIndicator
Jump in the gradient of a variable across element edges. A good "curvature" indicator that works well over a wide range of problems.

FluxJumpIndicator
Similar to GradientJump, except that a scalar coefficient (e.g. thermal conductivity) can be provided to produce a physical "flux" quantity.

LaplacianJumpIndicator
Jump in the second derivative of a variable. Only useful for shape functions.

AnalyticIndicator
Computes the difference between the finite element solution and a user-supplied Function representing the analytic solution to the problem.

Marker Objects

After an Indicator has computed the error for each element, a decision to refine or coarsen elements must be made using a Marker object.

ErrorFractionMarker
Selects elements based on their contribution to the total error.

ErrorToleranceMaker
Refine if error is greater than a specified value and coarsen if it is less.

ValueThresholdMarker
Refine if variable value is greater than a specific value and coarsen if it is less.

UniformMarker
Refine or coarsen all elements.

BoxMarker
Refine or coarsen inside or outside a given box.

ComboMarker
Combine several of the above Markers.

Input Syntax

[Adaptivity]
  initial_steps = 2
  cycles_per_step = 2
  marker = marker
  initial_marker = marker
  max_h_level = 2
  [Indicators/indicator]
    [Indicators/indicator]
      type = GradientJumpIndicator
      variable = u
    []
  []
  [Markers/marker]
    [Markers/marker]
      type = ErrorFractionMarker
      indicator = indicator
      coarsen = 0.1
      refine = 0.7
    []
  []
[]

Step 7: Mesh Adaptivity

(continued)

Step 7a: Coarse Solution

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 30
  ny = 3
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = temperature
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  exodus = true
[]

Step 7a: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step07_adaptivity
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step7a_coarse.i

Step 7b: Fine Solution

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 30
  ny = 3
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
  uniform_refine = 3
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = temperature
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  exodus = true
[]

Step 7b: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step07_adaptivity
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step7b_fine.i

Step 7c: Adaptive Mesh Solution

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 30
  ny = 3
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
  uniform_refine = 3
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []

  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = temperature
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  exodus = true
[]

[Adaptivity]
  marker = error_frac
  max_h_level = 3
  [Indicators]
    [temperature_jump]
      type = GradientJumpIndicator
      variable = temperature
      scale_by_flux_faces = true
    []
  []
  [Markers]
    [error_frac]
      type = ErrorFractionMarker
      coarsen = 0.15
      indicator = temperature_jump
      refine = 0.7
    []
  []
[]

Step 7c: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step07_adaptivity
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step7a_adapt.i

Step 7d: Multiple Subdomains

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 40
  ny = 4
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
  uniform_refine = 3
[]

[MeshModifiers]
  [bottom]
    type = SubdomainBoundingBox
    location = inside
    bottom_left = '0 0 0'
    top_right = '0.304 0.01285 0'
    block_id = 1
  []
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  viscosity_file = data/water_viscosity.csv
  density_file = data/water_density.csv
  thermal_conductivity_file = data/water_thermal_conductivity.csv
  specific_heat_file = data/water_specific_heat.csv

  [column_bottom]
    type = PackedColumn
    block = 1
    radius = 1.15
    temperature = temperature
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_thermal_conductivity_file = ${thermal_conductivity_file}
    fluid_specific_heat_file = ${specific_heat_file}
  []
  [column_top]
    type = PackedColumn
    block = 0
    radius = 1
    temperature = temperature
    porosity = '0.25952 + 0.7*x/0.304'
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_thermal_conductivity_file = ${thermal_conductivity_file}
    fluid_specific_heat_file = ${specific_heat_file}
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Adaptivity]
  marker = error_frac
  max_h_level = 3
  [Indicators]
    [temperature_jump]
      type = GradientJumpIndicator
      variable = temperature
      scale_by_flux_faces = true
    []
  []
  [Markers]
    [error_frac]
      type = ErrorFractionMarker
      coarsen = 0.025
      indicator = temperature_jump
      refine = 0.9
    []
  []
[]

[Outputs]
  [out]
    type = Exodus
    output_material_properties = true
  []
[]

Step 8: Postprocessors

Aggregate values based on simulation data are useful for understanding the simulation as well as defining coupling values across coupled equations.

There are two main systems for aggregating data: Postprocessors and VectorPostprocessors.

UserObject System

A system for defining an arbitrary interface between MOOSE objects.

The UserObject system provides data and calculation results to other MOOSE objects.

  • Postprocessors are UserObjects that compute a single scalar value.

  • VectorPostprocessors are UserObjects that compute vectors of data.

  • UserObjects define their own interface, which other MOOSE objects can call to retrieve data.

Execution

UserObjects are computed at specified "times" by the execute_on option in the input file:

execute_on = 'initial timestep_end'
execute_on = linear
execute_on = nonlinear
execute_on = 'timestep_begin final failed'\\

They can be restricted to specific blocks, sidesets, and nodesets

UserObject Types

There are various types of UserObjects:

  • ElementUserObject: execute on elements

  • NodalUserObject: execute on nodes

  • SideUserObject: execute on boundaries

  • InternalSideUserObject: execute on internal sides

  • InterfaceUserObject: execute on interfaces

  • GeneralUserObject: execute once

UserObject Anatomy

virtual void initialize();
Called once before beginning the UserObject calculation.

virtual void execute();
Called once on each geometric entity (element, node, etc.) or once per calculation for a GeneralUserObject.

virtual void threadJoin(const UserObject & uo);
During threaded execution this function is used to "join" together calculations generated on different threads.

  • Cast uo to a const reference of the specific UserObject type, then extract data and aggregate it to the data in "this" object.

  • This is not required for a GeneralUserObject because it is not threaded.

virtual void finalize();
The last function called after all calculations have been completed.

  • Take data from all calculations performed in execute() and perform an operation to get the final value(s)

  • Perform parallel communication where necessary to ensure all processors compute the same value(s)

User Defined Interface

A UserObject defines its own interface by defining const functions.

For example, if a UserObject is computing the average value of a variable on every block in the mesh, it might provide a function like:


Real averageValue(SubdomainID block) const;

Another MooseObject needing this UserObject would then call averageValue() to get the result of the calculation.

Using a UserObject

Any MOOSE object can retrieve a UserObject in a manner similar to retrieving a Function.

Generally, it is a good idea to take the name of the UserObject to from the input file:


InputParameters
BlockAverageDiffusionMaterial::validParams()
{
  InputParameters params = Material::validParams();
  params.addRequiredParam<UserObjectName>("block_average_userobject", "Computes the ...");
  return params;
}

A UserObject comes through as a const reference of the UserObject type. So, in your object:


const BlockAverageValue & _block_average_value;

The reference is set in the initialization list of your object by calling the templated getUserObject() method:


BlockAverageDiffusionMaterial::BlockAverageDiffusionMaterial(const InputParameters & parameters) :
    Material(parameters),
    _block_average_value(getUserObject<BlockAverageValue>("block_average_userobject"))
{}

Use the reference by calling some of the interface functions defined by the UserObject:


_diffusivity[_qp] = 0.5 * _block_average_value.averageValue(_current_elem->subdomain_id());

Postprocessor System

A system for computing a "reduction" or "aggregation" calculation based on the solution variables that results in a single scalar value.

Types of Postprocessors

ElementPostprocessor: operate on each element

NodalPostprocessor: operate on each node

SidePostprocessor: operate on boundaries

InternalSidePostprocessor: operate on internal element sides

InterfacePostprocessor: operator on subdomain interfaces

GeneralPostprocessor: operates once per execution

Postprocessor Anatomy

Postprocessor is a UserObject, so initialize, execute, threadJoin, and finalize methods are used for implementing the aggregation operation.

Real getValue()
This is called internally within MOOSE to retrieve the final scalar value, the value returned by this function is referenced by all other objects that are using the postprocessor.

Aggregation Routines

If the Postprocessor created has custom data it must be ensured that the value is communicated properly in (both MPI and thread-based) parallel simulations.

For MPI several utility methods exist to perform common aggregation operations:

  • gatherSum(scalar): sum across all processors.

  • gatherMin(scalar): min from all processors.

  • gatherMax(scalar): max from all processors.

Built-in Postprocessor Types

MOOSE includes a large number built-in Postprocessors: ElementAverageValue, SideAverageValue, ElementL2Error, ElementH1Error, and many more

By default, Postprocessors will output to a formatted table on the screen and optionally using the [Outputs] block be stored in CSV file.


[Output]
  csv = true
[]

Using a Postprocessor

Postprocessor values are used within an object by creating a const reference to a PostprocessorValue and initializing the reference in the initialization list.

  const PostprocessorValue & _pps_value;
    _pps_value(getPostprocessorValue("postprocessor")),

Default Postprocessor Values

It is possible to set default values for Postprocessors to allow an object to operate without creating Postprocessor object.


params.addParam<PostprocessorName>("postprocessor", 1.2345, "Doc String");

Additionally, a value may be supplied in the input file in lieu of a Postprocessor name.

VectorPostprocessor System

A system for "reduction" or "aggregation" calculations based on the solution variables that results in one or many vectors of values.

Types of VectorPostprocessors

ElementVectorPostprocessor: operate on each element

NodalVectorPostprocessor: operate on each node

SideVectorPostprocessor: operate on boundaries

InternalSideVectorPostprocessor: operate on internal element sides

GeneralVectorPostprocessor: operates once per execution

VectorPostprocessor Anatomy

Postprocessor is a UserObject, so initialize, execute, threadJoin, and finalize methods are used for implementing the aggregation operation.

virtual VectorPostprocessorValue & getVector (const std::string &vector_name) This is called internally within MOOSE to retrieve the final vector value for the given name, the value returned by this function is referenced by all other objects that are using the vector postprocessor.

VectorPostprocessor objects operate a bit like Material objects, each vector is declared and then within the "initialize", "execute", "threadJoin", and "finalize" methods the vectors are updated with the desired data.

Create a member variable, as a reference, for the vector data

  VectorPostprocessorValue & _pid;

Initialize the reference using the declareVector method with a name

    _pid(declareVector("pid")),

Built-in VectorPostprocessor Types

MOOSE includes a large number built-in VectorPostprocessors: NodalValueSampler, LineValueSampler, PointValueSampler, and many more.

VectorPostprocessors output is optionally enabled using the [Outputs] block. A CSV file for each vector and timestep will be created.


[Output]
  csv = true
[]

Using a VectorPostprocessor

Postprocessor values are used within an object by creating a const reference to a VectorPostprocessorValue and initializing the reference in the initialization list.

  const VectorPostprocessorValue & _x_values;
    _x_values(getVectorPostprocessorValue("vectorpostprocessor", _x_name)),

Step 8: Postprocessors

(continued)

Step 8: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 30
  ny = 3
  xmax = 0.304 # Length of test chamber
  ymax = 0.0257 # Test chamber radius
  uniform_refine = 2
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = left
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = right
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = left
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = right
  []
[]

[Materials]
  [column]
    type = PackedColumn
    radius = 1
    temperature = temperature
    porosity = '0.25952 + 0.7*y/0.0257'
  []
[]

[Postprocessors]
  [average_temperature]
    type = ElementAverageValue
    variable = temperature
  []
  [outlet_heat_flux]
    type = ADSideFluxIntegral
    variable = temperature
    boundary = right
    diffusivity = thermal_conductivity
  []
[]

[VectorPostprocessors]
  [temperature_sample]
    type = LineValueSampler
    num_points = 500
    start_point = '0.1 0      0'
    end_point =   '0.1 0.0257 0'
    variable = temperature
    sort_by = y
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
  rz_coord_axis = X
[]

[Executioner]
  type = Transient
  solve_type = NEWTON
  automatic_scaling = true

  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'

  end_time = 100
  dt = 0.25
  start_time = -1

  steady_state_tolerance = 1e-5
  steady_state_detection = true

  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  exodus = true
  csv = true
[]

Step 8: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step08_postprocessors
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step8.i

Step 9: Mechanics

Mechanics

Compute the elastic and thermal strain if the tube is only allowed to expand along the axial (y) direction.

where is the Cauchy stress tensor, is an additional source of stress (such as pore pressure), is the displacement vector, is the body force, is the unit normal to the boundary, is the prescribed displacement on the boundary and is the prescribed traction on the boundary.

