In this document we re-visit the collapsible channel problem yet again – this time to demonstrate the use of spatial adaptivity in fluid-structure interaction problems. In such problems, two additional issues have to be addressed:
We start with a brief reminder of
oomph-lib's mesh adaptation procedures to highlight what additional complications arise in fluid-structure interaction problems, and then explain how these problems are addressed.
We first discussed the use of spatial adaptivity for time-dependent problems in the context of the unsteady heat equation. We showed that whenever a new node is created,
oomph-lib's mesh adaptation procedures automatically assign the nodal values and "history values" (the auxiliary values that are used by the
TimeStepper to approximate time-derivatives of the nodal values) for the newly-created
Node by interpolating between the corresponding values in the new
Node's father element.
Similarly, an initial assignment for the newly-created
Node's current and previous positions (required for the evaluation of the mesh-velocities in the ALE formulation of the time-derivatives) is made by interpolating between the current and previous nodal positions of the new
Node's father element. This default assignment is subsequently overwritten if the father element is associated with a
MacroElement, in which case the newly-created
Node's current position is determined by the father element's
MacroElement representation. This ensures that the mesh refinement process respects curvilinear domain boundaries, as discussed
elsewhere. The same strategy is used to over-write the default assignment for a new
Node's previous positions: They are re-assigned, based on the father element's
MacroElement - representation, evaluated at the relevant previous timesteps.
To illustrate the process, consider the sketch below and assume that the time-integration of the Navier-Stokes equations is performed with a
BDF<2> timestepper – a timestepper that requires two history values (the solution and the nodal positions at two previous timesteps) to evaluate the time-derivative in the momentum equations. The position of the nodes in the collapsible part of the channel is determined by the
MacroElement - based representation of the
CollapsibleChannelDomain, using the wall shape obtained from the compound
MeshAsGeomObject that we created from the discretisation of the elastic wall, shown in green.
Assume that the initial mesh is sufficiently fine to resolve the solution at and . At , the automatic mesh adaptation splits one of the fluid elements, creating the five new
Nodes, shown in red (for simplicity we only show the fluid elements' vertex nodes). Their position is determined by the father element's
MacroElement mapping, using the current position of the
MeshAsGeomObject, obtained from the interpolation between the nodal positions of its
SolidNodes (shown as green circles).
So far, so good! A subtle problem arises when we try to assign the positional history values for the newly-created
Nodes. The evaluation of the
MacroElement mapping at the previous timesteps (required to determine the positions the newly-created
Nodes would have had, if they had already existed at previous timesteps) requires access to the previous wall shapes. In the non-FSI problem discussed earlier, the wall shape was given analytically and could therefore be evaluated at arbitrary times. In the FSI problem considered here, the previous wall shape is not available as the previous positions of the
SolidNodes are not required (and are therefore not stored) for the solution of the (steady!) wall equations.
The solution to the problem is simple: Recall that the final entry in the argument list of
oomph-lib's mesh constructors specifies the
TimeStepper to be used for the evaluation of any time-derivatives. The
TimeStepper's member function
TimeStepper::ntstorage() specifies the total number of values (the current value plus the number of history values) required to evaluate the time-derivatives; it is used by the
FiniteElement::construct_node(...) function to create the required amount of storage at the elements'
Nodes when the
Nodes are created in the mesh constructor. To maximise the potential for code-reuse, we always provide a default argument for the pointer to the
TimeStepper – a pointer to a static instantiation of
Steady<0>. This ensures that the "user" can use the mesh for steady problems without having to artificially create a dummy
TimeStepper that would be completely irrelevant for his/her problem.
For instance, the full interface to the constructor of the
OneDLagrangianMesh, defined in one_d_lagrangian_mesh.template.h is given by
Thus, when we constructed the wall mesh in the non-adaptive version of the driver code fsi_collapsible_channel.cc, using the statements
the use of the dummy
Steady<0> was implied. All time-derivatives computed by this
TimeStepper evaluate to zero, and the
TimeStepper does not require (or request) any storage for history values. This is a sensible default for problems that are either inherently steady (such as problems involving the Poisson equations, say) or for steady versions of time-dependent PDEs (such as the steady Navier-Stokes equations). In the present problem, we wish to retain the dummy character of the
TimeStepper so that all time-derivatives in the
FSIHermiteBeamElements are set to zero, while retaining a limited history of the
SolidNode's previous positions so that the wall shape at previous timesteps can be evaluated. This is possible by creating a
Steady timestepper with a non-zero template argument: The class
provides a dummy
TimeStepper that requires (and maintains)
NSTEPS history values that represent the nodal positions (or nodal values) at
NSTEPS previous timesteps. However, these history values are not used to evaluate any time-derivatives – all time-derivatives computed by this
TimeStepper are zero.
