problem.md

title: DuMu^x^ applications

Example application

Gas injection / immiscible two phase flow

Mass balance equations for two fluid phases:

$\begin{aligned} \frac{\partial \left(\phi \varrho_\alpha S_\alpha \right)}{\partial t}

\nabla \cdot \boldsymbol{v}_\alpha

q_\alpha = 0, \quad \alpha \in \lbrace w, n \rbrace. \end{aligned}$

Momentum balance equations (multiphase-phase Darcy's law):

\begin{aligned} \boldsymbol{v}_\alpha = \varrho_\alpha \frac{k_{r\alpha}}{\mu_\alpha} \mathbf{K} \left(\nabla\, p_\alpha - \varrho_{\alpha} \mathbf{g} \right), \quad \alpha \in \lbrace w, n \rbrace. \end{aligned}

Gas injection / immiscible two phase flow

$\begin{aligned} \frac{\partial \left(\phi \varrho_\alpha S_\alpha \right)}{\partial t}

\nabla \cdot \left( \varrho_\alpha \frac{k_{r\alpha}}{\mu_\alpha} \mathbf{K} \left(\nabla, p_\alpha - \varrho_{\alpha} \mathbf{g} \right) \right)

q_\alpha = 0 \end{aligned}$

• p_w, p_n: wetting and non-wetting fluid phase pressure
• \varrho_\alpha, \mu_\alpha: fluid phase density and dynamic viscosity
• \phi, \mathbf{K}, k_{r\alpha}: porosity, intrinsic permeability, relative permeability
• S_w, S_n: wetting and non-wetting saturation
• \mathbf{g}, q_\alpha: gravitational potential, source term

Gas injection / immiscible two phase flow

$\begin{aligned} \frac{\partial \left(\phi \varrho_\alpha S_\alpha \right)}{\partial t}

\nabla \cdot \left( \varrho_\alpha \frac{k_{r\alpha}}{\mu_\alpha} \mathbf{K} \left(\nabla, p_\alpha - \varrho_{\alpha} \mathbf{g} \right) \right)

q_\alpha = 0 \end{aligned}$

• Constitutive relations: p_n := p_w + p_c, p_c := p_c(S_w), k_{r\alpha} = k_{r\alpha}(S_w)
• Physical constraint (no free space): S_w + S_n = 1
• Primary variables: p_w, S_n (wetting phase pressure, non-wetting phase saturation)

A DuMu^x^ application

A DuMu^x^ application

The source code for a typical DuMu^x^ application consists of:

• Property specializations (e.g. properties.hh)
• Problem class definition (e.g. problem.hh) and often a spatial parameter class definition (e.g. spatialparams.hh)
• A parameter configuration file (e.g. params.input)
• The main program (e.g. main.cc)
• CMakeLists.txt (CMake build system configuration)

Property specializations

Properties

"Compile-time configuration"

"Tell DuMu^x^ what type of classes to use"

Details on properties in Part II: Property system

*properties*.hh

Create tag, choose model and discretization scheme:

namespace Dumux::Properties::TTag {

// the application type tag (choose any name)
struct Injection2pCC { using InheritsFrom = std::tuple<TwoP, CCTpfaModel>; };

} // end namespace Dumux::Properties::TTag

Specialize the Grid property for tag TTag::Injection2pCC to set the grid type:

namespace Dumux::Properties {

template<class TypeTag>
struct Grid<TypeTag, TTag::Injection2pCC>
{ using type = Dune::YaspGrid<2>; }; // Yet Another Structured Parallel Grid

} // end namespace Dumux::Properties

Specialize the Problem property to set the problem type:

namespace Dumux::Properties {

template<class TypeTag>
struct Problem<TypeTag, TTag::Injection2pCC>
{ using type = InjectionProblem2P<TypeTag>; };

} // end namespace Dumux::Properties

The problem class InjectionProblem2P is discussed in one of the following sections.