Modules

Chemical Reactions

The chemical reactions module provides a set of tools for the calculation of multicomponent aqueous reactive transport in porous media, originally developed as the MOOSE application RAT (Guo et al., 2013).

Contact

The MOOSE contact module provides the necessary tools for modeling mechanical contact using algorithms to enforce constraints between surfaces in the mesh, to prevent penetration and develop contact forces.

External PETSc Solver

The External PETSc Solver module provides support for stand-alone native PETSc applications that to be coupled with moose-based applications.

Fluid Properties

The Fluid Properties module provides a consistent interface to fluid properties such as density, viscosity, enthalpy and many others, as well as derivatives with respect to the primary variables. The consistent interface allows different fluids to be used in an input file by simply swapping the name of the Fluid Properties UserObject in a plug-and-play manner.

Functional Expansion Tools

A MOOSE module for continuous, mesh-agnostic, high-fidelity, reduced-data MultiApp coupling

Functional expansions (FXs) are a methodology that represent information as moments of a functional series (Flusser et al., 2016). This is is related to a Fourier series representation of cyclic data. Moments are generated via numerical integration for each term in the functional series to represent the field of interest. These moments can then be used to reconstruct the field in a separate app (Wendt et al., 2018; Wendt and Kerby, 2017; Kerby et al., 2017).

Heat Conduction

Basic utilities for solving the transient heat conduction equation:

Level Set

The level set module provides basic functionality to solve the level set equation, which is simply the multi-dimensional advection equation:

The MOOSE Navier-Stokes module is a library for the implementation of simulation tools that solve the Navier-Stokes equations using the continuous Galerkin finite element (CGFE) method. The Navier-Stokes equations are usually solved using either the pressure-based, incompressible formulation (assuming a constant fluid density), or the density-based, compressible formulation.

Phase Field

The MOOSE phase field module is a library for simplifying the implementation of simulation tools that employ the phase field model.

Porous Flow

The PorousFlow module is a library of physics for fluid and heat flow in porous media. It is formulated in an extremely general manner, so is capable of solving problems with an arbitrary number of phases (gas, liquid, etc) and fluid components (species present in each fluid phase), using any set of primary variables.

Reconstructed Discontinuous Galerkin (rDG)

The MOOSE rDG module is a library for the implementation of simulation tools that solve convection-dominated problems using the class of so-called reconstructed discontinuous Galerkin (rDG) methods. The specific rDG method implemented in this module is rDG(P0P1), which is equivalent to the second-order cell-centered finite volume method (FVM).

Stochastic Tools

The stochastic tools module is a toolbox designed for performing stochastic analysis for MOOSE-based applications.

Tensor Mechanics

The Tensor Mechanics module is a library of simulation tools that solve continuum mechanics problems. The module can be used to simulation both linear and finite strain mechanics, including Elasticity and Cosserat elasticity, Plasticity and micromechanics plasticity, Creep, and Damage due to cracking and property degradation.

Extended Finite Element Method (XFEM)

A MOOSE-based implementation of the extended finite element method, which is a numerical method that is especially designed for treating discontinuities.

Step 9: Mechanics

(continued)

PackedColumn.h


#pragma once

#include "ADMaterial.h"

// A helper class from MOOSE that linear interpolates x,y data
#include "LinearInterpolation.h"

/**
 * Material-derived objects override the computeQpProperties()
 * function.  They must declare and compute material properties for
 * use by other objects in the calculation such as Kernels and
 * BoundaryConditions.
 */
class PackedColumn : public ADMaterial
{
public:
  static InputParameters validParams();

  PackedColumn(const InputParameters & parameters);

protected:
  /**
   * Necessary override.  This is where the values of the properties
   * are computed.
   */
  virtual void computeQpProperties() override;

  /**
   * Helper function for reading CSV data for use in an interpolator object.
   */
  bool initInputData(const std::string & param_name, ADLinearInterpolation & interp);

  /// The radius of the spheres in the column
  const Function & _input_radius;

  /// The input porosity
  const Function & _input_porosity;

  /// Temperature
  const ADVariableValue & _temperature;

  /// Compute permeability based on the radius (mm)
  LinearInterpolation _permeability_interpolation;

  /// Fluid viscosity
  bool _use_fluid_mu_interp;
  const Real & _fluid_mu;
  ADLinearInterpolation _fluid_mu_interpolation;

  /// Fluid thermal conductivity
  bool _use_fluid_k_interp = false;
  const Real & _fluid_k;
  ADLinearInterpolation _fluid_k_interpolation;

  /// Fluid density
  bool _use_fluid_rho_interp = false;
  const Real & _fluid_rho;
  ADLinearInterpolation _fluid_rho_interpolation;

  /// Fluid specific heat
  bool _use_fluid_cp_interp;
  const Real & _fluid_cp;
  ADLinearInterpolation _fluid_cp_interpolation;

  /// Fluid thermal expansion coefficient
  bool _use_fluid_cte_interp;
  const Real & _fluid_cte;
  ADLinearInterpolation _fluid_cte_interpolation;

  /// Solid thermal conductivity
  bool _use_solid_k_interp = false;
  const Real & _solid_k;
  ADLinearInterpolation _solid_k_interpolation;

  /// Solid density
  bool _use_solid_rho_interp = false;
  const Real & _solid_rho;
  ADLinearInterpolation _solid_rho_interpolation;

  /// Solid specific heat
  bool _use_solid_cp_interp;
  const Real & _solid_cp;
  ADLinearInterpolation _solid_cp_interpolation;

  /// Solid thermal expansion coefficient
  bool _use_solid_cte_interp;
  const Real & _solid_cte;
  ADLinearInterpolation _solid_cte_interpolation;

  /// The permeability (K)
  ADMaterialProperty<Real> & _permeability;

  /// The porosity (eps)
  ADMaterialProperty<Real> & _porosity;

  /// The viscosity of the fluid (mu)
  ADMaterialProperty<Real> & _viscosity;

  /// The bulk thermal conductivity
  ADMaterialProperty<Real> & _thermal_conductivity;

  /// The bulk heat capacity
  ADMaterialProperty<Real> & _specific_heat;

  /// The bulk density
  ADMaterialProperty<Real> & _density;

  /// The bulk thermal expansion coefficient
  ADMaterialProperty<Real> & _thermal_expansion;
};

PackedColumn.C


#include "PackedColumn.h"
#include "Function.h"
#include "DelimitedFileReader.h"

registerMooseObject("DarcyThermoMechApp", PackedColumn);

InputParameters
PackedColumn::validParams()
{
  InputParameters params = ADMaterial::validParams();
  params.addRequiredCoupledVar("temperature", "The temperature (C) of the fluid.");

  // Add a parameter to get the radius of the spheres in the column
  // (used later to interpolate permeability).
  params.addParam<FunctionName>("radius",
                                "1.0",
                                "The radius of the steel spheres (mm) that are packed in the "
                                "column for computing permeability.");

  // http://en.wikipedia.org/wiki/Close-packing_of_equal_spheres
  params.addParam<FunctionName>(
      "porosity", 0.25952, "Porosity of porous media, default is for closed packed spheres.");

  // Fluid properties
  params.addParam<Real>(
      "fluid_viscosity", 1.002e-3, "Fluid viscosity (Pa s); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_viscosity_file",
      "The name of a file containing the fluid viscosity (Pa-s) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("fluid_thermal_conductivity",
                        0.59803,
                        "Fluid thermal conductivity (W/(mK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_thermal_conductivity_file",
      "The name of a file containing fluid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_density", 998.21, "Fluid density (kg/m^3); default is for water at 20C).");
  params.addParam<FileName>("fluid_density_file",
                            "The name of a file containing fluid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_specific_heat", 4157.0, "Fluid specific heat (J/(kgK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_specific_heat_file",
      "The name of a file containing fluid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("fluid_thermal_expansion",
                        2.07e-4,
                        "Fluid thermal expansion coefficient (1/K); default is for water at 20C).");
  params.addParam<FileName>("fluid_thermal_expansion_file",
                            "The name of a file containing fluid thermal expansion coefficient "
                            "(1/K) as a function of temperature "
                            "(C); if provided the constant value is ignored.");

  // Solid properties
  // https://en.wikipedia.org/wiki/Stainless_steel#Properties
  params.addParam<Real>("solid_thermal_conductivity",
                        15.0,
                        "Solid thermal conductivity (W/(mK); default is for AISI/ASTIM 304 "
                        "stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_thermal_conductivity_file",
      "The name of a file containing solid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_density",
      7900,
      "Solid density (kg/m^3); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>("solid_density_file",
                            "The name of a file containing solid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_specific_heat",
      500,
      "Solid specific heat (J/(kgK); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_specific_heat_file",
      "The name of a file containing solid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("solid_thermal_expansion",
                        17.3e-6,
                        "Solid thermal expansion coefficient (1/K); default is for water at 20C).");
  params.addParam<FileName>("solid_thermal_expansion_file",
                            "The name of a file containing solid thermal expansion coefficient "
                            "(1/K) as a function of temperature "
                            "(C); if provided the constant value is ignored.");
  return params;
}

PackedColumn::PackedColumn(const InputParameters & parameters)
  : ADMaterial(parameters),
    // Get the one parameter from the input file
    _input_radius(getFunction("radius")),
    _input_porosity(getFunction("porosity")),
    _temperature(adCoupledValue("temperature")),

    // Fluid
    _fluid_mu(getParam<Real>("fluid_viscosity")),
    _fluid_k(getParam<Real>("fluid_thermal_conductivity")),
    _fluid_rho(getParam<Real>("fluid_density")),
    _fluid_cp(getParam<Real>("fluid_specific_heat")),
    _fluid_cte(getParam<Real>("fluid_thermal_expansion")),

    // Solid
    _solid_k(getParam<Real>("solid_thermal_conductivity")),
    _solid_rho(getParam<Real>("solid_density")),
    _solid_cp(getParam<Real>("solid_specific_heat")),
    _solid_cte(getParam<Real>("solid_thermal_expansion")),

    // Material Properties being produced by this object
    _permeability(declareADProperty<Real>("permeability")),
    _porosity(declareADProperty<Real>("porosity")),
    _viscosity(declareADProperty<Real>("viscosity")),
    _thermal_conductivity(declareADProperty<Real>("thermal_conductivity")),
    _specific_heat(declareADProperty<Real>("specific_heat")),
    _density(declareADProperty<Real>("density")),
    _thermal_expansion(declareADProperty<Real>("thermal_expansion"))
{
  // Set data for permeability interpolation
  std::vector<Real> sphere_sizes = {1, 3};
  std::vector<Real> permeability = {0.8451e-9, 8.968e-9};
  _permeability_interpolation.setData(sphere_sizes, permeability);

  // Fluid viscosity, thermal conductivity, density, and specific heat
  _use_fluid_mu_interp = initInputData("fluid_viscosity_file", _fluid_mu_interpolation);
  _use_fluid_k_interp = initInputData("fluid_thermal_conductivity_file", _fluid_k_interpolation);
  _use_fluid_rho_interp = initInputData("fluid_density_file", _fluid_rho_interpolation);
  _use_fluid_cp_interp = initInputData("fluid_specific_heat_file", _fluid_cp_interpolation);
  _use_fluid_cte_interp = initInputData("fluid_thermal_expansion_file", _fluid_cte_interpolation);