If the Navier-Stokes equations are discretised with a
BDF<2> timestepper, the evaluation of the mesh velocity in the ALE representation of the time-derivatives requires the nodal position at the two previous timesteps. This is achieved by passing a pointer to a specifically-constructed
Steady<2> timestepper to the wall mesh. Here is the relevant code fragment from the Problem constructor in the driver code fsi_collapsible_channel_adapt.cc:
When discussing the non-FSI version of the collapsible channel problem we explained how
oomph-lib's mesh adaptation procedures assign the node-update data for newly-created
AlgebraicNodes. Recall that the node-update data comprises:
AlgebraicMeshthat implements the node-update function.
AlgebraicMeshare updated by different node-update functions. The ID has a default value of 0; this is used if there is only a single node-update function, as in the
GeomObjectsthat are involved in the node update.
By default, we assume that a newly-created
AlgebraicNode is updated by the same node-update function as the
AlgebraicNodes in its father element. Therefore we pass the pointer to the
AlgebraicMesh, the node-update function ID, and the vector of pointers to
GeomObjects to the newly-created
AlgebraicNodes, and interpolate the reference values between those stored at the
AlgebraicNodes in the father elements.
In most cases this provides a sensible default. For instance, it is hard to imagine a situation in which it would be sensible to update the position of newly-created
AlgebraicNodes by a procedure that differs from that used for the surrounding
AlgebraicNodes that already existed in the father element. Similarly, since the reference values vary from node to node (if they were constant we would not store them in the
AlgebraicNodes' node-update data but in the
AlgebraicMesh that implements the node update!) it makes sense to assign the values at newly-created
AlgebraicNodes by interpolation. For instance, in the
AlgebraicCollapsibleChannelMesh one of the reference values is the - coordinate of the reference point on the fixed lower wall. For the
AlgebraicNodes that already existed in the coarse base mesh, this value is given by the the
AlgebraicNodes' - coordinate in the undeformed mesh. Interpolation of this value for the newly-created
AlgebraicNodes results in an axially uniform subdivision of the refined elements.
The same procedure may be used to assign the reference value that represents the intrinsic coordinate of the reference point on the upper wall – at least as long as the upper wall is only ever addressed as a compound
GeomObject, as in our original (slow!) code that employed a
MacroElement - based node update. The procedure is illustrated in the sketch below: The upper wall is parametrised by a compound
GeomObject in which the beam's Lagrangian coordinate doubles as the
GeomObject's intrinsic coordinate The green arrows indicate the reference points for nodes I, II, III, IV and V in the coarse initial mesh. The reference values are stored in the node-update data of nodes I,...,V, respectively. The red arrow identifies the reference point for the newly-created node VI whose reference coordinate is created by interpolation between the reference values of nodes II, III, IV and V, i.e. the nodes in its father element.
Unfortunately, the default assignment is not appropriate for nodes that are updated by the (much faster) algebraic node update procedure implemented in the
AlgebraicNodes store pointers to the sub-
GeomObjects (i.e. the
FSIHermiteBeamElements in the wall mesh) that contain their reference points, and the values of the local coordinate at which the reference points are located. This is illustrated in the sketch below in which the sub-
GeomObjects, parametrised by their local coordinates are shown in magenta. Note that the reference points for nodes II and IV are located in one sub-
GeomObject, those for nodes III and V are located in another.
It obviously does not make sense to create the reference value for the newly-created node VI by interpolation. The node update data must be created from scratch in two steps:
MeshAsGeomObject(i.e. the continuous beam's Lagrangian coordinate), by interpolation. (Recall that the
AlgebraicNodesin the non-refineable
AlgebraicCollapsibleChannelMeshalready stored this coordinate, even though it was not used during the node-update itself).
GeomObject::locate_zeta(...)function to determine sub-
GeomObjectand the local coordinate within it, at which the reference point with Lagrangian coordinate is located.
To ensure that this procedure is performed automatically after every mesh adaptation, it should be implemented in the function
AlgebraicMesh::update_node_update(...). This function is defined as a pure virtual function in the
AlgebraicMesh base class in order to force the mesh writer to assess if the default procedure for the assignment of the node-update data for newly-created
AlgebraicNodes, described above, is appropriate. If it is, the function may, of course, be implemented as an empty function. We note that the function
AlgebraicMesh::update_node_update(...) is called after the default values for the node-update data have been assigned. It is therefore only necessary to correct those values for which the default procedure is inappropriate.
