From 337bbae4fb958f05f7842c1a1e22fa47672bc7fe Mon Sep 17 00:00:00 2001
From: Farid Mohammadi <farid.mohammadi@iws.uni-stuttgart.de>
Date: Tue, 31 Mar 2020 17:42:16 +0200
Subject: [PATCH] Cleanup/Checkup for release 3.2
---
exercises/exercise-basic/README.md | 11 ++---
.../exercise-basic/injection2pniproblem.hh | 4 +-
.../exercise-biomineralization/README.md | 10 ++---
exercises/exercise-coupling-ff-pm/README.md | 34 ++++++++-------
.../interface/freeflowsubproblem.hh | 19 ++++++---
.../exercise-coupling-ff-pm/interface/main.cc | 5 ++-
.../interface/porousmediumsubproblem.hh | 4 +-
.../models/porousmediumsubproblem.hh | 33 +++++++++++++--
.../turbulence/freeflowsubproblem.hh | 16 ++++++++
.../turbulence/main.cc | 10 +++--
exercises/exercise-dunemodule/README.md | 6 +--
exercises/exercise-fluidsystem/2pproblem.hh | 10 +++--
exercises/exercise-fluidsystem/README.md | 24 +++++------
.../components/mycompressiblecomponent.hh | 21 +++++-----
.../components/myincompressiblecomponent.hh | 16 ++++----
.../h2omycompressiblecomponent.hh | 8 ++--
.../exercise-fluidsystem/spatialparams.hh | 4 ++
exercises/exercise-fractures/README.md | 7 ++--
.../exercise-fractures/fractureproblem.hh | 3 +-
.../fracturespatialparams.hh | 9 ++--
exercises/exercise-fractures/matrixproblem.hh | 9 ++--
exercises/exercise-grids/README.md | 14 ++-----
exercises/exercise-grids/problem.hh | 11 +++--
exercises/exercise-mainfile/1pproblem.hh | 4 +-
exercises/exercise-mainfile/README.md | 41 ++++++++++---------
.../exercise-mainfile/exercise1pamain.cc | 6 +--
exercises/exercise-properties/README.md | 13 +++---
.../exercise-properties/mylocalresidual.hh | 6 ++-
exercises/exercise-properties/problem.hh | 7 +++-
exercises/exercise-runtimeparams/README.md | 8 ++--
exercises/exercise-runtimeparams/problem.hh | 17 +++++---
31 files changed, 235 insertions(+), 155 deletions(-)
diff --git a/exercises/exercise-basic/README.md b/exercises/exercise-basic/README.md
index 7dab4bb7..035e0eef 100644
--- a/exercises/exercise-basic/README.md
+++ b/exercises/exercise-basic/README.md
@@ -1,5 +1,6 @@
# Exercise Basics (DuMuX course)
<br>
+
## Problem set-up
N$`_2`$ is injected in an aquifer previously saturated with water with an injection rate of 0.0001 kg/(s*m$`^2`$).
@@ -25,7 +26,7 @@ Locate all the files you will need for this exercise
* The shared __spatial parameters file__: `injection2pspatialparams.hh`
* The shared __input file__: `params.input`
-<hr><br>
+<br><br>
### Task 2: Compiling and running an executable
<hr>
@@ -54,7 +55,7 @@ make exercise_basic_2p exercise_basic_2p2c
paraview injection-2p2c.pvd
```
-<hr><br>
+<br><br>
### Task 3: Setting up a new executable (for a non-isothermal simulation)
<hr>
@@ -76,21 +77,21 @@ make # should rerun cmake
make exercise_basic_2pni # builds new executable
```
-<hr><br>
+<br><br>
### Task 4: Setting up a non-isothermal __2pni__ test problem
<hr>
* Open the file `injection2pniproblem.hh`. It is a copy of the `injection2pproblem.hh` with some useful comments on how to implement a non-isothermal model. Look for comments containing
```c++
-// TODO: dumux-course-task
+// TODO: dumux-course-task 4
```
* The following set-up should be realized:
__Boundary conditions:__ Dirichlet conditions at the left boundary. For the primary variable 'temperature' use a varying temperature of <br/>
$`\displaystyle T(y) = 283~\text{K} + 0.03~\frac{\text{K}}{\text{m}} \cdot \left( d_\text{aquifer} - y \right) `$, <br/>
-with the aquifer depth
+with the aquifer depth
$`\displaystyle d_\text{aquifer}=2700~\text{m}`$.
Assign Neumann no-flow for the energy balance to the rest of the boundaries.
diff --git a/exercises/exercise-basic/injection2pniproblem.hh b/exercises/exercise-basic/injection2pniproblem.hh
index 82967461..a56d804c 100644
--- a/exercises/exercise-basic/injection2pniproblem.hh
+++ b/exercises/exercise-basic/injection2pniproblem.hh
@@ -43,8 +43,8 @@ class Injection2PNIProblem;
namespace Properties
{
/*!
-* TODO:dumux-course-task:
-* inherit from the TwoPNI model instead of TwoP here
+* TODO:dumux-course-task 4
+* Inherit from the TwoPNI model instead of TwoP here
*/
// Create new type tags
namespace TTag {
diff --git a/exercises/exercise-biomineralization/README.md b/exercises/exercise-biomineralization/README.md
index 329fc531..b4697c0e 100644
--- a/exercises/exercise-biomineralization/README.md
+++ b/exercises/exercise-biomineralization/README.md
@@ -1,6 +1,6 @@
-# Exercise Biomineralization
+# Exercise Biomineralization (DuMuX Course)
-The aim of this exercise is to get a first glimpse at the _DuMuX_ way of implementing mineralization and reaction processes. In the scope of this exercise, the setting of boundary conditions is revisited and a new reaction term is implemented.
+The aim of this exercise is to get a first glimpse at the _DuMu<sup>x</sup>_ way of implementing mineralization and reaction processes. In the scope of this exercise, the setting of boundary conditions is revisited and a new reaction term is implemented.
## Problem set-up
@@ -37,7 +37,7 @@ There are two types of solid components. Reactive and inert. For each reactive c
### 2. Implement a chemical equation
-In the following the basic steps required to set the new chemical equation are outlined. Here, this is done in the __chemistry__ folder in the prepared file: `simplebiominreactions.hh` within the function reactionSource().
+In the following the basic steps required to set the new chemical equation are outlined. Here, this is done in the __chemistry__ folder in the prepared file: `simplebiominreactions.hh` within the function ``reactionSource()``.
Please be aware, that the chemistry file already provides some convenience functions (e.g. ``moleFracToMolality()``).
__Task__
@@ -74,7 +74,7 @@ To enable your newly created chemical equation, the chemistry file has to be inc
#include "chemistry/simplebiominreactions.hh" // chemical reactions
```
-Additionally the TypeTag of your chemistry file needs to be set in the problem file, within the class ExerciseFourBioMinProblem:
+Additionally the TypeTag of your chemistry file needs to be set in the problem file, within the class ``ExerciseFourBioMinProblem``:
```c++
using Chemistry = typename Dumux::SimpleBiominReactions<NumEqVector, VolumeVariables>;
@@ -82,7 +82,7 @@ using Chemistry = typename Dumux::SimpleBiominReactions<NumEqVector, VolumeVaria
__Task__
-Now the source/sink term can be updated in the problem file in its function source(). You can access the newly created chemistry file and call the reactionSource()-function from it. Make sure to call the chemistry.reactionSource()-function with the correct arguments. Return the updated source terms in the end.
+Now the source/sink term can be updated in the problem file in its function ``source()``. You can access the newly created chemistry file and call the ``reactionSource()``-function from it. Make sure to call the ``chemistry.reactionSource()``-function with the correct arguments. Return the updated source terms in the end.
The volume variables can be set using the element volume variables and the sub control volume:
```c++
diff --git a/exercises/exercise-coupling-ff-pm/README.md b/exercises/exercise-coupling-ff-pm/README.md
index f25fe088..f5ae0cc6 100644
--- a/exercises/exercise-coupling-ff-pm/README.md
+++ b/exercises/exercise-coupling-ff-pm/README.md
@@ -1,4 +1,4 @@
-# Exercise Coupling free flow/porous medium flow
+# Exercise Coupling free flow/porous medium flow (DuMuX Course)
The aim of this exercise is to get familiar with setting up coupled free flow/porous medium flow problems.
@@ -113,7 +113,7 @@ if (couplingManager().isCoupledEntity(CouplingManager::darcyIdx, scvf))
```
This should make the flow go from left to right.
-You can also delete the initial vertical velocity from initialAtPos(), to be consistent with the new boundary conditions.
+You can also delete the initial vertical velocity from `initialAtPos()`, to be consistent with the new boundary conditions.
__Task B: Include slip-condition__
@@ -137,7 +137,7 @@ values.setBJS(Indices::momentumXBalanceIdx);
at the position where the coupling boundary conditions are set in `interface/freeflowsubproblem.hh`.