  // Solid thermal conductivity, density, and specific heat
  _use_solid_k_interp = initInputData("solid_thermal_conductivity_file", _solid_k_interpolation);
  _use_solid_rho_interp = initInputData("solid_density_file", _solid_rho_interpolation);
  _use_solid_cp_interp = initInputData("solid_specific_heat_file", _solid_cp_interpolation);
  _use_solid_cte_interp = initInputData("solid_thermal_expansion_file", _solid_cte_interpolation);
}

void
PackedColumn::computeQpProperties()
{
  // Current temperature
  ADReal temp = _temperature[_qp] - 273.15;

  // Permeability
  Real radius_value = _input_radius.value(_t, _q_point[_qp]);
  mooseAssert(radius_value >= 1 && radius_value <= 3,
              "The radius range must be in the range [1, 3], but " << radius_value << " provided.");
  _permeability[_qp] = _permeability_interpolation.sample(radius_value);

  // Porosity
  Real porosity_value = _input_porosity.value(_t, _q_point[_qp]);
  mooseAssert(porosity_value > 0 && porosity_value <= 1,
              "The porosity range must be in the range (0, 1], but " << porosity_value
                                                                     << " provided.");
  _porosity[_qp] = porosity_value;

  // Fluid properties
  _viscosity[_qp] =
      _use_fluid_mu_interp ? _fluid_mu_interpolation.sample(raw_value(temp)) : _fluid_mu;
  ADReal fluid_k = _use_fluid_k_interp ? _fluid_k_interpolation.sample(raw_value(temp)) : _fluid_k;
  ADReal fluid_rho =
      _use_fluid_rho_interp ? _fluid_rho_interpolation.sample(raw_value(temp)) : _fluid_rho;
  ADReal fluid_cp =
      _use_fluid_cp_interp ? _fluid_cp_interpolation.sample(raw_value(temp)) : _fluid_cp;
  ADReal fluid_cte =
      _use_fluid_cte_interp ? _fluid_cte_interpolation.sample(raw_value(temp)) : _fluid_cte;

  // Solid properties
  ADReal solid_k = _use_solid_k_interp ? _solid_k_interpolation.sample(raw_value(temp)) : _solid_k;
  ADReal solid_rho =
      _use_solid_rho_interp ? _solid_rho_interpolation.sample(raw_value(temp)) : _solid_rho;
  ADReal solid_cp =
      _use_solid_cp_interp ? _solid_cp_interpolation.sample(raw_value(temp)) : _solid_cp;
  ADReal solid_cte =
      _use_solid_cte_interp ? _solid_cte_interpolation.sample(raw_value(temp)) : _solid_cte;

  // Compute the heat conduction material properties as a linear combination of
  // the material properties for fluid and steel.
  _thermal_conductivity[_qp] = _porosity[_qp] * fluid_k + (1.0 - _porosity[_qp]) * solid_k;
  _density[_qp] = _porosity[_qp] * fluid_rho + (1.0 - _porosity[_qp]) * solid_rho;
  _specific_heat[_qp] = _porosity[_qp] * fluid_cp + (1.0 - _porosity[_qp]) * solid_cp;
  _thermal_expansion[_qp] = _porosity[_qp] * fluid_cte + (1.0 - _porosity[_qp]) * solid_cte;
}

bool
PackedColumn::initInputData(const std::string & param_name, ADLinearInterpolation & interp)
{
  if (isParamValid(param_name))
  {
    const std::string & filename = getParam<FileName>(param_name);
    MooseUtils::DelimitedFileReader reader(filename, &_communicator);
    reader.setComment("#");
    reader.read();
    interp.setData(reader.getData(0), reader.getData(1));
    return true;
  }
  return false;
}

Step 9: Input File

[GlobalParams]
  displacements = 'disp_r disp_z'
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  ny = 200
  nx = 10
  ymax = 0.304 # Length of test chamber
  xmax = 0.0257 # Test chamber radius
[]

[MeshModifiers]
  [bottom]
    type = SubdomainBoundingBox
    location = inside
    bottom_left = '0 0 0'
    top_right = '0.01285 0.304 0'
    block_id = 1
  []
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Modules/TensorMechanics/Master]
  [all]
    # This block adds all of the proper Kernels, strain calculators, and Variables
    # for TensorMechanics in the correct coordinate system (autodetected)
    add_variables = true
    strain = FINITE
    eigenstrain_names = eigenstrain
    use_automatic_differentiation = true
    generate_output = 'vonmises_stress elastic_strain_xx elastic_strain_yy strain_xx strain_yy'
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = bottom
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = top
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = bottom
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = top
  []
  [hold_inlet]
    type = DirichletBC
    variable = disp_z
    boundary = bottom
    value = 0
  []
  [hold_center]
    type = DirichletBC
    variable = disp_r
    boundary = left
    value = 0
  []
  [hold_outside]
    type = DirichletBC
    variable = disp_r
    boundary = right
    value = 0
  []
[]

[Materials]
  viscosity_file = data/water_viscosity.csv
  density_file = data/water_density.csv
  thermal_conductivity_file = data/water_thermal_conductivity.csv
  specific_heat_file = data/water_specific_heat.csv
  thermal_expansion_file = data/water_thermal_expansion.csv

  [column_top]
    type = PackedColumn
    block = 0
    temperature = temperature
    radius = 1.15
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_thermal_conductivity_file = ${thermal_conductivity_file}
    fluid_specific_heat_file = ${specific_heat_file}
    fluid_thermal_expansion_file = ${thermal_expansion_file}
  []
  [column_bottom]
    type = PackedColumn
    block = 1
    temperature = temperature
    radius = 1
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_thermal_conductivity_file = ${thermal_conductivity_file}
    fluid_specific_heat_file = ${specific_heat_file}
    fluid_thermal_expansion_file = ${thermal_expansion_file}
  []

  [elasticity_tensor]
    type = ADComputeIsotropicElasticityTensor
    youngs_modulus = 200e9 # (Pa) from wikipedia
    poissons_ratio = .3 # from wikipedia

  []
  [elastic_stress]
    type = ADComputeFiniteStrainElasticStress
  []
  [thermal_strain]
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    eigenstrain_name = eigenstrain
    temperature = temperature
    thermal_expansion_coeff = 1e-5 # TM modules doesn't support material property, but it will
  []
[]

[Postprocessors]
  [average_temperature]
    type = ElementAverageValue
    variable = temperature
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
[]

[Executioner]
  type = Transient
  start_time = -1
  end_time = 200
  steady_state_tolerance = 1e-7
  steady_state_detection = true
  dt = 0.25
  solve_type = PJFNK
  automatic_scaling = true
  compute_scaling_once = false
  petsc_options_iname = '-pc_type'
  petsc_options_value = 'lu'
  #petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
  #petsc_options_value = 'hypre boomeramg 500'
  line_search = none
  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  [out]
    type = Exodus
    elemental_as_nodal = true
  []
[]

Step 9: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step09_mechanics
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step9.i

Step 9: Results

Step 10: Multiscale Simulation

Run full simulation but compute thermal conductivity and porosity from micro-structure

MultiApp System

A system for performing multiple simulations within a main simulation.

MOOSE was originally created to solve fully-coupled systems of PDEs, but not all systems need to be/are fully coupled:

  • Multiscale systems are generally loosely coupled between scales

  • Systems with both fast and slow physics can be decoupled in time

  • Simulations involving input from external codes may be solved

The MultiApp system creates simulations of loosely-coupled systems of fully-coupled equations

MultiApp Hierarchy

Each "app" is considered to be a solve that is independent, and there is always a "main" that is driving the simulation

  • The "main" app can have any number of MultiApp objects

  • Each MultiApp can represent many sub-applications ("sub-apps")

Each sub-app can solve for different physics from the main application

  • A sub-app can be another MOOSE application or could be an external application

  • A sub-app can have MultiApps, thus create a multi-level solve

Input File Syntax

MultiApp objects are declared in the [MultiApps] block

app_type
The name of the MooseApp derived application to run (e.g., "AnimalApp")

positions
List of 3D coordinates describing the offset of the sub-application into the physical space of the main application

execute_on
Allows control when sub-applications are executed: INITIAL, LINEAR, NONLINEAR, TIMESTEP_BEGIN, TIMESTEP_END

input_files
One input file can be supplied for all the sub-apps or a file can be provided for each

[MultiApps]
  [micro]
    type = TransientMultiApp
    app_type = DarcyThermoMechApp
    positions = '0.01285 0.0    0
                 0.01285 0.0608 0
                 0.01285 0.1216 0
                 0.01285 0.1824 0
                 0.01285 0.2432 0
                 0.01285 0.304  0'
    input_files = step10_micro.i
    execute_on = 'timestep_end'
  []
[]

Parallel

The MultiApp system is designed for efficient parallel execution of hierarchical problems.

  • The main application utilizes all processors

  • The processors are split among each sub-apps within each MultiApp and are run simultaneously

  • Multiple MultiApps will be executed one after another

Transfer System

A system to move data to and from the "master" and "sub-applications" of a MultiApp.

Transferred data typically is handled by the Auxiliary and Postprocessor systems.

The data on the receiving application should couple to these values in the normal way and each sub-application should be able to solve on its own

Field Interpolation

  • An "interpolation" Transfer should be used when the domains have some overlapping geometry.

  • The source field is evaluated at the destination points (generally nodes or element centroids).

  • The evaluations are then put into the receiving AuxVariable field named variable.

  • All MultiAppTransfers take a direction parameter to specify the flow of information. Options are: from_multiapp or to_multiapp.

[Transfers]
  [from_sub]
    source_variable = sub_u
    direction = from_multiapp
    variable = transferred_u
    type = MultiAppMeshFunctionTransfer
    multi_app = sub
    execute_on = 'initial timestep_end'
  []
  [elemental_from_sub]
    source_variable = sub_u
    direction = from_multiapp
    variable = elemental_transferred_u
    type = MultiAppMeshFunctionTransfer
    multi_app = sub
  []
[]

UserObject Interpolation

  • Many UserObjects compute spatially-varying data that is not associated directly with a mesh

  • Any UserObject can override Real spatialValue(Point &) to provide a value given a point in space

  • A UserObjectTransfer can sample this spatially-varying data from one app and put the values into an AuxVariable in another

[Transfers]
  [layered_transfer_to_sub_app]
    type = MultiAppUserObjectTransfer
    direction = to_multiapp
    user_object = master_uo
    variable = sub_app_var
    multi_app = sub_app
    displaced_target_mesh = true
  []
  [layered_transfer_from_sub_app]
    type = MultiAppUserObjectTransfer
    direction = from_multiapp
    user_object = sub_app_uo
    variable = from_sub_app_var
    multi_app = sub_app
    displaced_source_mesh = true
  []
[]

Postprocessor Transfer

A Postprocessor transfer allows a transfer of scalar values between applications

  • When transferring to a MultiApp, the value can either be put into a Postprocessor value or can be put into a constant AuxVariable field

  • When transferring from a MultiApp to the master, the value can be interpolated from all the sub-apps into an auxiliary field

[Transfers]
  [pp_transfer]
    type = MultiAppPostprocessorTransfer
    direction = to_multiapp
    multi_app = pp_sub
    from_postprocessor = average
    to_postprocessor = from_master
  []
[]

Step 10: Multiscale Simulation

(continued)