Specialize the SpatialParams property to set the spatial parameter type:

namespace Dumux::Properties {

template<class TypeTag>
struct SpatialParams<TypeTag, TTag::Injection2pCC>
{
    using GridGeometry
        = GetPropType<TypeTag, Properties::GridGeometry>;
    using Scalar
        = GetPropType<TypeTag, Properties::Scalar>;
    using type = InjectionSpatialParams<GridGeometry, Scalar>;
};

} // end namespace Dumux::Properties

Specialize the FluidSystem property to set the fluid system type:

namespace Dumux::Properties {

template<class TypeTag>
struct FluidSystem<TypeTag, TTag::Injection2pCC>
{
    using Scalar = GetPropType<TypeTag, Properties::Scalar>;
    using Policy = FluidSystems::H2ON2DefaultPolicy<
        /*fastButSimplifiedRelations=*/true>;
    using type = FluidSystems::H2ON2<Scalar, Policy>;
};

} // end namespace Dumux::Properties

Problem definition

Problem

A "problem" class in DuMu^x^ implements a specific scenario:

*problem*.hh

template<class TypeTag>
class InjectionProblem2P : public PorousMediumFlowProblem<TypeTag>
{
    // - boundary conditions
    // - initial conditions
    // - source terms
    // - scenario name (for output)
}

Inherit from base class PorousMediumFlowProblem, only override scenario-specific functions (static polymorphism).

The boundary condition types:

BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
{
    BoundaryTypes bcTypes;
    // Use Dirichlet boundary conditions on the left
    if (globalPos[0] < eps_)
        bcTypes.setAllDirichlet();
    // Use Neumann boundary conditions on the rest of the boundary
    else
        bcTypes.setAllNeumann();
    return bcTypes;
}

Dirichlet boundary condition values (only called on Dirichlet boundaries)

PrimaryVariables dirichletAtPos(const GlobalPosition& globalPos) const
{ return initialAtPos(globalPos); }

PrimaryVariables is an array of primary variables (here, the size of the array is 2).

Neumann boundary condition values / boundary fluxes (only called on Neumann boundaries)

NumEqVector neumannAtPos(const GlobalPosition& globalPos) const
{
    NumEqVector values(0.0);
    if (injectionActive() && onInjectionBoundary(globalPos))
    {
        values[Indices::conti0EqIdx + FluidSystem::N2Idx] = -1e-4;
        values[Indices::conti0EqIdx + FluidSystem::H2OIdx] = 0.0;
    }

    return values;
}

NumEqVector is an array of equations (here, the size of the array is 2).

Initial conditions:

PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const
{
    PrimaryVariables values(0.0);
    const Scalar densityW
        = FluidSystem::H2O::liquidDensity(temperature(), 1.0e5);
    const Scalar pw
        = 1.0e5 - densityW*this->gravity()[dimWorld-1]
                  *(aquiferDepth_ - globalPos[dimWorld-1]);
    values[Indices::pressureIdx] = pw;
    values[Indices::saturationIdx] = 0.0;
    return values;
}

Source/sink terms:

NumEqVector sourceAtPos(const GlobalPosition &globalPos) const
{ return NumEqVector(0.0); }

Spatial Parameters definition

Spatial parameters

*spatialparams*.hh

template<class FVGridGeometry, class Scalar>
class InjectionSpatialParams
: public FVPorousMediumFlowSpatialParamsMP<
    FVGridGeometry, Scalar,
    InjectionSpatialParams<FVGridGeometry, Scalar>
> {
// parameters that are typically position-dependent
// e.g. porosity, permeability
};

Inherit from FVPorousMediumFlowSpatialParamsMP where FV: finite volumes, MP: multi-phase flow.

A function returning the instrinsic permeability K:

auto permeabilityAtPos(const GlobalPosition& globalPos) const
{
    if (isInAquitard_(globalPos))
        return aquitardK_;
    return aquiferK_;
}

A function returning the porosity:

Scalar porosityAtPos(const GlobalPosition& globalPos) const
{
    // here, either aquitard or aquifer porosity are returned
    if (isInAquitard_(globalPos))
        return aquitardPorosity_;
    return aquiferPorosity_;
}

A function returning a parameterized constitutive law describing fluid-matrix interactions (p_c(S_w), k_r(S_w)):

auto fluidMatrixInteractionAtPos(const GlobalPosition& globalPos) const
{
    if (isInAquitard_(globalPos))
        return makeFluidMatrixInteraction(aquitardPcKrSwCurve_);
    return makeFluidMatrixInteraction(aquiferPcKrSwCurve_);
}

Set the (constant) temperature field in the domain:

Scalar temperatureAtPos(const GlobalPosition& globalPos) const
{
    return 273.15 + 20.0;  // 20°C
}

Runtime parameters

Runtime parameters

Dune INI syntax ([Group] and Key = Value pairs)

params.input

[Grid]
LowerLeft = 0 0
UpperRight = 60 40
Cells = 24 16

[Problem]
Name = test

See Part I: Runtime parameters for details.