To check if the simulation behaves as expected, we can compare the velocity profile $`v_x(y)`$ with the analytical solution provided by [Beavers and Joseph (1967)](https://doi.org/10.1017/S0022112067001375).
-For doing so, we uncomment line 212 in `exerciseinterfacecouplingffpm.cc`.
+For doing so, we uncomment the following line in `main.cc` in the subfolder `interface`.
```cpp
stokesVtkWriter.addField(stokesProblem->getAnalyticalVelocityX(), "analyticalV_x");
```
@@ -145,11 +145,9 @@ stokesVtkWriter.addField(stokesProblem->getAnalyticalVelocityX(), "analyticalV_x
After re-compiling and re-running the executable, we should be able to see also
the analytical solution of $`v_x`$ on the free flow domain. Play around with the grid resolution to see how that affects the velocity profile.
-__Task C: Cange shape of interface__
+__Task C: Change the shape of interface__
-Now we want to include a non-flat interface between the two domains. We use `dune-subgrid` to construct
-two grids for the two domains from one common host grid. Comment out lines 96-106 in `exerciseinterfacecouplingffpm.cc` and comment lines 114-149 in the same file. This will instantiate a host grid and define two helper lambda functions that are used to choose elements from to host grid for the respective sub grid. In the given case,
-the domain is split in two haves, separated by a sinusoidal interface.
+Now we want to include a non-flat interface between the two domains. We use `dune-subgrid` to construct two grids for the two domains from one common host grid. To do so, open `main.cc` in the subfolder `interface` again and search for `TODO: dumux-course-task 1.C`. Comment out the first code block and uncomment the second. This will instantiate a host grid and define two helper lambda functions that are used to choose elements from to host grid for the respective sub grid. In the given case, the domain is split in two haves, separated by a sinusoidal interface.
```cpp
auto elementSelectorStokes = [&](const auto& element)
@@ -185,7 +183,9 @@ values.setCouplingNeumann(Indices::momentumYBalanceIdx);
```cpp
values.setCouplingNeumann(scvf.directionIndex());
```
-The same if true for the BJS condition, however, here we need to consider the tangential direction:
+in `main.cc` in the subfolder `interface`.
+
+The same is true for the BJS condition, however, here we need to consider the tangential direction:
```cpp
values.setBJS(1 - scvf.directionIndex());
```
@@ -219,7 +219,7 @@ Although a 2p2c system is plugged in, we still want to simulate the same situati
The following changes have to be made in the porous-medium model (`models/porousmediumsubproblem.hh`):
* Include the 2pnc model: include the respective headers and inherit from the new model `TwoPNC`
* Exchange the spatial parameters for the 1-phase system by those for a 2-phase system (hint: two occurrences).
-* Since two phases are involved now, we do not need to use the OnePAdapter anymore. Change to property of the FluidSystem such that `H2OAir` is used directly.
+* Since two phases are involved now, we do not need to use the `OnePAdapter` anymore. Change to property of the `FluidSystem` such that `H2OAir` is used directly.
Afterwards, set the `transportCompIdx` to `Indices::switchIdx`.
One big difference between the 1p and 2p model is, that the primary variables for which
@@ -237,21 +237,19 @@ struct Formulation<TypeTag, TTag::DarcyOnePNC>
In contrast to the formulation, which stays the same during one simulation, the meaning of
the primary variables may vary during one simulation.
-In the case we are investigating, we want to use the gas pressure and the liquid saturation as primary variables.
+In the case under investigation, we want to use the gas pressure and the liquid saturation as primary variables.
However, if only the gas phase is present, the liquid saturation is always zero.
In this case, the chosen formulation will set the given value as the mole fraction of water vapor in the gas phase.
* To tell to program which phases are present in which parts of the domain at the beginning of the simulation,
- you have to call `values.setState(MY_PHASE_PRESENCE);` in `initialAtPos()`. Have a look at the `indices.hh`
- in the `2pnc` model (as the 2p2c model is a special case of the 2pnc model) to figure out which is the correct value of `MY_PHASE_PRESENCE` for the presence of
- a gas-phase only (hint: the numbering of phase indices begins with 0, the numbering of the phase presence states begins
- with 1. Take a look at your formulation to find out which phase index to use for the gas phase.)
+ you have to call `values.setState(MY_PHASE_PRESENCE);` in `initialAtPos()`. `MY_PHASE_PRESENCE` should be replaced with the correct value for the case where only a gas-phase is present.
+ Have a look at the `indices.hh` in the `2pnc` model (as the 2p2c model is a special case of the 2pnc model) in the subfolder `porousmediumflow` in your DuMuX directory. (hint: the numbering of phase indices begins with 0, the numbering of the phase presence states begins with 1. Take a look at your formulation to find out which phase index to use for the gas phase.)
__Task B: Add output__:
In the next step, we want to add some output to the simulation.
First we want to know the water mass in the (porous-medium) system.
Therefore, we evaluate the storage term of the water component.
-* Have a look at the function `evaluateWaterMassStorageTerm()` in the porous medium subproblem.
+* Have a look at the function `evaluateWaterMassStorageTerm()` in the `porousmediumsubproblem.hh`.
Then implement a calculation of the total water mass:
$`\sum_{\alpha \in \textrm{g,l}} \left( \phi S_\alpha X^\text{w}_\alpha \varrho_\alpha V_\textrm{scv} \right)`$.
Afterwards, adapt the method `init()` such that the variable `initialWaterContent_` is initialized correctly using the `evaluateWaterMassStorageTerm()` method and assign that value also to the variable `lastWaterMass_`.
@@ -300,9 +298,9 @@ describe an algorithm to switch the primary variables, if phases should appear o
Now you are able to simulate a complete drying of the porous medium.
-### 4. Use a turbulence model in the free flow domain
+### 3. Use a turbulence model in the free flow domain
-Several RANS turbulence models are implemented in DuMuX.
+Several RANS turbulence models are implemented in DuMu<sup>x</sup>.
This part of the exercise consists of the following steps:
* replacing the Navier-Stokes model by the zero equation turbulence model,
* switching to a symmetry boundary condition,
@@ -355,7 +353,7 @@ These dynamic interactions are to be updated by calling
```cpp
stokesProblem->updateDynamicWallProperties(stokesSol);
```
-in the time loop (after `// update dynamic wall properties`).
+in the time loop (after `// Update dynamic wall properties`).
Compile and run your new coupled problem and take a look at the results in Paraview.