RandomCorrosion.h


#pragma once

// MOOSE includes
#include "AuxKernel.h"
#include "libmesh/bounding_box.h"

/**
 * Creates artificial, temperature driven corrosion.
 *
 * Consider a multi-phase system represented by a field-variable varying
 * from 0 to 1. This class randomly sets points within the field to have
 * a value of 0. Additionally, there is a contrived relationship with the
 * number of points where "corrosion" occurs, the greater the difference
 * between the supplied postprocessor and the reference the more points
 * that are used.
 */
class RandomCorrosion : public AuxKernel
{
public:
  static InputParameters validParams();

  /**
   * Class constructor
   * @param parameters The input parameters for the RandomCorrosion object.
   */
  RandomCorrosion(const InputParameters & parameters);

  /**
   * At each timestep randomly create a vector of points to apply "corrosion".
   */
  void timestepSetup() override;

protected:
  /**
   * Computes the "corrosion" for the supplied phase variable.
   * @return The compute "phase" variable
   */
  virtual Real computeValue() override;

  /**
   * A helper method for getting random points in the domiain.
   * @return A random point within the bounding box of the domain
   */
  Point getRandomPoint();

private:
  /// The vector of random points to apply "corrosion"
  std::vector<Point> _points;

  /// The bounding box of the domain, used for generating "corrosion" points
  BoundingBox _box;

  /// Nodal tolerance for determining if "corrosion" should occur at the current node
  const Real & _nodal_tol;

  /// Minimum  number of "corrosion" points to apply
  const unsigned int & _num_points;

  /// Reference temperature, used for creating a temperature dependence and corrosion
  const Real & _ref_temperature;

  /// System temperature, used for creating a temperature dependence and corrosion
  const PostprocessorValue & _temperature;
};

RandomCorrosion.C


// MOOSE includes
#include "RandomCorrosion.h"
#include "MooseMesh.h"

#include "libmesh/mesh_tools.h"

registerMooseObject("DarcyThermoMechApp", RandomCorrosion);

InputParameters
RandomCorrosion::validParams()
{
  InputParameters params = AuxKernel::validParams();
  params.addParam<Real>("tolerance",
                        1e-3,
                        "When acting as a nodal AuxKernel determine if the "
                        "random point to apply corrosion is located at the "
                        "current node.");
  params.addParam<unsigned int>("num_points",
                                10,
                                "The number of random points to apply artificial "
                                "corrosion. The number of points is increased by "
                                "a factor as the supplied temperatures diverge.");
  params.addParam<Real>("reference_temperature",
                        273.15,
                        "Temperature at which corrosion begins, "
                        "the greater the 'temperature' drifts "
                        "from this the greater the amount of "
                        "corrosion locations that occurs.");
  params.addParam<PostprocessorName>(
      "temperature",
      274.15,
      "The temperature value to used for computing the temperature "
      "multiplication factor for the number of corrosion locations.");
  return params;
}

RandomCorrosion::RandomCorrosion(const InputParameters & parameters)
  : AuxKernel(parameters),
    _box(MeshTools::create_bounding_box(_mesh)),
    _nodal_tol(getParam<Real>("tolerance")),
    _num_points(getParam<unsigned int>("num_points")),
    _ref_temperature(getParam<Real>("reference_temperature")),
    _temperature(getPostprocessorValue("temperature"))
{
  // This class only works with Nodal aux variables
  if (!isNodal())
    mooseError("RandomCorrosion only operates using nodal aux variables.");

  // Setup the random number generation
  setRandomResetFrequency(EXEC_TIMESTEP_BEGIN);
}

void
RandomCorrosion::timestepSetup()
{
  // Increase the number of points as the temperature differs from the reference
  Real factor = 1;
  if (_temperature > _ref_temperature)
    factor = 1 + (_temperature - _ref_temperature) * 0.1;

  // Generater the random points to apply "corrosion"
  _points.clear();
  for (unsigned int i = 0; i < _num_points * factor; ++i)
    _points.push_back(getRandomPoint());
}

Real
RandomCorrosion::computeValue()
{

  // If the current node is at a "corrosion" point, set the phase variable to zero
  for (const Point & pt : _points)
    if (_current_node->absolute_fuzzy_equals(pt, _nodal_tol))
      return 0.0;

  // Do nothing to the phase variable if not at a "corrosion" point
  return _u[_qp];
}

Point
RandomCorrosion::getRandomPoint()
{
  // Generates a random point within the domain
  const Point & min = _box.min();
  const Point & max = _box.max();

  Real x = getRandomReal() * (max(0) - min(0)) + min(0);
  Real y = getRandomReal() * (max(1) - min(1)) + min(1);
  Real z = getRandomReal() * (max(2) - min(2)) + min(2);

  return Point(x, y, z);
}

Step 10: Micro-scale Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 10
  ymax = 0.1
  xmax = 0.1
  uniform_refine = 0
[]

[Adaptivity]
  max_h_level = 4
  initial_steps = 6
  initial_marker = error_marker
  cycles_per_step = 2
  marker = error_marker
  [Indicators]
    [phi_jump]
      type = GradientJumpIndicator
      variable = phi
    []
  []
  [Markers]
    [error_marker]
      type = ErrorFractionMarker
      indicator = phi_jump
      refine = 0.8
      coarsen = 0.1
    []
  []
[]

[Variables]
  [temperature]
    initial_condition = 300
  []
[]

[AuxVariables]
  [phi]
  []
  [por_var]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [corrosion]
    type = RandomCorrosion
    variable = phi
    reference_temperature = 300
    temperature = temperature_in
    execute_on = 'INITIAL TIMESTEP_END'
  []
  [por_var]
    type = ADMaterialRealAux
    variable = por_var
    property = porosity
    execute_on = 'INITIAL TIMESTEP_END'
  []
[]

[Kernels]
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
[]

[BCs]
  [left]
    type = PostprocessorDirichletBC
    variable = temperature
    boundary = left
    postprocessor = temperature_in
  []
  [right]
    type = NeumannBC
    variable = temperature
    boundary = right
    value = 100 # prescribed flux
  []
[]

[Materials]
  [column]
    type = PackedColumn
    temperature = temperature
    radius = 1 # mm
    phase = phi
  []
[]

[Postprocessors]
  [temperature_in]
    type = Receiver
    default = 301
  []
  [k_eff]
    type = ThermalConductivity
    variable = temperature
    T_hot = temperature_in
    flux = 100
    dx = 0.1
    boundary = right
    length_scale = 1
    k0 = 12.05
    execute_on = 'INITIAL TIMESTEP_END'
  []
  [por_var]
    type = ElementAverageValue
    variable = por_var
    execute_on = 'INITIAL TIMESTEP_END'
  []
  [t_right]
    type = SideAverageValue
    boundary = right
    variable = temperature
    execute_on = 'INITIAL TIMESTEP_END'
  []
[]

[Executioner]
  type = Transient
  end_time = 1000
  dt = 1
  steady_state_tolerance = 1e-9
  steady_state_detection = true
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  automatic_scaling = true
[]

[Outputs]
  execute_on = 'initial timestep_end'
  exodus = true
[]

[ICs]
  [close_pack]
    radius = 0.01 # meter
    outvalue = 0  # water
    variable = phi
    invalue = 1   # steel
    type = ClosePackIC
  []
[]

Step 10: Run and Visualize Micro-scale


cd ~/projects/moose/tutorials/darcy-thermo_mech/step10_multiapps
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step10_micro.i

Step 10: Micro-scale Results

PackedColumn.h


#pragma once

#include "ADMaterial.h"

// A helper class from MOOSE that linear interpolates x,y data
#include "LinearInterpolation.h"

/**
 * Material-derived objects override the computeQpProperties()
 * function.  They must declare and compute material properties for
 * use by other objects in the calculation such as Kernels and
 * BoundaryConditions.
 */
class PackedColumn : public ADMaterial
{
public:
  static InputParameters validParams();

  PackedColumn(const InputParameters & parameters);

protected:
  /**
   * Necessary override.  This is where the values of the properties
   * are computed.
   */
  virtual void computeQpProperties() override;

  /**
   * Helper function for reading CSV data for use in an interpolator object.
   */
  bool initInputData(const std::string & param_name, ADLinearInterpolation & interp);

  /// The radius of the spheres in the column
  const Function & _input_radius;

  /// The input porosity
  const Function & _input_porosity;

  /// Temperature
  const ADVariableValue & _temperature;

  /// Compute permeability based on the radius (mm)
  LinearInterpolation _permeability_interpolation;

  /// Fluid viscosity
  bool _use_fluid_mu_interp;
  const Real & _fluid_mu;
  ADLinearInterpolation _fluid_mu_interpolation;

  /// Fluid thermal conductivity
  bool _use_fluid_k_interp = false;
  const Real & _fluid_k;
  ADLinearInterpolation _fluid_k_interpolation;

  /// Fluid density
  bool _use_fluid_rho_interp = false;
  const Real & _fluid_rho;
  ADLinearInterpolation _fluid_rho_interpolation;

  /// Fluid specific heat
  bool _use_fluid_cp_interp;
  const Real & _fluid_cp;
  ADLinearInterpolation _fluid_cp_interpolation;

  /// Fluid thermal expansion coefficient
  bool _use_fluid_cte_interp;
  const Real & _fluid_cte;
  ADLinearInterpolation _fluid_cte_interpolation;

  /// Solid thermal conductivity
  bool _use_solid_k_interp = false;
  const Real & _solid_k;
  ADLinearInterpolation _solid_k_interpolation;

  /// Solid density
  bool _use_solid_rho_interp = false;
  const Real & _solid_rho;
  ADLinearInterpolation _solid_rho_interpolation;

  /// Fluid specific heat
  bool _use_solid_cp_interp;
  const Real & _solid_cp;
  ADLinearInterpolation _solid_cp_interpolation;

  /// Solid thermal expansion coefficient
  bool _use_solid_cte_interp;
  const Real & _solid_cte;
  ADLinearInterpolation _solid_cte_interpolation;

  /// The permeability (K)
  ADMaterialProperty<Real> & _permeability;

  /// The porosity (eps)
  ADMaterialProperty<Real> & _porosity;

  /// The viscosity of the fluid (mu)
  ADMaterialProperty<Real> & _viscosity;

  /// The bulk thermal conductivity
  ADMaterialProperty<Real> & _thermal_conductivity;

  /// The bulk heat capacity
  ADMaterialProperty<Real> & _specific_heat;

  /// The bulk density
  ADMaterialProperty<Real> & _density;

  /// The bulk thermal expansion coefficient
  ADMaterialProperty<Real> & _thermal_expansion;

  /// Flag for using the phase for porosity
  bool _use_phase_variable;

  /// The coupled phase variable
  const VariableValue & _phase;

  /// Flag for using a variable for thermal conductivity
  bool _use_variable_conductivity;

  /// The coupled thermal conductivity
  const VariableValue & _conductivity_variable;
};

PackedColumn.C


#include "PackedColumn.h"
#include "Function.h"
#include "DelimitedFileReader.h"

registerMooseObject("DarcyThermoMechApp", PackedColumn);

InputParameters
PackedColumn::validParams()
{
  InputParameters params = ADMaterial::validParams();
  params.addRequiredCoupledVar("temperature", "The temperature (C) of the fluid.");

  // Add a parameter to get the radius of the spheres in the column
  // (used later to interpolate permeability).
  params.addParam<FunctionName>("radius",
                                "1.0",
                                "The radius of the steel spheres (mm) that are packed in the "
                                "column for computing permeability.");

  // http://en.wikipedia.org/wiki/Close-packing_of_equal_spheres
  params.addParam<FunctionName>(
      "porosity", 0.25952, "Porosity of porous media, default is for closed packed spheres.");