Main program and main function

Main program

• Each problem has one main file (test_name.cc or main.cc)
• Contains the main function (mandatory in C/C++ programs)

Main function

Calling Dumux::initialize is mandatory at the beginning of each DuMu^x^ program to make sure the environment is correctly set up.

int main(int argc, char** argv)
{
    // initialize MPI+X backends (mandatory)
    Dumux::initialize(argc, argv);

Parse runtime parameters:

// parse command line arguments and input file
Dumux::Parameters::init(argc, argv);

See Part I: Runtime parameters for details.

Define an alias for the test problem type tag

using namespace Dumux;
using TypeTag = Properties::TTag::Injection2pCC;

The tag (tag alias) is used to extract types and values via the property system (details on properties in Part II: Property system).

Create the computational grid:

// create a grid (take parameters from input file)
GridManager<GetPropType<TypeTag, Properties::Grid>> gridManager;
gridManager.init();

// obtain the grid and a grid view
const auto& grid = gridManager.grid();
const auto& leafGridView = grid.leafGridView();

More details on the grid in Part I: Grid.

GridGeometry and Problem instantiation:

// create the finite volume grid geometry
// (represents the chosen discretization scheme)
using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
auto gridGeometry = std::make_shared<GridGeometry>(leafGridView);

// the problem (initial and boundary conditions)
using Problem = GetPropType<TypeTag, Properties::Problem>;
auto problem = std::make_shared<Problem>(gridGeometry);

Initial solution and secondary variables:

// the solution vector
using SolutionVector
    = GetPropType<TypeTag, Properties::SolutionVector>;
SolutionVector x(gridGeometry->numDofs());

// the grid variables
using GridVariables = GetPropType<TypeTag, Properties::GridVariables>;
auto gridVariables
    = std::make_shared<GridVariables>(problem, gridGeometry);
gridVariables->init(x);

Setting up VTK output:

// initialize the vtk output module
VtkOutputModule<GridVariables, SolutionVector>
    vtkWriter(*gridVariables, x, problem->name());

// optionally add a velocity post-processor
using VelocityOutput
    = GetPropType<TypeTag, Properties::VelocityOutput>;
vtkWriter.addVelocityOutput(
    std::make_shared<VelocityOutput>(*gridVariables));

// add input/output defaults for the chosen model
using IOFields = GetPropType<TypeTag, Properties::IOFields>;
IOFields::initOutputModule(vtkWriter);

Some typical main function structures:

• Steady-state linear problems
• Steady-state non-linear problems
• Time-dependent non-linear problems

Assembling the system for a steady-state linear problem:

// the assembler for stationary problems
using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
auto assembler = std::make_shared<Assembler>(
    problem, gridGeometry, gridVariables);

// the discretization matrices for stationary linear problems
using JacobianMatrix
    = GetPropType<TypeTag, Properties::JacobianMatrix>;
auto A = std::make_shared<JacobianMatrix>();
auto r = std::make_shared<SolutionVector>();
assembler->setLinearSystem(A, r);
assembler->assembleJacobianAndResidual(x);

and solve it using an iterative method:

using LinearSolver = ILUBiCGSTABIstlSolver<
    LinearSolverTraits<GridGeometry>,
    LinearAlgebraTraitsFromAssembler<Assembler>>;
auto linearSolver = std::make_shared<LinearSolver>(
    gridGeometry->gridView(), gridGeometry->dofMapper());

(*r) *= -1.0; // solve Ax = -r to save update and copy
linearSolver->solve(*A, x, *r);

Simplified code for steady-state linear problem using Dumux::LinearPDESolver

auto assembler = ...;  // construct as before
auto linearSolver = ...;  // construct as before

using Solver = LinearPDESolver<Assembler, LinearSolver>;
Solver solver(assembler, linearSolver);

// assemble & solve
solver.solve(x);

For steady-state non-linear problems, use Dumux::NewtonSolver:

auto assembler = ...;  // construct as before
auto linearSolver = ...;  // construct as before

using Solver = NewtonSolver<Assembler, LinearSolver>;
Solver solver(assembler, linearSolver);

// linearize & solve
solver.solve(x);

For time-dependent problems, pass a TimeLoop instance and a solution vector carrying the solution on the previous/initial time level to the assembler:

SolutionVector xOld = x;

auto timeLoop = std::make_shared<TimeLoop<Scalar>(0.0, dt, tEnd);
timeLoop->setMaxTimeStepSize(maxDt);

using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
auto assembler = std::make_shared<Assembler>(
    problem, gridGeometry, gridVariables,
    timeLoop, xOld // <-- new arguments
);

// assemble linear/non-linear problem as before
// ...

