Found no facets matching domain for boundary condition.(TF_csm)

[kvslab]

Found no facets matching domain for boundary condition.(TF_csm)

[jorgensd]

This is down to the numerical accuracy of the mesh.
i.e. this can be reproduced with:

from dolfin import *

mesh = Mesh("TF_cfd.xml.gz")
R = 0.05       # Radius of the circle
c_x = 0.2       # Center of the circle x-direction
c_y = 0.2       # Center of the circle y-direction
mesh = refine(mesh)
Barwall = AutoSubDomain(lambda x: (
    (x[0] - c_x)**2 + (x[1] - c_y)**2 < R**2 + DOLFIN_EPS * 1e8))


def Down(x, on_boundary):
    return near(x[1], 0.19) and on_boundary


def Up(x, on_boundary):
    return near(x[1], 0.21, DOLFIN_EPS) and on_boundary


def Right(x, on_boundary):
    return near(x[0], 0.60) and on_boundary


Downwall = AutoSubDomain(Down)
Upwall = AutoSubDomain(Up)
Rightwall = AutoSubDomain(Right)

boundaries = MeshFunction("size_t", mesh, mesh.geometry().dim() - 1)
boundaries.set_all(0)
#Barwall.mark(boundaries, 1)
#Downwall.mark(boundaries, 2)
Upwall.mark(boundaries, 3)
#Rightwall.mark(boundaries, 4)


File("facet_function.pvd") << boundaries

if you change

def Up(x, on_boundary):
    return near(x[1], 0.21, DOLFIN_EPS) and on_boundary

to

def Up(x, on_boundary):
    return near(x[1], 0.21, 1e8*DOLFIN_EPS) and on_boundary

the boundary will be marked correctly.

Similarly, you should use tolerances for the other near operators

Barwall = AutoSubDomain(lambda x: (
    (x[0] - c_x)**2 + (x[1] - c_y)**2 < R**2 + DOLFIN_EPS * 1e8))


def Down(x, on_boundary):
    return near(x[1], 0.19, DOLFIN_EPS*1e8) and on_boundary


def Up(x, on_boundary):
    return near(x[1], 0.21, DOLFIN_EPS*1e8) and on_boundary


def Right(x, on_boundary):
    return near(x[0], 0.60, DOLFIN_EPS*1e8) and on_boundary

[keiyamamo]

Hi @zhangmuElias

Thank you for supplying the code!
I can see that the top and right boundary cannot be marked for some reason. As you said, I tested the bottom and it worked fine, so there seems to be something wrong with the top and right boundary. Although it is not immediately clear for me if it comes from the original mesh or the way we try to define the boundary...

In fact, the original csm mesh is not actually rectangular (left boundary is curved), but if you only need rectangular domain, I would suggest to use RectangleMesh. If not, I can further try to identify why top and right are not working, so please let me know.

[keiyamamo]

I can see that you're using your own solver. Can you check if the same error happens with the original solver by only changing the way of marking the boundary? If the error happens with the original solver, please post the problem here that can reproduce the error so that I can test it. Without minimum working example, it is hard to debug the code.

[zhangmuElias]

Yes, sure. The same error happens with the original solver by only changing the way of marking the boundary.

hwloc/linux: Ignoring PCI device with non-16bit domain.
Pass --enable-32bits-pci-domain to configure to support such devices
(warning: it would break the library ABI, don't enable unless really needed).
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Compute Jacobian matrix
Newton iteration 0: r (atol) = 2.760e-01 (tol = 1.000e-07), r (rel) = 1.674e-03 (tol = 1.000e-07) 
Newton iteration 1: r (atol) = 1.712e-11 (tol = 1.000e-07), r (rel) = 2.601e-15 (tol = 1.000e-07) 
Distance x: 1.817850e-18
Distance y: -1.000000e-04

Although it will go on calculating, the contour result is wrong.
The not working case file is here, you can run it with original turtleFSI to see the errors.
TF_csm_topfix.txt

I think the proposed TF_csm.xml.gz file has some problems with identifying the top boundary.
Because I tested using different ways to build the mesh for the original TF_CSM case, like:

    p1 = Point(0.25, 0.19)
    p2 = Point(0.6, 0.21)
    mesh = RectangleMesh(p1, p2, 175, 10)

Then the top boundary can be chosen using:

    Barwall = AutoSubDomain(lambda x: (near(x[0], 0.25)))
    Topwall = AutoSubDomain(lambda x: (near(x[1], 0.21)))
    boundaries = MeshFunction("size_t", mesh, mesh.geometry().dim() - 1)
    boundaries.set_all(0)
    Barwall.mark(boundaries, 1)
    Topwall.mark(boundaries, 2)

Then the displacement contour is:

[zhangmuElias]

Dear @keiyamamo
Thank you, RectangleMesh will fit my need for now. I am just testing my code. You don't need to change now. (^_^)
I think it is not an important problem since it goes well for the left fixed condition. And users will use their own mesh files when they solve their own projects.

[zhangmuElias]

Dear @jorgensd

Thank you! I see!