  // Fluid properties
  params.addParam<Real>(
      "fluid_viscosity", 1.002e-3, "Fluid viscosity (Pa s); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_viscosity_file",
      "The name of a file containing the fluid viscosity (Pa-s) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("fluid_thermal_conductivity",
                        0.59803,
                        "Fluid thermal conductivity (W/(mK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_thermal_conductivity_file",
      "The name of a file containing fluid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_density", 998.21, "Fluid density (kg/m^3); default is for water at 20C).");
  params.addParam<FileName>("fluid_density_file",
                            "The name of a file containing fluid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "fluid_specific_heat", 4157.0, "Fluid specific heat (J/(kgK); default is for water at 20C).");
  params.addParam<FileName>(
      "fluid_specific_heat_file",
      "The name of a file containing fluid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("fluid_thermal_expansion",
                        2.07e-4,
                        "Fluid thermal expansion coefficient (1/K); default is for water at 20C).");
  params.addParam<FileName>("fluid_thermal_expansion_file",
                            "The name of a file containing fluid thermal expansion coefficient "
                            "(1/K) as a function of temperature "
                            "(C); if provided the constant value is ignored.");

  // Solid properties
  // https://en.wikipedia.org/wiki/Stainless_steel#Properties
  params.addParam<Real>("solid_thermal_conductivity",
                        15.0,
                        "Solid thermal conductivity (W/(mK); default is for AISI/ASTIM 304 "
                        "stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_thermal_conductivity_file",
      "The name of a file containing solid thermal conductivity (W/(mK)) as a function of "
      "temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_density",
      7900,
      "Solid density (kg/m^3); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>("solid_density_file",
                            "The name of a file containing solid density (kg/m^3) as a function "
                            "of temperature (C); if provided the constant value is ignored.");

  params.addParam<Real>(
      "solid_specific_heat",
      500,
      "Solid specific heat (J/(kgK); default is for AISI/ASTIM 304 stainless steel at 20C).");
  params.addParam<FileName>(
      "solid_specific_heat_file",
      "The name of a file containing solid specific heat (J/(kgK) as a function of temperature "
      "(C); if provided the constant value is ignored.");

  params.addParam<Real>("solid_thermal_expansion",
                        17.3e-6,
                        "Solid thermal expansion coefficient (1/K); default is for water at 20C).");
  params.addParam<FileName>("solid_thermal_expansion_file",
                            "The name of a file containing solid thermal expansion coefficient "
                            "(1/K) as a function of temperature "
                            "(C); if provided the constant value is ignored.");

  // Optional phase variable
  params.addCoupledVar("phase",
                       "The variable indicating the phase (steel=1 or water=0). If "
                       "supplied this is used to compute the porosity instead of the "
                       "supplied value.");

  // Optional thermal conductivity variable
  params.addCoupledVar("thermal_conductivity",
                       "When supplied the variable be will be used for "
                       "thermal conductivity rather than being computed.");
  return params;
}

PackedColumn::PackedColumn(const InputParameters & parameters)
  : ADMaterial(parameters),
    // Get the one parameter from the input file
    _input_radius(getFunction("radius")),
    _input_porosity(getFunction("porosity")),
    _temperature(adCoupledValue("temperature")),

    // Fluid
    _fluid_mu(getParam<Real>("fluid_viscosity")),
    _fluid_k(getParam<Real>("fluid_thermal_conductivity")),
    _fluid_rho(getParam<Real>("fluid_density")),
    _fluid_cp(getParam<Real>("fluid_specific_heat")),
    _fluid_cte(getParam<Real>("fluid_thermal_expansion")),

    // Solid
    _solid_k(getParam<Real>("solid_thermal_conductivity")),
    _solid_rho(getParam<Real>("solid_density")),
    _solid_cp(getParam<Real>("solid_specific_heat")),
    _solid_cte(getParam<Real>("solid_thermal_expansion")),

    // Material Properties being produced by this object
    _permeability(declareADProperty<Real>("permeability")),
    _porosity(declareADProperty<Real>("porosity")),
    _viscosity(declareADProperty<Real>("viscosity")),
    _thermal_conductivity(declareADProperty<Real>("thermal_conductivity")),
    _specific_heat(declareADProperty<Real>("specific_heat")),
    _density(declareADProperty<Real>("density")),
    _thermal_expansion(declareADProperty<Real>("thermal_expansion")),

    // Optional phase variable
    _use_phase_variable(isParamValid("phase")),
    _phase(_use_phase_variable ? coupledValue("phase") : _zero),

    // Optional thermal conductivity variable
    _use_variable_conductivity(isParamValid("thermal_conductivity")),
    _conductivity_variable(_use_variable_conductivity ? coupledValue("thermal_conductivity")
                                                      : _zero)
{
  // Set data for permeability interpolation
  std::vector<Real> sphere_sizes = {1, 3};
  std::vector<Real> permeability = {0.8451e-9, 8.968e-9};
  _permeability_interpolation.setData(sphere_sizes, permeability);

  // Fluid viscosity, thermal conductivity, density, and specific heat
  _use_fluid_mu_interp = initInputData("fluid_viscosity_file", _fluid_mu_interpolation);
  _use_fluid_k_interp = initInputData("fluid_thermal_conductivity_file", _fluid_k_interpolation);
  _use_fluid_rho_interp = initInputData("fluid_density_file", _fluid_rho_interpolation);
  _use_fluid_cp_interp = initInputData("fluid_specific_heat_file", _fluid_cp_interpolation);
  _use_fluid_cte_interp = initInputData("fluid_thermal_expansion_file", _fluid_cte_interpolation);

  // Solid thermal conductivity, density, and specific heat
  _use_solid_k_interp = initInputData("solid_thermal_conductivity_file", _solid_k_interpolation);
  _use_solid_rho_interp = initInputData("solid_density_file", _solid_rho_interpolation);
  _use_solid_cp_interp = initInputData("solid_specific_heat_file", _solid_cp_interpolation);
  _use_solid_cte_interp = initInputData("solid_thermal_expansion_file", _solid_cte_interpolation);
}

void
PackedColumn::computeQpProperties()
{
  // Current temperature
  ADReal temp = _temperature[_qp] - 273.15;

  // Permeability
  Real radius_value = _input_radius.value(_t, _q_point[_qp]);
  mooseAssert(radius_value >= 1 && radius_value <= 3,
              "The radius range must be in the range [1, 3], but " << radius_value << " provided.");
  _permeability[_qp] = _permeability_interpolation.sample(radius_value);

  // Porosity
  if (_use_phase_variable)
    _porosity[_qp] = 1 - _phase[_qp];
  else
  {
    Real porosity_value = _input_porosity.value(_t, _q_point[_qp]);
    mooseAssert(porosity_value > 0 && porosity_value <= 1,
                "The porosity range must be in the range (0, 1], but " << porosity_value
                                                                       << " provided.");
    _porosity[_qp] = porosity_value;
  }

  // Fluid properties
  _viscosity[_qp] = _use_fluid_mu_interp ? _fluid_mu_interpolation.sample(temp) : _fluid_mu;
  ADReal fluid_rho = _use_fluid_rho_interp ? _fluid_rho_interpolation.sample(temp) : _fluid_rho;
  ADReal fluid_cp = _use_fluid_cp_interp ? _fluid_cp_interpolation.sample(temp) : _fluid_cp;
  ADReal fluid_cte = _use_fluid_cte_interp ? _fluid_cte_interpolation.sample(temp) : _fluid_cte;

  // Solid properties
  ADReal solid_rho = _use_solid_rho_interp ? _solid_rho_interpolation.sample(temp) : _solid_rho;
  ADReal solid_cp = _use_solid_cp_interp ? _solid_cp_interpolation.sample(temp) : _solid_cp;
  ADReal solid_cte = _use_solid_cte_interp ? _solid_cte_interpolation.sample(temp) : _solid_cte;

  // Compute the heat conduction material properties as a linear combination of
  // the material properties for fluid and steel.
  if (_use_variable_conductivity)
    _thermal_conductivity[_qp] = _conductivity_variable[_qp];
  else
  {
    ADReal fluid_k = _use_fluid_k_interp ? _fluid_k_interpolation.sample(temp) : _fluid_k;
    ADReal solid_k = _use_solid_k_interp ? _solid_k_interpolation.sample(temp) : _solid_k;
    _thermal_conductivity[_qp] = _porosity[_qp] * fluid_k + (1.0 - _porosity[_qp]) * solid_k;
  }

  _density[_qp] = _porosity[_qp] * fluid_rho + (1.0 - _porosity[_qp]) * solid_rho;
  _specific_heat[_qp] = _porosity[_qp] * fluid_cp + (1.0 - _porosity[_qp]) * solid_cp;
  _thermal_expansion[_qp] = _porosity[_qp] * fluid_cte + (1.0 - _porosity[_qp]) * solid_cte;
}

bool
PackedColumn::initInputData(const std::string & param_name, ADLinearInterpolation & interp)
{
  if (isParamValid(param_name))
  {
    const std::string & filename = getParam<FileName>(param_name);
    MooseUtils::DelimitedFileReader reader(filename, &_communicator);
    reader.setComment("#");
    reader.read();
    interp.setData(reader.getData(0), reader.getData(1));
    return true;
  }
  return false;
}

Step 10: Multi-scale Input File

[GlobalParams]
  displacements = 'disp_r disp_z'
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 10
  ny = 100
  ymax = 0.304 # Length of test chamber
  xmax = 0.0257 # Test chamber radius
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[AuxVariables]
  [k_eff]
    initial_condition = 15.0 # water at 20C
  []
  [velocity]
    order = CONSTANT
    family = MONOMIAL_VEC
  []
[]

[Modules/TensorMechanics/Master]
  [all]
    # This block adds all of the proper Kernels, strain calculators, and Variables
    # for TensorMechanics in the correct coordinate system (autodetected)
    add_variables = true
    strain = FINITE
    eigenstrain_names = eigenstrain
    use_automatic_differentiation = true
    generate_output = 'vonmises_stress elastic_strain_xx elastic_strain_yy strain_xx strain_yy'
  []
[]

[Kernels]
  [darcy_pressure]
    type = DarcyPressure
    variable = pressure
  []
  [heat_conduction]
    type = ADHeatConduction
    variable = temperature
  []
  [heat_conduction_time_derivative]
    type = ADHeatConductionTimeDerivative
    variable = temperature
  []
  [heat_convection]
    type = DarcyAdvection
    variable = temperature
    pressure = pressure
  []
[]

[AuxKernels]
  [velocity]
    type = DarcyVelocity
    variable = velocity
    execute_on = timestep_end
    pressure = pressure
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = bottom
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = top
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = bottom
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = top
  []
  [hold_inlet]
    type = DirichletBC
    variable = disp_z
    boundary = bottom
    value = 0
  []
  [hold_center]
    type = DirichletBC
    variable = disp_r
    boundary = left
    value = 0
  []
  [hold_outside]
    type = DirichletBC
    variable = disp_r
    boundary = right
    value = 0
  []
[]

[Materials]
  viscosity_file = data/water_viscosity.csv
  density_file = data/water_density.csv
  specific_heat_file = data/water_specific_heat.csv
  thermal_expansion_file = data/water_thermal_expansion.csv
  [column]
    type = PackedColumn
    temperature = temperature
    radius = 1
    thermal_conductivity = k_eff # Use the AuxVariable instead of calculating
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_specific_heat_file = ${specific_heat_file}
    fluid_thermal_expansion_file = ${thermal_expansion_file}
  []