In addition to the standard variables and parameters, you can now analyze turbulence model specific quantities
diff --git a/exercises/exercise-coupling-ff-pm/interface/freeflowsubproblem.hh b/exercises/exercise-coupling-ff-pm/interface/freeflowsubproblem.hh
index 4e579e2d..8c22118b 100644
--- a/exercises/exercise-coupling-ff-pm/interface/freeflowsubproblem.hh
+++ b/exercises/exercise-coupling-ff-pm/interface/freeflowsubproblem.hh
@@ -25,9 +25,9 @@
#include <dune/grid/yaspgrid.hh>
-// TODO: dumux-course-task
+// TODO: dumux-course-task 1.C
//****** uncomment for the last exercise *****//
-// #include <dumux/io/grid/subgridmanager.hh>
+// #include <dumux/io/grid/gridmanager_sub.hh>
#include <dumux/material/fluidsystems/1pliquid.hh>
#include <dumux/material/components/simpleh2o.hh>
@@ -64,7 +64,7 @@ struct Grid<TypeTag, TTag::StokesOneP>
using Scalar = GetPropType<TypeTag, Properties::Scalar>;
using TensorGrid = Dune::YaspGrid<2, Dune::TensorProductCoordinates<Scalar, dim> >;
-// TODO: dumux-course-task
+// TODO: dumux-course-task 1.C
//****** comment out for the last exercise *****//
using type = TensorGrid;
@@ -161,8 +161,8 @@ public:
const auto& globalPos = scvf.dofPosition();
- // TODO: dumux-course-task
- // change the boundary conditions here as described in the exercise
+ // TODO: dumux-course-task 1.A
+ // Change the boundary conditions here as described in the exercise
if(onUpperBoundary_(globalPos))
{
values.setDirichlet(Indices::velocityXIdx);
@@ -181,7 +181,14 @@ public:
{
values.setCouplingNeumann(Indices::conti0EqIdx);
values.setCouplingNeumann(Indices::momentumYBalanceIdx);
+ // TODO: dumux-course-task 1.B
+ // Replace Dirichlet BC with Beavers-Joseph-Saffman slip condition for the tangential momentum balance
values.setDirichlet(Indices::velocityXIdx); // assume no slip on interface
+
+ // TODO: dumux-course-task 1.C
+ // set the Beaver-Joseph-Saffman slip condition for the tangential momentum balance equation,
+ // consider orientation of face automatically
+
}
return values;
@@ -251,6 +258,8 @@ public:
{
PrimaryVariables values(0.0);
values[Indices::velocityYIdx] = -1e-6 * globalPos[0] * (this->gridGeometry().bBoxMax()[0] - globalPos[0]);
+ // TODO: dumux-course-task 1.A
+ // Set fixed pressures on the left and right boundary
return values;
}
diff --git a/exercises/exercise-coupling-ff-pm/interface/main.cc b/exercises/exercise-coupling-ff-pm/interface/main.cc
index 00719762..c675221c 100644
--- a/exercises/exercise-coupling-ff-pm/interface/main.cc
+++ b/exercises/exercise-coupling-ff-pm/interface/main.cc
@@ -88,8 +88,8 @@ int main(int argc, char** argv) try
using DarcyTypeTag = Properties::TTag::DarcyOneP;
-
- // TODO: dumux-course-task: comment-out this section for the last exercise **************** //
+ //TODO: dumux-course-task 1.C
+ // ******************** comment-out this section for the last exercise **************** //
// create two individual grids (from the given grid file or the input file)
// for both sub-domains
@@ -209,6 +209,7 @@ int main(int argc, char** argv) try
StaggeredVtkOutputModule<StokesGridVariables, decltype(stokesSol)> stokesVtkWriter(*stokesGridVariables, stokesSol, stokesName);
GetPropType<StokesTypeTag, Properties::IOFields>::initOutputModule(stokesVtkWriter);
+ //TODO: dumux-course-task 1.B
//****** uncomment the add analytical solution of v_x *****//
// stokesVtkWriter.addField(stokesProblem->getAnalyticalVelocityX(), "analyticalV_x");
diff --git a/exercises/exercise-coupling-ff-pm/interface/porousmediumsubproblem.hh b/exercises/exercise-coupling-ff-pm/interface/porousmediumsubproblem.hh
index 848178a0..2a9e2bf5 100644
--- a/exercises/exercise-coupling-ff-pm/interface/porousmediumsubproblem.hh
+++ b/exercises/exercise-coupling-ff-pm/interface/porousmediumsubproblem.hh
@@ -26,9 +26,9 @@
#include <dune/grid/yaspgrid.hh>
-// TODO: dumux-course-task
+// TODO: dumux-course-task 1.C
//****** uncomment for the last exercise *****//
-// #include <dumux/io/grid/subgridmanager.hh>
+// #include <dumux/io/grid/gridmanager_sub.hh>
#include <dumux/discretization/cctpfa.hh>
diff --git a/exercises/exercise-coupling-ff-pm/models/porousmediumsubproblem.hh b/exercises/exercise-coupling-ff-pm/models/porousmediumsubproblem.hh
index e4845cfb..2d3b64fd 100644
--- a/exercises/exercise-coupling-ff-pm/models/porousmediumsubproblem.hh
+++ b/exercises/exercise-coupling-ff-pm/models/porousmediumsubproblem.hh
@@ -33,8 +33,11 @@
#include <dumux/material/fluidmatrixinteractions/diffusivityconstanttortuosity.hh>
#include <dumux/porousmediumflow/problem.hh>
-
+// TODO: dumux-course-task 2.A
+// Include 2pnc model here
#include <dumux/porousmediumflow/1pnc/model.hh>
+// TODO: dumux-course-task 2.A
+// Include spatial params for a 2-phase system
#include "../1pspatialparams.hh"
namespace Dumux
@@ -46,6 +49,8 @@ namespace Properties
{
// Create new type tags
namespace TTag {
+ // TODO: dumux-course-task 2.A
+ // Change to property of the `FluidSystem` such that `H2OAir` is used directly.
struct DarcyOnePNC { using InheritsFrom = std::tuple<OnePNC, CCTpfaModel>; };
} // end namespace TTag
@@ -77,8 +82,14 @@ struct EffectiveDiffusivityModel<TypeTag, TTag::DarcyOnePNC>
template<class TypeTag>
struct Grid<TypeTag, TTag::DarcyOnePNC> { using type = Dune::YaspGrid<2>; };
+// TODO: dumux-course-task 2.A
+// Define new formulation for primary variables here.
+
+
// Set the spatial paramaters type
template<class TypeTag>
+// TODO: dumux-course-task 2.A
+// Adapt the spatial params here.
struct SpatialParams<TypeTag, TTag::DarcyOnePNC> {
using type = OnePSpatialParams<GetPropType<TypeTag, GridGeometry>, GetPropType<TypeTag, Scalar>>;
};
@@ -113,6 +124,8 @@ class PorousMediumSubProblem : public PorousMediumFlowProblem<TypeTag>
conti0EqIdx = Indices::conti0EqIdx,
pressureIdx = Indices::pressureIdx,
phaseIdx = 0,
+ // TODO: dumux-course-task 2.A
+ // set the `transportCompIdx` to `Indices::switchIdx`.
transportCompIdx = 1
};
@@ -152,7 +165,11 @@ public:
template<class SolutionVector, class GridVariables>
void init(const SolutionVector& curSol,
const GridVariables& gridVariables)
- { }
+ {
+ // TODO: dumux-course-task 2.B
+ // Initialize `initialWaterContent_` and assign that to `lastWaterMass_`.
+
+ }
template<class SolutionVector, class GridVariables>
void postTimeStep(const SolutionVector& curSol,
@@ -196,7 +213,9 @@ public:
for (auto&& scv : scvs(fvGeometry))
{
// const auto& volVars = elemVolVars[scv];
- // insert calculation of the water mass here
+
+ // TODO: dumux-course-task 2.B
+ // Insert calculation of the water mass here
waterMass += 0.0;
}
}
@@ -237,7 +256,9 @@ public:
if (!couplingManager().isCoupledEntity(CouplingManager::darcyIdx, scvf))
continue;
- NumEqVector flux(0.0); // use "massCouplingCondition" from the couplingManager here
+ // TODO: dumux-course-task 2.B
+ // Use "massCouplingCondition" from the couplingManager here
+ NumEqVector flux(0.0);
x.push_back(scvf.center()[0]);
y.push_back(flux[transportCompIdx]);
@@ -355,6 +376,10 @@ public:
static const Scalar stokesPressure = getParamFromGroup<Scalar>("Stokes", "Problem.Pressure");
PrimaryVariables values(0.0);
+
+ // TODO: dumux-course-task 2.A
+ // Declare here which phases are present.
+
values[Indices::pressureIdx] = stokesPressure;
values[transportCompIdx] = moleFraction_;
return values;
diff --git a/exercises/exercise-coupling-ff-pm/turbulence/freeflowsubproblem.hh b/exercises/exercise-coupling-ff-pm/turbulence/freeflowsubproblem.hh
index 34616705..d4aec3fa 100644
--- a/exercises/exercise-coupling-ff-pm/turbulence/freeflowsubproblem.hh
+++ b/exercises/exercise-coupling-ff-pm/turbulence/freeflowsubproblem.hh
@@ -29,6 +29,8 @@
#include <dumux/material/fluidsystems/h2oair.hh>
#include <dumux/discretization/staggered/freeflow/properties.hh>
+// TODO: dumux-course-task 3.A
+// Include headers for compositional zero equation turbulence model here.
#include <dumux/freeflow/compositional/navierstokesncmodel.hh>
#include <dumux/freeflow/navierstokes/problem.hh>
@@ -41,6 +43,8 @@ namespace Properties {
// Create new type tags
namespace TTag {
+ // TODO: dumux-course-task 3.A
+ // Change the entry in the `StokesZeroEq` definition accordingly.
struct StokesZeroEq { using InheritsFrom = std::tuple<NavierStokesNCNI, StaggeredFreeFlowModel>; };
} // end namespace TTag
@@ -80,6 +84,8 @@ struct EnableGridVolumeVariablesCache<TypeTag, TTag::StokesZeroEq> { static cons
* \brief The free-flow sub problem
*/
template <class TypeTag>
+// TODO: dumux-course-task 3.A
+// Adapt the inheritance of the problem class.
class FreeFlowSubProblem : public NavierStokesProblem<TypeTag>
{
using ParentType = NavierStokesProblem<TypeTag>;
@@ -181,6 +187,8 @@ public:
if (onUpperBoundary_(globalPos))
{
+ // TODO: dumux-course-task 3.B
+ // Replace all conditions here with symmetric BCs.
values.setDirichlet(Indices::velocityXIdx);
values.setDirichlet(Indices::velocityYIdx);
values.setNeumann(Indices::conti0EqIdx);
@@ -262,6 +270,12 @@ public:
const CouplingManager& couplingManager() const
{ return *couplingManager_; }
+ // TODO: dumux-course-task 3.A
+ // Tell the turbulence model, where the walls are located
+
+ // TODO: dumux-course-task 3.B
+ // Remove the condition `onUpperBoundary_(globalPos)` from the `isOnWallAtPos(globalPos)`
+
/*!