The skeleton of a time loop:

timeLoop->start(); do {

    // Time loop body

} while (!timeLoop->finished());

Solving a time step:

// time loop
timeLoop->start(); do
{
    // linearize & solve
    nonLinearSolver.solve(x, *timeLoop);
    // make the new solution the old solution
    xOld = x;
    gridVariables->advanceTimeStep();

Advancing the time loop to the next step:

    // advance to the time loop to the next step
    timeLoop->advanceTimeStep();
    // report statistics of this time step
    timeLoop->reportTimeStep();
    // set new dt as suggested by the newton solver
    timeLoop->setTimeStepSize(
        nonLinearSolver.suggestTimeStepSize(timeLoop->timeStepSize())
    );
} while (!timeLoop->finished());
// print final report
timeLoop->finalize(leafGridView.comm());

Build system (CMake)

Typical C++ build steps

1. configure
2. compile
3. install (copy programs to some location)

Step 3 is usually skipped by DuMu^x^ developers. But you can of course "install" Dune modules and DuMu^x^.

Build system - what is CMake?

• Open-source build system tool developed by KITware
• Offers a one-tool-solution to all building tasks, like configuring, building, linking, testing and packaging
• Is portable and supports cross-platform compilation
• Build file generator: Support various backends called generators (default: GNU Makefiles)
• Control files written in the CMake language

Build system - CMakeLists.txt

• Every directory in a project contains a file called CMakeLists.txt, which is written in the CMake language
• Upon configure, the top-level CMakeLists.txt is executed
• Subfolders are included with the add_subdirectory(...) function

Build system - configuring

• Configure build-time compiler parameters / linking information
• Create "targets" that can be build to create executables
• Find and link external libraries / software dependencies

Build system - dunecontrol

• For Dune, CMake is triggered via the dunecontrol script

dune-common/bin/dunecontrol [options] <command>

• useful commands:
  • configure: configure libraries, variables, paths, files
  • make all: build libraries
  • all: includes configure and make all

Build system - dunecontrol

• useful options:
  • --opts=<optionfile.opts> specify e.g. compiler flags; DuMu^x^ provides dumux/cmake.opts.
  • --build-dir=<build directory> specify path for out-of-source build; Default: every module contains its own build directory called build-cmake/
  • --only <module> only apply command to a specific module/s (comma-separated list)

Build system - dunecontrol

You may have to reconfigure (rerun dunecontrol) whenever a dependency changes or a Dune library is updated. CMake caches. To reconfigure, you may need to remove the cache first:

./dune-common/bin/dunecontrol bexec rm -r CMakeFiles CMakeCache.txt

removes the CMake cache files from all Dune modules. (Use --only <module> to only remove caches of specific modules.)

Build system - basic CMake functions

• Use add_subdirectory for recursively adding subdirectories
• Subdirectory must contain a CMakeLists.txt (can be empty)
• Executables are added via add_executable(<name> source1 [source2 ...])
• Tests are added via dumux_add_test which also add a test executable to the test suite
• Symlinks can be added via dune_symlink_to_source_files

Build system

CMakeLists.txt for an example application: create a test target test_2p_incompressible_box by defining name, source file and command line arguments:

dumux_add_test(
    NAME test_2p_incompressible_box
    SOURCES test_2p_fv.cc
    CMD_ARGS test_2p.input
)

Build system

Add extra compile definitions and commands (typical for DuMu^x^ regression tests):

dumux_add_test(
    NAME test_2p_incompressible_box
    SOURCES test_2p_fv.cc
    COMPILE_DEFINITIONS TYPETAG=TwoPIncompressibleBox
    COMMAND ${CMAKE_SOURCE_DIR}/bin/testing/runtest.py
    CMD_ARGS --script fuzzy
    --files ${CMAKE_SOURCE_DIR}/test/references/lensbox-reference.vtu
        ${CMAKE_CURRENT_BINARY_DIR}/2p_box-00007.vtu
    --command "${CMAKE_CURRENT_BINARY_DIR}/test_2p_incompressible_box
            test_2p.input -Problem.Name 2p_box"
)

Build system

Extra: Create linked parameter file in build-cmake folder, separately add executable and set compile definitions for an executable:

dune_symlink_to_source_files(FILES "params.input")
# using tpfa
add_executable(test_2p_incompressible_tpfa EXCLUDE_FROM_ALL main.cc)
target_compile_definitions(
    test_2p_incompressible_tpfa PUBLIC TYPETAG=TwoPIncompressibleTpfa
)

Build system

Useful resources:

• CMake online documentation
• Dune CMake online documentation for CMake functions available with Dune.

Parallelism