  [elasticity_tensor]
    type = ADComputeIsotropicElasticityTensor
    youngs_modulus = 200e9 # (Pa) from wikipedia
    poissons_ratio = .3 # from wikipedia
  []
  [elastic_stress]
    type = ADComputeFiniteStrainElasticStress
  []
  [thermal_strain]
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    thermal_expansion_coeff = 1e-6
    eigenstrain_name = eigenstrain
    temperature = temperature
  []
[]

[Postprocessors]
  [average_temperature]
    type = ElementAverageValue
    variable = temperature
  []
[]

[Executioner]
  type = Transient
  start_time = -1
  end_time = 200
  steady_state_tolerance = 1e-7
  steady_state_detection = true
  dt = 0.25
  solve_type = PJFNK
  automatic_scaling = true
  compute_scaling_once = false
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
  petsc_options_value = 'hypre boomeramg 500'
  line_search = none
  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[MultiApps]
  [micro]
    type = TransientMultiApp
    app_type = DarcyThermoMechApp
    positions = '0.01285 0.0    0
                 0.01285 0.0608 0
                 0.01285 0.1216 0
                 0.01285 0.1824 0
                 0.01285 0.2432 0
                 0.01285 0.304  0'
    input_files = step10_micro.i
    execute_on = 'timestep_end'
  []
[]

[Transfers]
  [keff_from_sub]
    type = MultiAppPostprocessorInterpolationTransfer
    direction = from_multiapp
    multi_app = micro
    variable = k_eff
    power = 1
    postprocessor = k_eff
    execute_on = 'timestep_end'
  []
  [temperature_to_sub]
    type = MultiAppVariableValueSamplePostprocessorTransfer
    direction = to_multiapp
    multi_app = micro
    source_variable = temperature
    postprocessor = temperature_in
    execute_on = 'timestep_end'
  []
[]

[Controls]
  [multiapp]
    type = TimePeriod
    disable_objects = 'MultiApps::micro Transfers::keff_from_sub Transfers::temperature_to_sub'
    start_time = '0'
    execute_on = 'initial'
  []
[]

[Outputs]
  [out]
    type = Exodus
    elemental_as_nodal = true
  []
[]

Step 10: Run and Visualize Multi-scale


cd ~/projects/moose/tutorials/darcy-thermo_mech/step10_multiapps
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step10.i

Step 10: Multi-scale Results

Step 11: Custom Syntax

Add custom syntax to build objects that are common to all Darcy thermal mecahnical problems:

  • Velocity auxiliary variables and kernels

  • Pressure kernel

  • Temperature kernels

Action System

A system for the programmatic creation of simulation objects and input file syntax.

Creating an Action

Inherit from Action or MooseObjectAction and override the act() method.

Notice, the constructor uses a copy of an InputParameters object. This is by design to allow the parameters to be manipulated and re-used during object creation.

Action Object

An action design to build specific objects, such as the case in Step 9: Mechanics for tensor mechanics.

[Modules/TensorMechanics/Master]
  [all]
    # This block adds all of the proper Kernels, strain calculators, and Variables
    # for TensorMechanics in the correct coordinate system (autodetected)
    add_variables = true
    strain = FINITE
    eigenstrain_names = eigenstrain
    use_automatic_differentiation = true
    generate_output = 'vonmises_stress elastic_strain_xx elastic_strain_yy strain_xx strain_yy'
  []
[]

Syntax and Tasks

The MOOSE action system operates on tasks, each task is connected to one or many actions.

For each task the act() method is called for each task, thus the act method can be used to create any number of objects.

In general, the following macros are called within an application registerAll method to create the necessary syntax and tasks to build the desired objects.

registerSyntax(action, action_syntax)
Creates input file syntax provided in "action_syntax" and associates with the "action" provided

registerSyntaxTask(action, action_syntax, task)
Same as above, but also creates a named task that will be executed.

registerTask(name, is_required)
Creates a named task that actions can be associated.

addTaskDependency(action, depends_on)
Create a dependency between two tasks to help control the order of operation of task execution

MooseObjectAction Object

An action designed to build one or many other MooseObjects, such as in the case of the [Dampers] block.

AddDamperAction.h


#pragma once

#include "MooseObjectAction.h"

class AddDamperAction;

template <>
InputParameters validParams<AddDamperAction>();

class AddDamperAction : public MooseObjectAction
{
public:
  static InputParameters validParams();

  AddDamperAction(InputParameters params);

  virtual void act() override;
};

AddDamperAction.C


#include "AddDamperAction.h"
#include "FEProblem.h"

registerMooseAction("MooseApp", AddDamperAction, "add_damper");

defineLegacyParams(AddDamperAction);

InputParameters
AddDamperAction::validParams()
{
  return MooseObjectAction::validParams();
}

AddDamperAction::AddDamperAction(InputParameters params) : MooseObjectAction(params) {}

void
AddDamperAction::act()
{
  _problem->addDamper(_type, _name, _moose_object_pars);
}

Moose.C

  registerSyntax("AddDamperAction", "Dampers/*");

Step 11: Custom Syntax

(continued)

SetupDarcySimulation.h


#pragma once

// MOOSE includes
#include "Action.h"

/**
 * An action for creating the necessary objects to perform a thermal mechanics problem using
 * Darcy's equation.
 * */
class SetupDarcySimulation : public Action
{
public:
  static InputParameters validParams();

  SetupDarcySimulation(InputParameters params);
  virtual void act() override;

protected:
  const bool _compute_velocity;
  const bool _compute_pressure;
  const bool _compute_temperature;
};

SetupDarcySimulation.C


#include "SetupDarcySimulation.h"

// MOOSE includes
#include "FEProblem.h"
#include "AuxiliarySystem.h"

// libMesh includes
#include "libmesh/fe.h"

registerMooseAction("DarcyThermoMechApp", SetupDarcySimulation, "setup_darcy");

InputParameters
SetupDarcySimulation::validParams()
{
  InputParameters params = Action::validParams();
  params.addParam<VariableName>("pressure", "pressure", "The pressure variable.");
  params.addParam<VariableName>("temperature", "temperature", "The temperature variable.");
  params.addParam<bool>(
      "compute_velocity", true, "Enable the auxiliary calculation of velocity from pressure.");
  params.addParam<bool>("compute_pressure", true, "Enable the computation of pressure.");
  params.addParam<bool>("compute_temperature", true, "Enable the computation of temperature.");
  return params;
}

SetupDarcySimulation::SetupDarcySimulation(InputParameters parameters)
  : Action(parameters),
    _compute_velocity(getParam<bool>("compute_velocity")),
    _compute_pressure(getParam<bool>("compute_pressure")),
    _compute_temperature(getParam<bool>("compute_temperature"))
{
}

void
SetupDarcySimulation::act()
{
  // Actual names of input variables
  const std::string pressure = getParam<VariableName>("pressure");
  const std::string temperature = getParam<VariableName>("temperature");

  // Velocity AuxVariables
  if (_compute_velocity && _current_task == "add_aux_variable")
  {
    InputParameters var_params = _factory.getValidParams("VectorMooseVariable");
    var_params.set<MooseEnum>("family") = "MONOMIAL_VEC";
    var_params.set<MooseEnum>("order") = "CONSTANT";

    _problem->addAuxVariable("VectorMooseVariable", "velocity", var_params);
  }

  // Velocity AuxKernels
  else if (_compute_velocity && _current_task == "add_aux_kernel")
  {
    InputParameters params = _factory.getValidParams("DarcyVelocity");
    params.set<ExecFlagEnum>("execute_on") = EXEC_TIMESTEP_END;
    params.set<std::vector<VariableName>>("pressure") = {pressure};

    params.set<AuxVariableName>("variable") = "velocity";
    _problem->addAuxKernel("DarcyVelocity", "velocity", params);
  }

  // Kernels
  else if (_current_task == "add_kernel")
  {
    // Flags for aux variables
    const bool is_pressure_aux = _problem->getAuxiliarySystem().hasVariable(pressure);
    const bool is_temperature_aux = _problem->getAuxiliarySystem().hasVariable(temperature);

    // Pressure
    if (_compute_pressure && !is_pressure_aux)
    {
      InputParameters params = _factory.getValidParams("DarcyPressure");
      params.set<NonlinearVariableName>("variable") = pressure;
      _problem->addKernel("DarcyPressure", "darcy_pressure", params);
    }

    // Temperature
    if (_compute_temperature && !is_temperature_aux)
    {
      {
        InputParameters params = _factory.getValidParams("ADHeatConduction");
        params.set<NonlinearVariableName>("variable") = temperature;
        _problem->addKernel("ADHeatConduction", "heat_conduction", params);
      }

      {
        InputParameters params = _factory.getValidParams("ADHeatConductionTimeDerivative");
        params.set<NonlinearVariableName>("variable") = temperature;
        _problem->addKernel("ADHeatConductionTimeDerivative", "heat_conduction_time", params);
      }

      {
        InputParameters params = _factory.getValidParams("DarcyAdvection");
        params.set<NonlinearVariableName>("variable") = temperature;
        params.set<std::vector<VariableName>>("pressure") = {pressure};
        _problem->addKernel("DarcyAdvection", "heat_advection", params);
      }
    }
  }
}

DarcyThermoMechApp.h


#pragma once

#include "MooseApp.h"

class DarcyThermoMechApp : public MooseApp
{
public:
  static InputParameters validParams();

  DarcyThermoMechApp(InputParameters parameters);

  static void registerApps();
  static void registerAll(Factory & factory, ActionFactory & action_factory, Syntax & syntax);
};

DarcyThermoMechApp.C


// Tutorial Includes
#include "DarcyThermoMechApp.h"

// MOOSE Includes
#include "AppFactory.h"
#include "MooseSyntax.h"
#include "ModulesApp.h"

template <>
InputParameters
validParams<DarcyThermoMechApp>()
{
  InputParameters params = validParams<MooseApp>();

  params.set<bool>("automatic_automatic_scaling") = false;

  // Sets DirichletBC default for preset = true
  // This will be removed in the future when the global default is changed
  params.set<bool>("use_legacy_dirichlet_bc") = false;

  return params;
}

DarcyThermoMechApp::DarcyThermoMechApp(InputParameters parameters) : MooseApp(parameters)
{
  DarcyThermoMechApp::registerAll(_factory, _action_factory, _syntax);
}

void
DarcyThermoMechApp::registerApps()
{
  registerApp(DarcyThermoMechApp);
}

void
DarcyThermoMechApp::registerAll(Factory & factory, ActionFactory & action_factory, Syntax & syntax)
{

  Registry::registerObjectsTo(factory, {"DarcyThermoMechApp"});
  Registry::registerActionsTo(action_factory, {"DarcyThermoMechApp"});
  ModulesApp::registerAll(factory, action_factory, syntax);

  registerSyntaxTask("SetupDarcySimulation", "DarcyThermoMech", "add_aux_variable");
  registerSyntaxTask("SetupDarcySimulation", "DarcyThermoMech", "add_aux_kernel");
  registerSyntaxTask("SetupDarcySimulation", "DarcyThermoMech", "add_kernel");
}

Step 11: Input File

[GlobalParams]
  displacements = 'disp_r disp_z'
[]

[Mesh]
  type = GeneratedMesh
  dim = 2
  ny = 200
  nx = 10
  ymax = 0.304 # Length of test chamber
  xmax = 0.0257 # Test chamber radius
[]

[Variables]
  [pressure]
  []
  [temperature]
    initial_condition = 300 # Start at room temperature
  []
[]

[DarcyThermoMech]
[]