* \name Volume terms
*/
@@ -285,6 +299,8 @@ public:
values[Indices::velocityXIdx] = refVelocity();
values[Indices::temperatureIdx] = refTemperature();
+ // TODO: dumux-course-task 3.B
+ // Remove the condition `onUpperBoundary_(globalPos)` here.
if(onUpperBoundary_(globalPos) || onLowerBoundary_(globalPos))
values[Indices::velocityXIdx] = 0.0;
diff --git a/exercises/exercise-coupling-ff-pm/turbulence/main.cc b/exercises/exercise-coupling-ff-pm/turbulence/main.cc
index c6d7249d..a0750fad 100644
--- a/exercises/exercise-coupling-ff-pm/turbulence/main.cc
+++ b/exercises/exercise-coupling-ff-pm/turbulence/main.cc
@@ -161,8 +161,11 @@ int main(int argc, char** argv) try
couplingManager->init(stokesProblem, darcyProblem, sol);
- // TODO: update static wall properties
- // TODO: update dynamic wall properties
+ // TODO: dumux-course-task 3.A
+ // Update static wall properties
+
+ // TODO: dumux-course-task 3.A
+ // Update dynamic wall properties
// the grid variables
using StokesGridVariables = GetPropType<StokesTypeTag, Properties::GridVariables>;
@@ -218,7 +221,8 @@ int main(int argc, char** argv) try
// make the new solution the old solution
solOld = sol;
- // TODO: update dynamic wall properties
+ // TODO: dumux-course-task 3.A
+ // Update dynamic wall properties
// post time step treatment of Darcy problem
darcyProblem->postTimeStep(sol[darcyIdx], *darcyGridVariables, timeLoop->timeStepSize());
diff --git a/exercises/exercise-dunemodule/README.md b/exercises/exercise-dunemodule/README.md
index e396be75..a12cfa33 100644
--- a/exercises/exercise-dunemodule/README.md
+++ b/exercises/exercise-dunemodule/README.md
@@ -21,7 +21,7 @@ workflow to develop code on top of DuMuX.
* a version at your choice (the version of your project, not of dumux.)
* your email address
-<hr><br><br>
+<br><br><br>
### Task 2: Rerun dunecontrol to configure your new project
<hr>
@@ -33,7 +33,7 @@ The following command will configure your new module
You need to run this command in the folder with content dumux, dumux-course, dune-common, dune-geometry, dune-grid, dune-istl, etc. `<opts file>` needs to be replaced (please replace the angle brackets also) by an options file, e.g., by `./dumux/cmake.opts`. Have a look at the comments in this file to see how you can adapt it to your needs.
-<hr><br><br>
+<br><br><br>
### Task 3: Create a new test case within your new DuMuX module
<hr>
@@ -77,7 +77,7 @@ cd appl
./test_1p_compressible_stationary_tpfa params.input
```
-<hr><br><br>
+<br><br><br>
### Task 4: Create a new GitLab project
<hr>
diff --git a/exercises/exercise-fluidsystem/2pproblem.hh b/exercises/exercise-fluidsystem/2pproblem.hh
index 28a36b1e..995075b0 100644
--- a/exercises/exercise-fluidsystem/2pproblem.hh
+++ b/exercises/exercise-fluidsystem/2pproblem.hh
@@ -44,6 +44,8 @@
#include <dumux/material/components/h2o.hh>
// The components that will be created in this exercise
+// TODO: dumux-course-task 2.2
+//****** Include the corresponding header for the task *****//
#include "components/myincompressiblecomponent.hh"
// #include "components/mycompressiblecomponent.hh"
@@ -94,10 +96,10 @@ private:
using Scalar = GetPropType<TypeTag, Properties::Scalar>;
using TabulatedH2O = Components::TabulatedComponent<Components::H2O<Scalar>>;
using LiquidWaterPhase = typename FluidSystems::OnePLiquid<Scalar, TabulatedH2O>;
- /*!
- * Uncomment first line and comment second line for using the incompressible component
- * Uncomment second line and comment first line for using the compressible component
- */
+
+ // TODO: dumux-course-task 2.2
+ //****** Select the corresponding component for the task *****//
+ // Uncomment first line and comment second line for using the compressible component
using LiquidMyComponentPhase = typename FluidSystems::OnePLiquid<Scalar, MyIncompressibleComponent<Scalar> >;
// using LiquidMyComponentPhase = typename FluidSystems::OnePLiquid<Scalar, MyCompressibleComponent<Scalar> >;
diff --git a/exercises/exercise-fluidsystem/README.md b/exercises/exercise-fluidsystem/README.md
index df8f82a0..438ce7b4 100644
--- a/exercises/exercise-fluidsystem/README.md
+++ b/exercises/exercise-fluidsystem/README.md
@@ -1,7 +1,6 @@
-# Exercise Fluidsystem
+# Exercise Fluidsystem (DuMuX Course)
-The aim of this exercise is to get familiar with the _DuMuX_ way of implementing new components (fluids) and fluid systems (mixtures). In the scope of this exercise, a new fictitious component is implemented
-(exercise fluidsystem a) as well as its mixture with water (exercise fluidsystem b).
+The aim of this exercise is to get familiar with the _DuMu<sup>x</sup>_ way of implementing new components (fluids) and fluid systems (mixtures). In the scope of this exercise, a new fictitious component is implemented (Section 2) as well as its mixture with water (Section 3).
## Problem set-up
@@ -91,9 +90,8 @@ This fluid system expects __phases__ as input and so far we have only included t
#include <dumux/material/fluidsystems/1pliquid.hh>
```
-which creates a _liquid phase_ from a given component. Finally, using all of the included classes we set the fluid system property by choosing that
-the water phase is liquid (OnePLiquid) and consists of the tabulated water component, and
-the other phase is liquid as well and consists of the incompressible fictitious component. Both will make up the immiscible fluid system (TwoPImmiscible):
+which creates a _liquid phase_ from a given component. Finally, using all of the included classes we set the fluid system property by choosing that the water phase is liquid (`OnePLiquid`) and consists of the tabulated water component, and
+the other phase is liquid as well and consists of the incompressible fictitious component. Both will make up the immiscible fluid system (`TwoPImmiscible`):
```c++
@@ -105,10 +103,10 @@ private:
using Scalar = GetPropType<TypeTag, Properties::Scalar>;
using TabulatedH2O = Components::TabulatedComponent<Components::H2O<Scalar>>;
using LiquidWaterPhase = typename FluidSystems::OnePLiquid<Scalar, TabulatedH2O>;
- /*!
- * Uncomment first line and comment second line for using the incompressible component
- * Uncomment second line and comment first line for using the compressible component
- */
+
+ // TODO: dumux-course-task 2.2
+ //****** Select the corresponding component for the task *****//
+ // Uncomment first line and comment second line for using the compressible component
using LiquidMyComponentPhase = typename FluidSystems::OnePLiquid<Scalar, MyIncompressibleComponent<Scalar> >;
// using LiquidMyComponentPhase = typename FluidSystems::OnePLiquid<Scalar, MyCompressibleComponent<Scalar> >;
@@ -164,7 +162,7 @@ We now want to implement a pressure-dependent density for our component. Open th
$`\displaystyle \rho_{MyComp} = \rho_{min} + \frac{ \rho_{max} - \rho_{min} }{ 1 + \rho_{min}*e^{-1.0*k*(\rho_{max} - \rho_{min})*p} } `$
-where $`p`$ is the pressure and $`\rho_{min} = 1440 `$, $`\rho_{max} = 1480 `$ and $`k = 5 \cdot 10^{-7} `$. Also, make sure the header is included in the `2pproblem.hh` file by uncommenting line 54. Furthermore, the new component has to be set as a liquid phase in the fluid system, i.e. comment line 109 and uncomment line 110. The density distribution of this phase (rhoN) at the final simulation time should look like this:
+where $`p`$ is the pressure and $`\rho_{min} = 1440 `$, $`\rho_{max} = 1480 `$ and $`k = 5 \cdot 10^{-7} `$. Also, make sure the header is included in the `2pproblem.hh` file by uncommenting the corresponding line. Furthermore, the new component has to be set as a liquid phase in the fluid system. To do so, search for `TODO: dumux-course-task 2.2`. Comment out the corresponding line and uncomment the other. The density distribution of this phase (rhoN) at the final simulation time should look like this:
@@ -224,7 +222,7 @@ Under the assumption that one molecule of `MyCompressibleComponent` displaces ex
$` \rho_{w} = \frac{ \rho_{w, pure} }{ M_{H_2O} }*(M_{H_2O}*x_{H_2O} + M_{MyComponent}*x_{MyComponent}) `$
-Implement this dependency in the `density()` method in the fluid system. In order to compile and execute the program run
+Implement this dependency in the `density()` method in the fluid system. In order to compile and execute the program, run the following commands:
```bash
cd build-cmake/exercises/exercise-fluidsystem
@@ -255,7 +253,7 @@ int wettingPhaseAtPos(const GlobalPosition& globalPos) const
}
```
-Change this function such that the the phase of our new component is the wetting phase __only__ within the lenses. Execute the program of task 3 again:
+Change this function such that the phase of our new component is the wetting phase __only__ within the lenses. Execute the program of task 3 again:
```bash
cd build-cmake/exercises/exercise-fluidsystem
diff --git a/exercises/exercise-fluidsystem/components/mycompressiblecomponent.hh b/exercises/exercise-fluidsystem/components/mycompressiblecomponent.hh
index 927f0468..ee8dc42c 100644
--- a/exercises/exercise-fluidsystem/components/mycompressiblecomponent.hh
+++ b/exercises/exercise-fluidsystem/components/mycompressiblecomponent.hh
@@ -50,12 +50,7 @@ public:
static std::string name()
{ return "MyCompressibleComponent"; }
- /*!