To illustrate the procedure, here is the class definition for the
RefineableAlgebraicCollapsibleChannelMesh. The mesh is derived by multiple inheritance from the non-refineable
AlgebraicCollapsibleChannelMesh and the
RefineableQuadMesh base class. The constructor calls the constructors of both underlying meshes and then sets up the
We overload the (empty) previous implementations of
AlgebraicMesh::update_node_update(...) with our own function:
Here is the actual implementation of this function. We start by extracting the reference values that were already assigned by the default procedure:
Recall from the discussion of the algebraic node-update strategy for the non-refineable version of the problem that reference values 0 and 1 store the - coordinate along the fixed bottom wall, and the fractional height of the node in the cross-channel direction, respectively. These values are interpolated correctly and do not have to be corrected. The third reference value is the intrinsic coordinate of the reference point in its sub-
GeomObject. This needs to be re-computed and we will assign the corrected value below. The fourth reference value is the intrinsic coordinate of the reference point within the compound
MeshAsGeomObject. We store this in a temporary variable:
Next, we extract vector of (pointers to the)
GeomObjects involved in this node's node-update from the node.
Now we use the
GeomObject::locate_zeta(...) function to obtain the pointer to the (sub-)
GeomObject and the intrinsic coordinate within it, at which the reference point (identified by its intrinsic coordinate
zeta in the compound
GeomObject) is located:
We over-write the first (and, in fact, only) entry in the vector of
GeomObjects that are involved in this node's node-update with the pointer to the (sub-)
GeomObject just located:
Similarly, we over-write the third reference value with the local coordinate of the reference point within its (sub-)
The incorrect entries in the two vectors
ref_value have now been corrected. We can wipe the node's node-update data and re-assign it:
The figure below shows a snapshot of the flow field during the early stages of the oscillation. The computation was performed with refineable Crouzeix-Raviart elements, using the
RefineableAlgebraicCollapsibleChannelMesh. Note how the automatic mesh adaptation has refined the mesh in the regions in which the Stokes layers create steep velocity gradients.
The driver code fsi_collapsible_channel_adapt.cc for the spatially adaptive problem is a trivial extension of the non-adaptive code fsi_collapsible_channel.cc, therefore we will not provide a detailed listing here. Comparing the two source codes (e.g. with
sdiff) shows that spatial adaptivity may be enabled with a few straightforward changes:
MacroElementNodeUpdateRefineableCollapsibleChannelMesh(or from the
Problem::actions_after_adapt(); see below.
Steady<2>timestepper for the wall mesh, as discussed above.
As in the non-FSI problem, we use the function
Problem::actions_before_adapt() to delete the applied traction elements before the mesh adaptation:
As usual, we then employ the function
Problem::actions_after_adapt() to re-attach traction elements to the fluid elements that are located at the mesh's inflow boundary (mesh boundary 5) when the mesh adaptation is complete.
Next, we pin the redundant pressure degrees of freedom (see another tutorial for details) and pass the function pointer to the function that defines the prescribed traction to the applied traction elements:
We specify the function
FSI_functions::apply_no_slip_on_moving_wall() as the auxiliary node-update function for all fluid nodes that are located on the FSI boundary (mesh boundary 3) – this ensures that the fluid velocity is updated (via the no-slip condition) whenever the position of a fluid node on this boundary is updated. For fluid nodes that already existed before the mesh adaptation this statement over-writes the function pointers already stored at those nodes. Note the use of compiler flags to distinguish between the two node-update strategies.
Finally, we re-generate the FSI lookup scheme that establishes which fluid elements are located next to the Gauss points in the beam elements. This is necessary because the previous lookup scheme, set up in the problem constructor, becomes invalid if any of the fluid elements next the wall are split during the refinement process.
doc_solution(...)outputs the wall shape at the present and the two previous timesteps: The output file
walli-j.at the i - th timestep and contains the wall shape at the j - th previous timestep. To check that the
Steady<2>timestepper correctly maintains the time-history of the wall displacement field, confirm that
wall3-2.datis identical to
Steady<2>timestepper is not specified explicitly. [Hint: Unless you have compiled the library with
-DRANGE_CHECKING, the code will die with a segmentation fault – use the debugger to determine where the segmentation fault occurs and explain what goes wrong.]
MacroElementNodeUpdateMeshesdo not require a
AlgebraicCollapsibleChannelMesh::update_node_update(...)is not overloaded in the derived refineable mesh
RefineableAlgebraicCollapsibleChannelMesh. [Hint: Inspect the plot of the initial conditions in the output file
soln0.datto see how the uniform refinement performed in the problem constructor fails if the function
RefineableAlgebraicCollapsibleChannelMesh::update_node_update(...)is not executed.]
A pdf version of this document is available.