[Modules/TensorMechanics/Master]
  [all]
    # This block adds all of the proper Kernels, strain calculators, and Variables
    # for TensorMechanics in the correct coordinate system (autodetected)
    add_variables = true
    strain = FINITE
    eigenstrain_names = eigenstrain
    use_automatic_differentiation = true
    generate_output = 'vonmises_stress elastic_strain_xx elastic_strain_yy strain_xx strain_yy'
  []
[]

[BCs]
  [inlet]
    type = DirichletBC
    variable = pressure
    boundary = bottom
    value = 4000 # (Pa) From Figure 2 from paper.  First data point for 1mm spheres.
  []
  [outlet]
    type = DirichletBC
    variable = pressure
    boundary = top
    value = 0 # (Pa) Gives the correct pressure drop from Figure 2 for 1mm spheres
  []
  [inlet_temperature]
    type = FunctionDirichletBC
    variable = temperature
    boundary = bottom
    function = 'if(t<0,350+50*t,350)'
  []
  [outlet_temperature]
    type = HeatConductionOutflow
    variable = temperature
    boundary = top
  []
  [hold_inlet]
    type = DirichletBC
    variable = disp_z
    boundary = bottom
    value = 0
  []
  [hold_center]
    type = DirichletBC
    variable = disp_r
    boundary = left
    value = 0
  []
  [hold_outside]
    type = DirichletBC
    variable = disp_r
    boundary = right
    value = 0
  []
[]

[Materials]
  viscosity_file = data/water_viscosity.csv
  density_file = data/water_density.csv
  thermal_conductivity_file = data/water_thermal_conductivity.csv
  specific_heat_file = data/water_specific_heat.csv
  thermal_expansion_file = data/water_thermal_expansion.csv

  [column]
    type = PackedColumn
    block = 0
    temperature = temperature
    radius = 1.15
    fluid_viscosity_file = ${viscosity_file}
    fluid_density_file = ${density_file}
    fluid_thermal_conductivity_file = ${thermal_conductivity_file}
    fluid_specific_heat_file = ${specific_heat_file}
    fluid_thermal_expansion_file = ${thermal_expansion_file}
  []

  [elasticity_tensor]
    type = ADComputeIsotropicElasticityTensor
    youngs_modulus = 200e9 # (Pa) from wikipedia
    poissons_ratio = .3 # from wikipedia

  []
  [elastic_stress]
    type = ADComputeFiniteStrainElasticStress
  []
  [thermal_strain]
    type = ADComputeThermalExpansionEigenstrain
    stress_free_temperature = 300
    eigenstrain_name = eigenstrain
    temperature = temperature
    thermal_expansion_coeff = 1e-5
  []
[]

[Postprocessors]
  [average_temperature]
    type = ElementAverageValue
    variable = temperature
  []
[]

[Problem]
  type = FEProblem
  coord_type = RZ
[]

[Executioner]
  type = Transient
  start_time = -1
  end_time = 200
  steady_state_tolerance = 1e-7
  steady_state_detection = true
  dt = 0.25
  solve_type = PJFNK
  automatic_scaling = true
  compute_scaling_once = false
  petsc_options_iname = '-pc_type -pc_hypre_type -ksp_gmres_restart'
  petsc_options_value = 'hypre boomeramg 500'
  line_search = none
  [TimeStepper]
    type = FunctionDT
    function = 'if(t<0,0.1,0.25)'
  []
[]

[Outputs]
  [out]
    type = Exodus
    elemental_as_nodal = true
  []
[]

Step 11: Run and Visualize


cd ~/projects/moose/tutorials/darcy-thermo_mech/step11_action
make -j 12 # use number of processors for you system
cd problems
~/projects/moose/python/peacock/peacock -i step11.i

Step 11: Results

Method of Manufactured Solutions (MMS)

The Method of Manufactured Solutions (MMS) is a useful tool for code verification (making sure that a mathematical model is properly solved)

MMS works by assuming a solution, substituting it into the PDE, and obtaining a forcing term

The modified PDE (with forcing term added) is then solved numerically; the result can be compared to the assumed solution

By checking the norm of the error on successively finer grids you can verify your code obtains the theoretical convergence rates

Example 14: MMS

PDE:

Assumed solution:

Forcing function:

Need to solve:

Example 14: Input File

[Mesh]
  type = GeneratedMesh
  dim = 2
  nx = 32
  ny = 32
  xmin = 0.0
  xmax = 1.0
  ymin = 0.0
  ymax = 1.0
[]

[Variables]
  [forced]
    order = FIRST
    family = LAGRANGE
  []
[]

[Functions]
  # A ParsedFunction allows us to supply analytic expressions directly in the input file
  [exact]
    type = ParsedFunction
    value = sin(alpha*pi*x)
    vars = alpha
    vals = 16
  []

  # This function is an actual compiled function
  [force]
    type = ExampleFunction
    alpha = 16
  []
[]

[Kernels]
  [diff]
    type = ADDiffusion
    variable = forced
  []

  # This Kernel can take a function name to use
  [forcing]
    type = ADBodyForce
    variable = forced
    function = force
  []
[]

[BCs]
  # The BC can take a function name to use
  [all]
    type = FunctionDirichletBC
    variable = forced
    boundary = 'bottom right top left'
    function = exact
  []
[]

[Executioner]
  type = Steady
  solve_type = NEWTON
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
[]

[Postprocessors]
  [h]
    type = AverageElementSize
  []
  [error]
    type = ElementL2Error
    variable = forced
    function = exact
  []
[]

[Outputs]
  execute_on = 'timestep_end'
  exodus = true
  csv = true
[]

Example 14: Run via Command-line


cd ~/projects/moose/examples/ex14_pps
make -j 12 # use number of processors for you system
./ex14-opt -i ex14.i

MMS Python Package


export PYTHONPATH=$PYTHONPATH:~/projects/moose/python

Example 14: Exact Solution

mms_exact.py

#!/usr/bin/env python3

import mms
fs,ss = mms.evaluate('-div(grad(u))', 'sin(a*pi*x)', scalars=['a'])
mms.print_fparser(fs)
mms.print_hit(fs, 'force')
mms.print_hit(ss, 'exact')

cd ~/projects/moose/examples/ex14_pps
./mms_exact.py

pi^2*a^2*sin(x*pi*a)
[force]
  type = ParsedFunction
  value = 'pi^2*a^2*sin(x*pi*a)'
  vars = 'a'
  vals = '1.0'
[]
[exact]
  type = ParsedFunction
  value = 'sin(x*pi*a)'
  vars = 'a'
  vals = '1.0'
[]

Error Analysis

To compare two solutions (or a solution and an analytical solution) and , the following expressions are frequently used:

From finite element theory, the convergence rates are known for these quantities on successively refined grids. These two calculations are computed in MOOSE by utilizing the ElementL2Error or ElementH1SemiError postprocessor objects, respectively.

Example 14: Convergence Study

mms_spatial.py

#!/usr/bin/env python3

import mms
df1 = mms.run_spatial('ex14.i', 4, executable='./ex14-opt')
df2 = mms.run_spatial('ex14.i', 4, 'Mesh/second_order=true', 'Variables/forced/order=SECOND', executable='./ex14-opt')

fig = mms.ConvergencePlot(xlabel='Element Size ($h$)', ylabel='$L_2$ Error')
fig.plot(df1, label='1st Order', marker='o', markersize=8)
fig.plot(df2, label='2nd Order', marker='o', markersize=8)
fig.save('ex14_mms.png')

Example 14: Convergence Results


cd ~/projects/moose/examples/ex14_pps
./mms_spatial.py

Debugging

A debugger is often more effective than print statements in helping to find bugs

Many debuggers exist: LLDB, GDB, Totalview, ddd, Intel Debugger, etc.

Typically it is best to use a debugger that is associated with your compiler

Here LLDB/GDB are used, both are simple to use and are included in the MOOSE package

Segmentation Fault

A "Segmentation fault," "Segfault," or "Signal 11" error denotes a memory bug (often array access out of bounds).


Segmentation fault: 11

A segfault is a "good" error to have, because a debugger can easily pinpoint the problem.

Example 21: Input File

[Mesh]
  file = reactor.e
  #Let's assign human friendly names to the blocks on the fly
  block_id = '1 2'
  block_name = 'fuel deflector'

  boundary_id = '4 5'
  boundary_name = 'bottom top'
[]

[Variables]
  #Use active lists to help debug problems. Switching on and off
  #different Kernels or Variables is extremely useful!
  active = 'diffused convected'
  [diffused]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.5
  []

  [convected]
    order = FIRST
    family = LAGRANGE
    initial_condition = 0.0
  []
[]

[Kernels]
  #This Kernel consumes a real-gradient material property from the active material
  active = 'convection diff_convected example_diff time_deriv_diffused time_deriv_convected'
  [convection]
    type = ExampleConvection
    variable = convected
  []

  [diff_convected]
    type = Diffusion
    variable = convected
  []

  [example_diff]
    type = ExampleDiffusion
    variable = diffused
    coupled_coef = convected
  []

  [time_deriv_diffused]
    type = TimeDerivative
    variable = diffused
  []

  [time_deriv_convected]
    type = TimeDerivative
    variable = convected
  []
[]

[BCs]
  [bottom_diffused]
    type = DirichletBC
    variable = diffused
    boundary = 'bottom'
    value = 0
  []

  [top_diffused]
    type = DirichletBC
    variable = diffused
    boundary = 'top'
    value = 5
  []

  [bottom_convected]
    type = DirichletBC
    variable = convected
    boundary = 'bottom'
    value = 0
  []

  [top_convected]
    type = NeumannBC
    variable = convected
    boundary = 'top'
    value = 1
  []
[]

[Materials]
  [example]
    type = ExampleMaterial
    block = 'fuel'
    diffusion_gradient = 'diffused'

    #Approximate Parabolic Diffusivity
    independent_vals = '0 0.25 0.5 0.75 1.0'
    dependent_vals = '1e-2 5e-3 1e-3 5e-3 1e-2'
  []

  [example1]
    type = ExampleMaterial
    block = 'deflector'
    diffusion_gradient = 'diffused'

    # Constant Diffusivity
    independent_vals = '0 1.0'
    dependent_vals = '1e-1 1e-1'
  []
[]

[Executioner]
  type = Transient
  solve_type = 'PJFNK'
  petsc_options_iname = '-pc_type -pc_hypre_type'
  petsc_options_value = 'hypre boomeramg'
  dt = 0.1
  num_steps = 10
[]

[Outputs]
  execute_on = 'timestep_end'
  exodus = true
[]

Example 21: Run Input File


cd ~/projects/moose/examples/ex21_debugging
make -j12
./ex21-opt -i ex21.i

Time Step  0, time = 0
                dt = 0

Time Step  1, time = 0.1
                dt = 0.1
Segmentation fault: 11

Debug Compile

To use a debugger with a MOOSE-based application, it must be compiled in something other than optimized mode (opt); debug (dbg) mode is recommended because it will produce full line number information in stack traces:


cd ~/projects/moose/examples/ex21_debugging
METHOD=dbg make -j12

This will create a "debug version" of and application: ex21-dbg

Running Debugger

The compiled debug application can be executed using either GDB (gcc) or LLDB (clang):


gdb --args ./ex21-dbg -i ex21.i

lldb -- ./ex21-dbg -i ex21.i

These commands will start debugger, load the executable, and open the debugger command prompt

Using GDB or LLDB

At any prompt in GDB or LLDB, you can type h and hit enter to get help

  1. Set a "breakpoint" in MPI_Abort so that the code pauses (maintaining the stack trace)

    
    (lldb) b MPI_Abort
    Breakpoint 1: where = libmpi.12.dylib`MPI_Abort, address = 0x000000010b18f460
    

  2. Run the application, type r and hit enter, the application will hit the breakpoint.

    
    (lldb) r
    Process 77675 launched: './ex21-dbg' (x86_64)
    

  3. When the application stops, get the backtrace

    
    (lldb) bt
     * thread #1, queue = 'com.apple.main-thread', stop reason = breakpoint 1.1
       * frame #0: 0x000000010b18f460 libmpi.12.dylib`MPI_Abort
         frame #1: 0x00000001000e5f8c libex21-dbg.0.dylib`MooseArray<double>::operator[](this=0x0000000112919388, i=0) const at MooseArray.h:276
         frame #2: 0x00000001000e580b libex21-dbg.0.dylib`ExampleDiffusion::computeQpResidual(this=0x0000000112918a18) at ExampleDiffusion.C:37
         frame #3: 0x0000000100486b99 libmoose-dbg.0.dylib`Kernel::computeResidual(this=0x0000000112918a18) at Kernel.C:99
    

The backtrace shows that in ExampleDiffusion::computeQpResidual() an attempt was made to access entry 0 of a MooseArray with 0 entries.


return _coupled_coef[_qp] * Diffusion::computeQpResidual();

There is only one item being indexed on that line: _coupled_coef; therefore, consider how _coupled_coef was declared

Bug

In ExampleDiffusion.h, the member variable _coupled_coef is a VariableValue that should be declared as a reference:


const VariableValue _coupled_coef;

Not storing this as a reference will cause a copy of the VariableValue to be made during construction. This copy will never be resized, nor will it ever have values written to it.