- * TODO: Copy the methods implemented in MyIncompressibleComponent and substitute
- * the density calculation by the expression given in the exercise description.
- */
-
- /*!
+ /*!
* \brief Returns true if the liquid phase is assumed to be compressible
*/
static constexpr bool liquidIsCompressible()
@@ -66,7 +61,10 @@ public:
*/
static Scalar molarMass()
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.2
+ // Copy the methods implemented in MyIncompressibleComponent and substitute
+ // the density calculation by the expression given in the exercise description.
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement molar mass");
}
@@ -79,7 +77,8 @@ public:
*/
static Scalar liquidDensity(Scalar temperature, Scalar pressure)
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.2:
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement liquid density");
}
@@ -104,7 +103,8 @@ public:
*/
static Scalar liquidViscosity(Scalar temperature, Scalar pressure)
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.2:
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement liquid viscosity");
}
@@ -116,7 +116,8 @@ public:
*/
static Scalar vaporPressure(Scalar t)
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 3
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement vapour pressure");
}
};
diff --git a/exercises/exercise-fluidsystem/components/myincompressiblecomponent.hh b/exercises/exercise-fluidsystem/components/myincompressiblecomponent.hh
index 37b04dad..fa6074b2 100644
--- a/exercises/exercise-fluidsystem/components/myincompressiblecomponent.hh
+++ b/exercises/exercise-fluidsystem/components/myincompressiblecomponent.hh
@@ -49,10 +49,6 @@ public:
static std::string name()
{ return "MyIncompressibleComponent"; }
- /*!
- * TODO: Implement the methods for the component data given in the exercise description.
- */
-
/*!
* \brief Returns true if the liquid phase is assumed to be compressible
*/
@@ -64,7 +60,9 @@ public:
*/
static Scalar molarMass()
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.1
+ // Implement the methods for the component data given in the exercise description.
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement molarMass()");
}
@@ -77,7 +75,9 @@ public:
*/
static Scalar liquidDensity(Scalar temperature, Scalar pressure)
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.1
+ // Implement the methods for the component data given in the exercise description.
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement liquidDensity()");
}
@@ -102,7 +102,9 @@ public:
*/
static Scalar liquidViscosity(Scalar temperature, Scalar pressure)
{
- // TODO: replace the line below by a meaningful return statement
+ // TODO: dumux-course-task 2.1
+ // Implement the methods for the component data given in the exercise description.
+ // Replace the line below by a meaningful return statement
DUNE_THROW(Dune::NotImplemented, "Todo: implement liquidViscosity()");
}
};
diff --git a/exercises/exercise-fluidsystem/fluidsystems/h2omycompressiblecomponent.hh b/exercises/exercise-fluidsystem/fluidsystems/h2omycompressiblecomponent.hh
index 62965b2a..f0ae0ea0 100644
--- a/exercises/exercise-fluidsystem/fluidsystems/h2omycompressiblecomponent.hh
+++ b/exercises/exercise-fluidsystem/fluidsystems/h2omycompressiblecomponent.hh
@@ -51,7 +51,7 @@ class H2OMyCompressibleComponent
{
using ThisType = H2OMyCompressibleComponent<Scalar, H2OType>;
using Base = Dumux::FluidSystems::Base<Scalar, ThisType>;
-
+
public:
using H2O = H2OType;
using MyCompressibleComponent = Dumux::MyCompressibleComponent<Scalar>;
@@ -229,9 +229,9 @@ public:
// Scalar x_H2O = fluidState.moleFraction(phase0Idx, H2OIdx);
// Scalar x_myComp = fluidState.moleFraction(phase0Idx, NAPLIdx);
- /*!
- * TODO: implement the composition-dependent water density from the exercise sheet.
- */
+ // TODO: dumux-course-task 3
+ // Implement the composition-dependent water density from the exercise sheet.
+
DUNE_THROW(Dune::NotImplemented, "Todo: implement composition-dependent density");
}
else
diff --git a/exercises/exercise-fluidsystem/spatialparams.hh b/exercises/exercise-fluidsystem/spatialparams.hh
index 1eda4bb1..b3caeaec 100644
--- a/exercises/exercise-fluidsystem/spatialparams.hh
+++ b/exercises/exercise-fluidsystem/spatialparams.hh
@@ -144,6 +144,10 @@ public:
// Our fluid system is H2OMyCompressibleComponent
// We want to define water as the wetting phase in
// the entire domain (see fluid system for the phase indices)
+
+ // TODO: dumux-course-task 4
+ // Adapt the following line so that the phase of our new component is
+ // the wetting phase, only within the lenses.
return FluidSystem::phase0Idx;
}
diff --git a/exercises/exercise-fractures/README.md b/exercises/exercise-fractures/README.md
index 8fb0703c..c5610c9c 100644
--- a/exercises/exercise-fractures/README.md
+++ b/exercises/exercise-fractures/README.md
@@ -155,7 +155,8 @@ BoundaryTypes interiorBoundaryTypes(const Element& element, const SubControlVolu
// the interior boundary conditions to Dirichlet.
// IMPORTANT: Note that you will never be asked to set any values at the interior boundaries!
// This simply chooses a different interface condition!
- // TODO Task C: Change coupling conditions!
+ // TODO dumux-course-task C
+ // Change coupling conditions!
values.setAllDirichlet();
return values;
@@ -180,7 +181,7 @@ Physical Line(1) = {6,7,9,11,12,13,14,15,16,17,18,19,20,21,23,25};
Physical Line(2) = {8,10,22,24,26};
```
-We now want to give all fracture elements that are tagged with domain marker 2 the properties for barriers and assign the parameters for open fractures to all other elements. The domain markers are read from the grid file and can be obtained from the `GridManager` subsequent to grid creation. The main file of this exercise has been implemented such that these markers are already passed to the spatial parameters of the sub-domains (see `main.cc`, lines 120-132). In the spatial parameters you will find a convenience function which allows you to obtain the domain marker for a given element (see `fracturespatialparams.hh`):
+We now want to give all fracture elements that are tagged with domain marker 2 the properties for barriers and assign the parameters for open fractures to all other elements. The domain markers are read from the grid file and can be obtained from the `GridManager` subsequent to grid creation. The main file of this exercise has been implemented such that these markers are already passed to the spatial parameters of the sub-domains (see `main.cc`, search for `// pass the model parameter group to the spatial params`). In the spatial parameters you will find a convenience function which allows you to obtain the domain marker for a given element (see `fracturespatialparams.hh`):
```cpp
//! returns the domain marker for an element
@@ -188,7 +189,7 @@ int getElementDomainMarker(const Element& element) const
{ return gridDataPtr_->getElementDomainMarker(element); }
```
-The domain markers are also already added to the output (see `main.cc`, lines 195-199). To visualize them, open any of your previously produced results with _Paraview_ and take a look at them by selecting __domainMarker__.
+The domain markers are also already added to the output (see `main.cc`, search for `// add domain markers to output`). To visualize them, open any of your previously produced results with _Paraview_ and take a look at them by selecting __domainMarker__.