ExampleDiffusion.h


#pragma once

#include "Diffusion.h"

// Forward Declarations
class ExampleDiffusion;

/**
 * validParams returns the parameters that this Kernel accepts / needs
 * The actual body of the function MUST be in the .C file.
 */
template <>
InputParameters validParams<ExampleDiffusion>();

class ExampleDiffusion : public Diffusion
{
public:
  ExampleDiffusion(const InputParameters & parameters);

protected:
  virtual Real computeQpResidual() override;
  virtual Real computeQpJacobian() override;

  /**
   * THIS IS AN ERROR ON PURPOSE!
   *
   * The "&" is missing here!
   *
   * Do NOT copy this line of code!
   */

  const VariableValue _coupled_coef;
};

ExampleDiffusion.C


#include "ExampleDiffusion.h"

/**
 * This function defines the valid parameters for
 * this Kernel and their default values
 */
registerMooseObject("ExampleApp", ExampleDiffusion);

template <>
InputParameters
validParams<ExampleDiffusion>()
{
  InputParameters params = validParams<Diffusion>();
  params.addRequiredCoupledVar(
      "coupled_coef", "The value of this variable will be used as the diffusion coefficient.");

  return params;
}

ExampleDiffusion::ExampleDiffusion(const InputParameters & parameters)
  : Diffusion(parameters), _coupled_coef(coupledValue("coupled_coef"))
{
}

Real
ExampleDiffusion::computeQpResidual()
{
  return _coupled_coef[_qp] * Diffusion::computeQpResidual();
}

Real
ExampleDiffusion::computeQpJacobian()
{
  return _coupled_coef[_qp] * Diffusion::computeQpJacobian();
}

Restart and Recovery System

Definitions

Restart
Running a simulation that uses data from a previous simulation, using different input files

Recover
Resuming an existing simulation after a premature termination

Solution file
A mesh format containing field data in addition to the mesh (i.e. a normal output file)

Checkpoint
A snapshot of the simulation including all meshes, solutions, and stateful data

N to N
In a restart context, this means the number of processors for the previous and current simulations match

N to M
In a restart context, different numbers of processors may be used for the previous and current simulations

Variable Initialization

This method is best suited for restarting a simulation when the mesh in the previous simulation exactly matches the mesh in the current simulation and only initial conditions need to be set for one more variables.

  • This method requires only a valid solution file

  • MOOSE supports N to M restart when using this method


[Mesh]
  # MOOSE supports reading field data from ExodusII, XDA/XDR, and mesh checkpoint files (.e, .xda, .xdr, .cp)
  file = previous.e
  # This method of restart is only supported on serial meshes
  distribution = serial
[]

[Variables/nodal]
  family = LAGRANGE
  order = FIRST
  initial_from_file_var = nodal
  initial_from_file_timestep = 10
[]

[AuxVariables/elemental]
  family = MONOMIAL
  order = CONSTANT
  initial_from_file_var = elemental
  initial_from_file_timestep = 10
[]

Checkpoints

Advanced restart and recovery in MOOSE require checkpoint files

To enable automatic checkpoints using the default options (every time step, and keep last two) in a simulation simply add the following flag to your input file:


[Outputs]
  checkpoint = true
[]

For more control over the checkpoint system, create a sub-block in the input file that will allow you to change the file format, suffix, frequency of output, the number of checkpoint files to keep, etc.

  • Set num_files to at least 2 to minimize the chance of ending up with a corrupt restart file

    [Outputs]
      exodus = true
      [out]
        type = Checkpoint
        interval = 3
        num_files = 2
      []
    []
    

Advanced Restart

This method is best suited for situations when the mesh from the previous simulation and the current simulation match and the variables and stateful data should be loaded from the pervious simulation.

  • Support for modifying some variables is supported such as dt and time_step. By default, MOOSE will automatically use the last values found in the checkpoint files

  • Only N to N restarts are supported using this method


[Mesh]
  # Serial number should match corresponding Executioner parameter
  file = out_cp/0010_mesh.cpr
  # This method of restart is only supported on serial meshes
  distribution = serial
[]

[Problem]
  # Note that the suffix is left off in the parameter below.
  restart_file_base = out_cp/LATEST  # You may also use a specific number here
[]

Reloading Data

It is possible to load and project data onto a different mesh from a solution file usually as an initial condition in a new simulation.

MOOSE supports this through the use of a SolutionUserObject

Recover

A simulation that has terminated due to a fault can be recovered simply by using the --recover command-line flag, but it requires a checkpoint file.


./frog-opt -i input.i --recover

Multiapp Restart

When running a multiapp simulation you do not need to enable checkpoint output in each sub app input file. The master app stores the restart data for all sub apps in its file.

MOOSE Pluggable Systems

Action System

A system for the programmatic creation of simulation objects and input file syntax.

Auxiliary System

A system for direct calculation of field variables ("AuxVariables") that is designed for postprocessing, coupling, and proxy calculations.

Boundary Condition System

System for computing residual contributions from boundary terms of a PDE.

Constraint System

A system for imposing constraints within a simulation, such as limiting the heat flux across a gap or fixing solution variables across an interface using mortar methods.

Control System

A system for pragmatically modifying the input parameters of objects during a simulation.

Damper System

A system to limit the computed change to the solution during each non-linear iteration to prevent the solver from dramatically alteration of the solution from one step to the next. This may prevent, for example, the solver from attempting to evaluate non-physical values such as negative temperature.

DGKernel System

A system for computing residual contributions for volume terms for the discontinuous Galerkin finite element method.

DiracKernel System

A system for computing residual calculations from point sources.

Distribution System

A system for defining statistical distribution (e.g., uniform, normal, Weibull) functions for use with the stochastic tools module.

Executioner System

A system for dictating the simulation solving strategy.

Function System

A system for defining analytic expressions based on the spatial location (, , ) and time, .

Geometric Search System

A system for locating geometric elements within a simulation such as the nearest node across a gap.

Initial Condition System

A system for initialize field variables (non-linear and auxiliary) prior to execution of a simulation.

Indicator System

A system for computing an error estimation for use with automatic mesh refinement and coarsening.

InterfaceKernel System

A system to assist in coupling different physics across sub-domains, such as setting the flux of two species to be equivalent across a boundary between two domains.

Kernel System

A system for computing the residual contribution from a volumetric term within a PDE using the Galerkin finite element method.

Line Search System

This system is meant for creating custom line searches for use during the non-linear solve.

Marker System

A system for setting status of an element to refine, coarsen, or remain the same for automatic mesh adaptivity.

Material System

A system for defining material properties to be used by multiple systems and allow for variable coupling.

Mesh System

A system for defining a finite element mesh.

Mesh Generator System

A system for generating a finite element mesh using successive geometric construction routines such as building a 2D grid and then extruding into 3D space.

MeshModifer System

A system for altering a finite element mesh such as adding a sub-domain or boundary.

MultiApp System

A system for performing multiple simulations within a main simulation.

Nodal Kernel System

A system for computing a residual contribution of a PDE at nodes within the finite element mesh.

Output System

A system for producing outputting simulation data to the screen or files.

Parser System

A system for converting input data into MOOSE objects for creating a simulation.

Partitioner System

A system for partitioning a finite element mesh for parallel execution of a simulation.

Postprocessor System

A system for computing a "reduction" or "aggregation" calculation based on the solution variables that results in a single scalar value.

Preconditioner System

A system for defining the preconditioning matrix for use with the non-linear solver.

Predictor System

A system for predicting the next iteration of a simulation based on previous solution iterates.

Problem System

A system for defining the numerical systems that comprise a simulation.

Relationship Manager System

A system is defining geometric or algebraic information needed to perform a calculations in parallel.

Sampler System

A system for defining distribution sampling strategies for use with the stochastic tools module.

Split System

A system for splitting the preconditioning matrix to optimize the non-linear solving for multiphysics problems.

Time Integrator System

A system for defining schemes for numerical integration in time.

Time Stepper System

A system for suggesting time steps for transient executioners.

Transfer System

A system to move data to and from the "master" and "sub-applications" of a MultiApp.

UserObject System

A system for defining an arbitrary interface between MOOSE objects.

VectorPostprocessor System

A system for "reduction" or "aggregation" calculations based on the solution variables that results in one or many vectors of values.

References

  1. Eric B Becker, Graham F Carey, and John Tinsley Oden. Finite Elements, An Introduction: Volume I. Prentice Hall, 6 edition, 1981.
  2. Jan Flusser, Tomáš Suk, and Barbara Zitová. 2D & 3D image analysis by moments. John Wiley & Sons, Inc., 2016. ISBN 1119039355.
  3. David F. Griffiths. The 'no boundary condition' outflow boundary condition. International Journal for Numerical Methods in Fluids, 24(4):393–411, 1997. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0363%2819970228%2924%3A4%3C393%3A%3AAID-FLD505%3E3.0.CO%3B2-O, doi:10.1002/(SICI)1097-0363(19970228)24:4<393::AID-FLD505>3.0.CO;2-O.
  4. Luanjing Guo, Hai Huang, Derek R Gaston, Cody J Permann, David Andrs, George D Redden, Chuan Lu, Don T Fox, and Yoshiko Fujita. A parallel, fully coupled, fully implicit solution to reactive transport in porous media using the preconditioned Jacobian-Free Newton-Krylov Method. Advances in Water Resources, 53:101–108, 2013.
  5. Leslie Kerby, Aaron G Tumulak, Jaakko Leppänen, and Ville Valtavirta. Preliminary Serpent—MOOSE Coupling and Implementation of Functional Expansion Tallies in Serpent. In International Conference on Mathematics & Computational Methods Applied to Nuclear Science and Engineering (M&C 2017). 2017.
  6. Dana A. Knoll and David E. Keyes. Jacobian-free newton-krylov methods: a survey of approaches and applications. J. Comput. Phys, 193:357–397, 2004.
  7. Brycen Wendt and Leslie Kerby. Multiapp transfers in the moose framework based on functional expansions. Transactions of the American Nuclear Society, 117(1):735–738, October 2017.
  8. Brycen Wendt, April Novak, Leslie Kerby, and Paul Romano. Integration of functional expansion methodologies as a moose module. In PHYSOR 2018: Reactor Physics paving the way towards more efficient systems. April 2018.