Adjust the functions for permeability, porosity and material law parameters in the `fracturespatialparams.hh` file such that they are selected depending on the domain marker of the elements. You will see in the results that the pressure jump across the first vertical fracture is now lower than before, because there are highly permeable fractures crossing it, allowing for a pressure release into the other parts of the domain.
diff --git a/exercises/exercise-fractures/fractureproblem.hh b/exercises/exercise-fractures/fractureproblem.hh
index 76493b12..2e2c2daf 100644
--- a/exercises/exercise-fractures/fractureproblem.hh
+++ b/exercises/exercise-fractures/fractureproblem.hh
@@ -140,7 +140,8 @@ public:
// However, there is one fracture reaching the top boundary. For this
// fracture tip we set Dirichlet Bcs as in the matrix domain
- // TODO Task A: Change boundary conditions
+ // TODO dumux-course-task A
+ // Change boundary conditions
if (globalPos[1] > this->gridGeometry().bBoxMax()[1] - 1e-6)
values.setAllDirichlet();
diff --git a/exercises/exercise-fractures/fracturespatialparams.hh b/exercises/exercise-fractures/fracturespatialparams.hh
index 76edd228..3431f351 100644
--- a/exercises/exercise-fractures/fracturespatialparams.hh
+++ b/exercises/exercise-fractures/fracturespatialparams.hh
@@ -98,7 +98,8 @@ public:
const SubControlVolume& scv,
const ElementSolution& elemSol) const
{
- // TODO Task B: change fracture properties
+ // TODO dumux-course-task B
+ // Change fracture properties
return permeability_;
}
@@ -108,7 +109,8 @@ public:
const SubControlVolume& scv,
const ElementSolution& elemSol) const
{
- // TODO Task B: change fracture properties
+ // TODO dumux-course-task B
+ // Change fracture properties
return porosity_;
}
@@ -118,7 +120,8 @@ public:
const SubControlVolume& scv,
const ElementSolution& elemSol) const
{
- // TODO Task B: change fracture properties
+ // TODO dumux-course-task B
+ // Change fracture properties
return materialLawParams_;
}
diff --git a/exercises/exercise-fractures/matrixproblem.hh b/exercises/exercise-fractures/matrixproblem.hh
index 07920241..1eb67c1d 100644
--- a/exercises/exercise-fractures/matrixproblem.hh
+++ b/exercises/exercise-fractures/matrixproblem.hh
@@ -144,7 +144,8 @@ public:
// we consider buoancy-driven upwards migration of nitrogen and set
// Dirichlet BCs on the top and bottom boundary
- // TODO Task A: Change boundary conditions and Dirichlet values!
+ // TODO dumux-course-task A
+ // Change boundary conditions and Dirichlet values!
values.setAllNeumann();
if (globalPos[1] < 1e-6 || globalPos[1] > this->gridGeometry().bBoxMax()[1] - 1e-6)
values.setAllDirichlet();
@@ -171,7 +172,8 @@ public:
// the interior boundary conditions to Dirichlet.
// IMPORTANT: Note that you will never be asked to set any values at the interior boundaries!
// This simply chooses a different interface condition!
- // TODO Task C: Change coupling conditions!
+ // TODO dumux-course-task C
+ // Change coupling conditions!
values.setAllDirichlet();
return values;
@@ -184,7 +186,8 @@ public:
auto values = initialAtPos(globalPos);
// nitrogen is in contact with the domain on the center half of the lower boundary
- // TODO Task A: Change boundary conditions and Dirichlet values!
+ // TODO dumux-course-task A
+ // Change boundary conditions and Dirichlet values!
if (globalPos[1] < 1e-6 && globalPos[0] > 25.0 && globalPos[0] < 75.0)
values[saturationIdx] = boundarySaturation_;
diff --git a/exercises/exercise-grids/README.md b/exercises/exercise-grids/README.md
index 4edb8961..5ab7966c 100644
--- a/exercises/exercise-grids/README.md
+++ b/exercises/exercise-grids/README.md
@@ -1,5 +1,6 @@
# Exercise Grids (DuMuX course)
<br>
+
## Problem set-up
Here we will expand on what we've covered in the basics exercise, and the problem set up will remain the same.
@@ -48,7 +49,7 @@ template<class TypeTag>
struct Grid<TypeTag, TTag::Injection2pTypeTag> { using type = Dune::YaspGrid<2>; };
```
-This sets the Grid, which belongs to the Injection2pTypeTag type tag, and calls the manager with a basic YaspGrid in the second dimension.
+This sets the Grid, which belongs to the `Injection2pTypeTag` type tag, and calls the manager with a basic `YaspGrid` in the second dimension.
If we look in the grid manager header file, `dumux/dumux/io/grid/gridmanager.hh`,
we will see that there are a few grid development options. Until now, we have used the most basic definition.
@@ -136,9 +137,9 @@ Grading1 = 1.0 -1.3 1.3 1.0
DuMuX can also read in grids from external files. There are two supported file types: `.dgf` grids, and `.msh` grids.
__`.dgf`__ grids (DUNE Grid Format grids) are developed within the dune environment and are often used in dumux tests.
-(see: `https://www.dune-project.org/doxygen/2.4.1/group__DuneGridFormatParser.html`)
+(see: [DUNE Grid Format grids](https://www.dune-project.org/doxygen/2.4.1/group__DuneGridFormatParser.html))
__`.msh`__ grids are made from the open-source Gmsh software, and is also supported by dumux.
-(see: `http://gmsh.info//` and `http://gmsh.info//doc/texinfo/gmsh.html`)
+(see: [Gmsh](http://gmsh.info//) and [Gmsh reference manual](http://gmsh.info//doc/texinfo/gmsh.html))
We can read in simple .dgf files using basic YaspGrids, but if we want to use more complicated external grids, we would need to use other grid formats, like UGGrid or ALUGrid.
For this example, we can rewrite our Grid Properties to develop an ALUGrid. The grid manager class takes the following form:
@@ -162,10 +163,3 @@ An example of an Unstructured grid is located in the `grid/` folder (`grid_unstr
This grid is made up of triangles (simplices of dimension 2). This element type can be set in the grid properties section.
* > __Task 5__: Change the grid property element type to include `Dune::simplex` instead of `Dune::cube`. Read in the unstructured grid via the input file and run the simulation.
-
-
-
-
-
-
-
diff --git a/exercises/exercise-grids/problem.hh b/exercises/exercise-grids/problem.hh
index 855d4c9e..8995c5da 100644
--- a/exercises/exercise-grids/problem.hh
+++ b/exercises/exercise-grids/problem.hh
@@ -51,9 +51,14 @@ struct Injection2pCC { using InheritsFrom = std::tuple<Injection2p, CCTpfaModel>
// Set the grid type
template<class TypeTag>
struct Grid<TypeTag, TTag::Injection2p> { using type = Dune::YaspGrid<2>; };
-// TODO: Task 2: Replace the above Grid Property definition with a more flexible grid (Use Dune::TensorProductCoordinates)
-// TODO: Task 4: Replace the above Grid Property definition to read in a external structured grid via a .msh file (Use Dune::ALUGrid and Dune:cube)
-// TODO: Task 5: Replace the above Grid Property definition to read in a external unstructured grid via a .msh file (Use Dune::ALUGrid and Dune::simplex)
+// TODO: dumux-course-task 2
+//Replace the above Grid Property definition with a more flexible grid (Use Dune::TensorProductCoordinates)
+
+// TODO: dumux-course-task 4
+// Replace the above Grid Property definition to read in a external structured grid via a .msh file (Use Dune::ALUGrid and Dune:cube)
+
+// TODO: dumux-course-task 5
+// Replace the above Grid Property definition to read in a external unstructured grid via a .msh file (Use Dune::ALUGrid and Dune::simplex)
// Set the problem property
template<class TypeTag>
diff --git a/exercises/exercise-mainfile/1pproblem.hh b/exercises/exercise-mainfile/1pproblem.hh
index 1f15312a..1b713337 100644
--- a/exercises/exercise-mainfile/1pproblem.hh
+++ b/exercises/exercise-mainfile/1pproblem.hh
@@ -36,7 +36,7 @@
#include <dumux/discretization/box.hh>
-// TODO: dumux-course-task
+// TODO: dumux-course-task 3
// uncomment the incompressiblelocalresidual which is a specialization of the standard immisible localresidual for one phase incompressible cases and provides an analytic jacobian.
// #include <dumux/porousmediumflow/1p/incompressiblelocalresidual.hh>
@@ -84,7 +84,7 @@ public:
using type = FluidSystems::OnePLiquid<Scalar, Components::SimpleH2O<Scalar> >;
};
-// TODO: dumux-course-task
+// TODO: dumux-course-task 3
// set the OneP Incompressible local residual for the OnePIncompressible type tag. This provides an analytic jacobian to be used for the analytic solution. Change that by setting:
// template<class TypeTag>
// struct LocalResidual<TypeTag, TTag::OnePIncompressible> { using type = OnePIncompressibleLocalResidual<TypeTag>; };
diff --git a/exercises/exercise-mainfile/README.md b/exercises/exercise-mainfile/README.md
index 1630d4d9..8119e960 100644
--- a/exercises/exercise-mainfile/README.md
+++ b/exercises/exercise-mainfile/README.md
@@ -1,14 +1,15 @@
# Exercise Mainfiles (DuMuX course)
<br>
+
## Problem set-up
-This exercise will make you familiar the program sequence in DuMux and how different levels of complexity can be realized in the main file according to the complexity of your physical problem.
+This exercise will make you familiar the program sequence in DuMuX and how different levels of complexity can be realized in the main file according to the complexity of your physical problem.
In order to do so, there are three examples of one phase flow problems. Two examples (a and b) are stationary problems and the third example (c) is an instationary problem.
-The stationary examples differ in the fluidssystems they are using which means they differ in the fluid properties (e.g. density, thermal conductivity etc). The first problem (a) uses an incompressible fluid which means that the density does not change when pressure changes. This makes it possible to solve the system linearly. The second problem uses a compressible fluid, that means the density is a function of pressure and we need to use a nonlinear solver.
+The stationary examples differ in the `fluidssystems` they are using, which means they differ in the fluid properties (e.g. density, thermal conductivity etc). The first problem (a) uses an incompressible fluid, i.e. the density does not change when pressure changes. This makes it possible to solve the system linearly. The second problem uses a compressible fluid, that means the density is a function of pressure and we need to use a nonlinear solver.
-To summarize the problems differ in:
+To summarize, the problems differ in:
* exercise mainfile a: a one-phase incompressible, stationary problem
* exercise mainfile b: a one-phase compressible, stationary problem
* exercise mainfile c: a one-phase compressible, instationary problem
@@ -17,7 +18,7 @@ The problem set-up for all three examples is always the same: It is a two dimens
<img src="https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course/raw/master/exercises/extradoc/exercise1_1p_setup.png" width="1000">
-In the beginning there is a uniform pressure of $`1\cdot 10^5 Pa`$ in the whole domain. On the top and the bottom border dirichlet boundary conditions are set with a pressure of $`1\cdot 10^5 Pa`$ on top and $`2 \cdot 10^5 Pa`$ on the bottom. At the sides there is no in- or outflow and there are no source terms.
+In the beginning, there is a uniform pressure of $`1\cdot 10^5 Pa`$ in the whole domain. On the top and the bottom border, dirichlet boundary conditions are set with a pressure of $`1\cdot 10^5 Pa`$ on top and $`2 \cdot 10^5 Pa`$ on the bottom. At the sides, there is no in- or outflow and there are no source terms.
## Preparing the exercise
@@ -37,25 +38,25 @@ Locate all the files you will need for this exercise
* The __input file__ for the __compressible, stationary__ problem: `exercise_mainfile_b.input`
* The __input file__ for the __compressible, instationary__ problem: `exercise_mainfile_c.input`
-Please pay special attention to the similarities and differences in the three main files. The first main file is solved linearly and does not need a newton solver or any other nonlinear solver method. The second problem is a nonlinear problem and uses newton's method to solve the system. The third problem is nonlinear and additionally instationary. Therefore a time loop needs to be included in the main file.
+Please pay special attention to the similarities and differences in the three main files. The first main file is solved linearly and does not need a newton solver or any other nonlinear solver method. The second problem is a nonlinear problem and uses newton's method to solve the system. The third problem is nonlinear and additionally instationary. Therefore, a time loop needs to be included in the main file.
-The general structure of any main file in DuMux is:
+The general structure of any main file in DuMuX is:
-* the specific problem TypeTag is defined for the problem. This example shows the TypeTag for the CompressibleProblem
+* the specific problem `TypeTag` is defined for the problem. This example shows the `TypeTag` for the `CompressibleProblem`:
```c++
// define the type tag for this problem
using TypeTag = Properties::TTag::OnePCompressible;
```
-The TypeTag is created in the `1pproblem.hh`. There you can see that it inherits from the __OneP__ and additionally from the __CCTpfaModel__ which defines the discretization method, which is in this case the cell-centered tpfa method.
+The `TypeTag` is created in the `1pproblem.hh`. There, you can see that it inherits from the __OneP__ and additionally from the __CCTpfaModel__. The latter defines the discretization method, which is in this case the cell-centered tpfa method.
-* a gridmanager tries to create the grid either from a grid file or the input file
+* A gridmanager tries to create the grid either from a grid file or the input file:
```c++
GridManager<GetPropType<TypeTag, Properties::Grid>> gridManager;
gridManager.init();
```
-* we create the finite volume grid geometry, the problem, solutionvector and the gridvariables and initialize them. Additionally we initialize the vtkoutput. Each model has a predefined model specific output with relevant parameters for that model.
+* We create the finite volume grid geometry, the problem, solution vector and the grid variables and initialize them. Additionally, we initialize the vtk output. Each model has a predefined model specific output with relevant parameters for that model:
```c++
// create the finite volume grid geometry
@@ -85,7 +86,7 @@ IOFields::initOutputModule(vtkWriter); //!< Add model specific output fields
vtkWriter.write(0.0);
```
-* then we need to assemble and solve the system. Depending on the problem this can be done with a linear solver or with a nonlinear solver. If the problem is time dependent we additionally need a time loop. An example for that is given in exercise_1p_c:
+* Then, we need to assemble and solve the system. Depending on the problem, this can be done with a linear solver or a nonlinear solver. If the problem is time dependent, we additionally need a time loop. An example for that is given in `exercise1pcmain.cc`:
```c++
// get some time loop parameters
@@ -144,7 +145,7 @@ timeLoop->start(); do
timeLoop->finalize(leafGridView.comm());
```
-<hr><br><br>
+<br><br><br>
### Task 2: Compiling and running an executable
<hr>
@@ -157,7 +158,7 @@ cd ../../build-cmake/exercises/exercise-mainfile
* Compile all three executables `exercise_mainfile_a` and `exercise_mainfile_b` and `exercise_mainfile_c`
```bash
-make exercise_1p_a exercise_1p_b exercise_1p_c
+make exercise_mainfile_a exercise_mainfile_b exercise_mainfile_c
```
* Execute the three problems and inspect the result
@@ -168,23 +169,23 @@ make exercise_1p_a exercise_1p_b exercise_1p_c
./exercise_mainfile_c
```
-* you can look at the results (e.g. for the first example) with paraview:
+* You can look at the results (e.g. for the first example) with paraview:
```bash
paraview 1p_incompressible_stationary.pvd
```
-<hr><br><br>
+<br><br><br>
### Task 3: Analytical differentiation
<hr>
-In the input file `exercise_1p_a.input` you will see that there is a variable BaseEpsilon. This defines the base for the epsilon used in the numeric differentiation. If that value is too small, you will see that the solution of the numeric differentiation is not correct. Change that value to $`1 \cdot 10^{-15}`$ and have a look at the solution.
+In the input file `exercise_1p_a.input`, you will see that there is a variable `BaseEpsilon`. This defines the base for the epsilon used in the numeric differentiation. If that value is too small, you will see that the solution of the numeric differentiation is not correct. Change that value to $`1 \cdot 10^{-15}`$ and have a look at the solution.
-For the incompressible one phase problem it is possible to also have an analytic solution method. Then the epsilon does not play a role anymore since the derivatives are calculated analytically. To implement that follow the directions in the `exercise1pamain.cc` and the `1pproblem.hh` marked by:
+For the incompressible one phase problem, it is also possible to have an analytic solution method. In this case, the epsilon does not play a role anymore, since the derivatives are calculated analytically. To implement that, follow the tips in the `exercise1pamain.cc` and the `1pproblem.hh` marked by:
```c++
-// TODO: dumux-course-task
+// TODO: dumux-course-task 3
```
-For the analytic solution of your immiscible problem you need analytic solutions for the derivatives of the jacobian. For that we have a special local residual, the `OnePIncompressibleLocalResidual` which provides that. You just need to include `incompressiblelocalresidual.hh` in your `1pproblem.hh` and use that instead of the `immisciblelocalresidual.hh` which is used as a standard for all immiscible models.
+For the analytic solution of your immiscible problem, you need analytic solutions for the derivatives of the jacobian. For that, we have a special local residual, the `OnePIncompressibleLocalResidual` which provides that. You just need to include `incompressiblelocalresidual.hh` in your `1pproblem.hh` and use that instead of the `immisciblelocalresidual.hh` which is used as a default for all immiscible models.
-Additionally you need to set the differentiation method in the main file `exercise1pamain.cc` to analytic.
+Additionally, you need to set the differentiation method in the main file `exercise1pamain.cc` to analytic.
diff --git a/exercises/exercise-mainfile/exercise1pamain.cc b/exercises/exercise-mainfile/exercise1pamain.cc
index 6cfe2dc4..208ffef7 100644
--- a/exercises/exercise-mainfile/exercise1pamain.cc
+++ b/exercises/exercise-mainfile/exercise1pamain.cc
@@ -105,11 +105,11 @@ int main(int argc, char** argv) try
using IOFields = GetPropType<TypeTag, Properties::IOFields>;
IOFields::initOutputModule(vtkWriter); //!< Add model specific output fields
vtkWriter.write(0.0);
-
+
Dune::Timer timer;
- // TODO: dumux-course-task
- // change the differentiation method to analytic by changing from DiffMethod::numeric to DiffMethod::analytic
+ // TODO: dumux-course-task 3
+ // Change the differentiation method to analytic by changing from DiffMethod::numeric to DiffMethod::analytic
// the assembler for stationary problems
using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>;
diff --git a/exercises/exercise-properties/README.md b/exercises/exercise-properties/README.md
index 8419bf83..b676f489 100644
--- a/exercises/exercise-properties/README.md
+++ b/exercises/exercise-properties/README.md
@@ -1,5 +1,6 @@
# Exercise Properties (DuMuX course)
<br>
+
## Problem set-up
The problem setup is identical to the two-phase incompressible test from DuMu<sup>x</sup>.
@@ -23,7 +24,7 @@ Locate all the files you will need for this exercise
* a custom __local residual__ in: `mylocalresidual.hh`
-<hr><br><br>
+<br><br><br>
### Task 2: Compiling and running the program
<hr>
@@ -44,15 +45,14 @@ make exercise_properties
```bash
./exercise_properties
```
-Note: Because the input file has the same name as the
-executable, DuMu<sup>x</sup> will find it automatically.
+Note: Because the input file has the same name as the executable, DuMu<sup>x</sup> will find it automatically.
-<hr><br><br>
+<br><br><br>
### Task 3: Implement a custom local residual
<hr>
-Types that are properties can be changed on the problem level by using the property system. In the following task we implement our own 2p local residual, i.e. the class that computes the element residual in every Newton iteration. The file `mylocalresidual.hh` contains a copy of the original local residual class used for all immiscible models renamed to `template<class TypeTag> class MyLocalResidual`.
+Types that are properties can be changed on the problem level by using the property system. In the following task, we implement our own 2p local residual, i.e. the class that computes the element residual in every Newton iteration. The file `mylocalresidual.hh` contains a copy of the original local residual class used for all immiscible models renamed to `template<class TypeTag> class MyLocalResidual`.
* Make DuMu<sup>x</sup> use this new local residual by including the header `mylocalresidual.hh` and setting the corresponding property in the `Property` namespace in the file `problem.hh`
@@ -69,7 +69,6 @@ Simplify the original local residual by using the assumption that only incompres
* Eliminate the density from the `computeStorage` and the `computeFlux` methods.
-* Adapt the relevant routine in the problem file such that volume instead of mass is injected. The density of the employed NAPL is 1460 kg/m^3 . For a first try, you can use the hardcoded value.
+* Adapt the relevant routine in the problem file such that volume instead of mass is injected. The density of the employed NAPL is 1460 kg/m<sup>3</sup> . For a first try, you can use the hardcoded value.
* Generalize your approach by using the component's `liquidDensity(t, p)` function instead of the hardcoded value.
-
diff --git a/exercises/exercise-properties/mylocalresidual.hh b/exercises/exercise-properties/mylocalresidual.hh
index 67c390b4..d6c75f81 100644
--- a/exercises/exercise-properties/mylocalresidual.hh
+++ b/exercises/exercise-properties/mylocalresidual.hh
@@ -70,7 +70,8 @@ public:
* \note The volVars can be different to allow computing
* the implicit euler time derivative here
*/
- // TODO: eliminate density from the storage term
+ // TODO: dumux-course-task 3
+ // Eliminate density from the storage term
NumEqVector computeStorage(const Problem& problem,
const SubControlVolume& scv,
const VolumeVariables& volVars) const
@@ -105,7 +106,8 @@ public:
* \param scvf The sub control volume face to compute the flux on
* \param elemFluxVarsCache The cache related to flux compuation
*/
- // TODO: eliminate the density from the flux term
+ // TODO: dumux-course-task
+ // Eliminate the density from the flux term
NumEqVector computeFlux(const Problem& problem,
const Element& element,
const FVElementGeometry& fvGeometry,
diff --git a/exercises/exercise-properties/problem.hh b/exercises/exercise-properties/problem.hh
index 23c67f48..1fec9082 100644
--- a/exercises/exercise-properties/problem.hh
+++ b/exercises/exercise-properties/problem.hh
@@ -40,7 +40,8 @@
#include "spatialparams.hh"
-// TODO: include the local residual header
+// TODO: dumux-course-task 3
+// Include the local residual header
namespace Dumux {
// forward declarations
@@ -61,7 +62,9 @@ struct Grid<TypeTag, TTag::TwoPIncompressible> { using type = Dune::YaspGrid<2>;
template<class TypeTag>
struct Problem<TypeTag, TTag::TwoPIncompressible> { using type = TwoPTestProblem<TypeTag>; };
-// TODO: use MyLocalResidual as LocalResidual
+// TODO: dumux-course-task 3
+// Use MyLocalResidual as LocalResidual
+
// Set the fluid system
template<class TypeTag>
diff --git a/exercises/exercise-runtimeparams/README.md b/exercises/exercise-runtimeparams/README.md
index 78875fd5..595f2bb6 100644
--- a/exercises/exercise-runtimeparams/README.md
+++ b/exercises/exercise-runtimeparams/README.md
@@ -1,5 +1,6 @@
# Exercise Runtime Parameters (DuMuX course)
<br>
+
## Problem set-up
Here we will expand on what we've covered in the basics exercise, and the problem set up will remain the same.
@@ -47,9 +48,9 @@ EntryPressureAquitard = 4.5e4 # Pa
PermeabilityAquifer = 1e-12 # m^2
EntryPressureAquifer = 1e4 # Pa
```
-When a parameter is defined directly within your program, you'll need to recompile your program everytime you change the value. When a parameter is passed via the input file, this is not the case. If we decided to vary the entry pressure in our geologic units a few times via the parameters listed above, there would be no need to recompile between simulation runs.
+When a parameter is defined directly within your program, you'll need to recompile your program every time you change the value. When a parameter is passed via the input file, this is not the case. If we decided to vary the entry pressure in our geologic units a few times via the parameters listed above, there would be no need to recompile between simulation runs.
-* > __Task 1__: Change the aquitard's entry pressure in the input file to a lower value and compare the results with the previous solution. You don't need to recompile the executable.
+* > __Task 1__: Change the aquitard's entry pressure in the input file to a lower value and compare the results with the previous solution. You do not need to recompile the executable.
<br><br>
### Task 2: Setting a variable to collect a runtime parameter
@@ -64,8 +65,7 @@ values[Indices::conti0EqIdx + FluidSystem::N2Idx]= -1e-4/FluidSystem::molarMass(
values[Indices::conti0EqIdx + FluidSystem::H2OIdx] = 0.0;
```
-This parameter may need to change, and if we choose to always change this within the class,
-we will need to recompile every time.
+This parameter may need to change, and if we choose to always change this within the class, we will need to recompile every time.
Instead of hard defining this parameter within the function, we can set a variable to read into our parameter tree via the input file and use this in our function instead.
To do this, there are two functions defined in `dumux/dumux/common/parameters.hh`, `getParam()` and `getParamFromGroup()`. They use the following format:
diff --git a/exercises/exercise-runtimeparams/problem.hh b/exercises/exercise-runtimeparams/problem.hh
index 8cd8ddec..922e375d 100644
--- a/exercises/exercise-runtimeparams/problem.hh
+++ b/exercises/exercise-runtimeparams/problem.hh
@@ -131,9 +131,14 @@ public:
aquiferDepth_ = getParam<Scalar>("Problem.AquiferDepth");
// the duration of the injection, units: second
injectionDuration_ = getParamFromGroup<Scalar>("Problem","InjectionDuration");
- //TODO: Task 2: Set a variable "TotalAreaSpecificInflow" to read in a value from the parameter tree via the input file
- //TODO: Task 3: Set a default value for the above parameter.
- //TODO: Task 4: Provide output describing where the parameter value comes from using parameter bool functions.
+ // TODO: dumux-course-task 2
+ // Set a variable "TotalAreaSpecificInflow" to read in a value from the parameter tree via the input file
+
+ // TODO: dumux-course-task 3
+ // Set a default value for the above parameter.
+
+ // TODO: dumux-course-task 4
+ // Provide output describing where the parameter value comes from using parameter bool functions.
}
/*!
@@ -213,7 +218,8 @@ public:
{
// inject nitrogen. negative values mean injection
// units kg/(s*m^2)
- //TODO: Task 2: incorporate "totalAreaSpecificInflow_" into the injection boundary condition
+ // TODO: dumux-course-task 2
+ // Incorporate "totalAreaSpecificInflow_" into the injection boundary condition
values[Indices::conti0EqIdx + FluidSystem::N2Idx]= -1e-4/FluidSystem::molarMass(FluidSystem::N2Idx);
values[Indices::conti0EqIdx + FluidSystem::H2OIdx] = 0.0;
}
@@ -262,7 +268,8 @@ private:
std::string name_; //! Problem name
Scalar aquiferDepth_; //! Depth of the aquifer in m
Scalar injectionDuration_; //! Duration of the injection in seconds
- //TODO: Task 2: Set a variable "totalAreaSpecificInflow_" to read in a value from the parameter tree via the input file
+ // TODO: dumux-course-task 2
+ // Set a variable "totalAreaSpecificInflow_" to read in a value from the parameter tree via the input file
Scalar time_;
};
--
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