Sean,
I am not familiar with the matrix-free framework, but I wanted to say that if
you figure out how to make this work, we would certainly very much like it if
you could submit your fixes as a patch to deal.II! It sounds like you're doing
a good job working your way through the code and understanding what needs to
be fixed -- that is work that would be useful for others as well!
Best
Wolfgang
On 12/9/24 15:45, Sean Johnson wrote:
*** Caution: EXTERNAL Sender ***
I misspoke. The first problem isn't line 220 it is around 816.
It didn't fully fix the problem as one of the values was populated with the
wrong value but I would bet this has to do with my renumbering of the Degrees
of Freedom.
On Monday, December 9, 2024 at 2:15:54 PM UTC-7 Sean Johnson wrote:
I have found what I believe to be the cause of the problem. Its in the
dealii file face_setup_internal.h which is inside the matrix_free folder.
To account for adaptive meshes, when creating faces the files checks if
the neighbor has any children to know if it might be further refined. If
so, it then passes through the children of the face and flips a flag on
them. The problem is in 1D the cell does have children; however, the faces
return 0 for the number of children so no flags get flipped. This is all
around line 220 of the file. In addition, the create_face function in the
same file then also needs a slight tweak in the if statement around line
994 that has the condition "cell->level() > neighbor->level()". The else
statement (which will be where a normal 1D adaptive mesh face will go to)
uses a function that is not intended for 1D meshes. I just changed it to
an else if statement that required the dim to be larger than 1.
I am in the process of testing if this works in an actual problem being
solved. Previously, matrix free adaptive meshes just would never evaluate
the integral on faces between different refinement levels which obviously
causes large errors. The solution mentioned above fixed the issue in my
simplest version of the problem script that I provided in the first
message. The script just printed which faces were visited by the the
matrix_free operator and which faces did exist in the dof_handler.
I'll update if it doesn't fully resolve my original issue.
Sean Johnson
On Wednesday, December 4, 2024 at 4:39:56 PM UTC-7 Sean Johnson wrote:
Hey,
Sorry I am still digging through trying to find out why this happens.
I have confirmed that the matrix free operator thinks there are 2
batches of interior faces with the first one containing a pair of
interior faces and the second just containing one face. There are 4
pairs of interior faces so this still implies that deal.ii in matrix
free 1D with an adaptive mesh misses the face between refinement levels.
I was trying to read the code of how the matrix free operator is
initialized but it uses a function called internal_reinit() and I
can't find the actual code defining this function anywhere in
matrix_free.h
Any help would be greatly appreciated.
Thanks,
Sean Johnson
On Wednesday, November 6, 2024 at 5:58:13 PM UTC-7 Sean Johnson wrote:
Wolfgang,
Thanks for responding. Of course I can explain. So as stated my
code creates a mesh from 0 to 16 with 5 cells. First from 0 to 4,
then 4 to 8, then 8 to 12, then 12 to 14, and finally 14 to 16.
The code first outputs all the coordinate of all the face values
just by iterating over them using the dof_handler cell/face
iterator. So it prints:
############# Printing X values of center of faces ################
Face at x_val: 0
Face at x_val: 4
Face at x_val: 4
Face at x_val: 8
Face at x_val: 8
Face at x_val: 12
Face at x_val: 12
Face at x_val: 14
Face at x_val: 14
Face at x_val: 16
Then, it creates a matrix free operator and goes through applying
the matrix free operator to a vector of zeros. The matrix free
operator is built to do nothing for the cell and boundary face
loops. However, for the interior face loops it is just supposed to
print the coordinates of the quadrature points (since the face is
just a point in 1D it should print the coordinate of the face).
What it prints is:
#######################################################
Matrix Free Face Iteration
#######################################################
x_val: 4
x_val: 8
x_val: 14
x_val: 14
Then just to verify that the matrix free operator didn't change
anything and I didn't have stray code changing anything I repeat
the first part of the code that uses the dof_handler and it prints
the exact same thing.
So what I expect to be different is this second part with the
matrix free operator. I would expect it to print:
#######################################################
Matrix Free Face Iteration
#######################################################
x_val: 4
x_val: 8
x_val: 12
x_val: 14
Or basically to have "x_val: 12" anywhere in this section because
12 is the coordinate of an interior face of the mesh and is not
currently included in the output of the code.. This only happens
at the face between two cells of different refinement levels and
only in 1D from my testing.
Thanks for your time,
Sean Johnson
On Wednesday, November 6, 2024 at 4:54:32 PM UTC-7 Wolfgang
Bangerth wrote:
On 11/5/24 13:53, Sean Johnson wrote:
>
> In 1D for adaptive meshes, the matrix free operator is not
iterating
> over the face/point that is between refinement levels.
>
> I attached a code that basically just makes a mesh and
refines the last
> cell. I use the dof_handler to print out all the
coordinates of the
> faces. It does iterate over all the faces. However, the
matrix free
> operator in its face iterator doesn't recognize the point
between
> refinement levels as a face so I have it print out all the
coordinates
> of faces and its obviously missing one.
>
> The "mesh" is just a line from [0,16]. First it is divided
into 4 cells.
> Then the final cell is further refined so there should be
faces at:
> 0,4,8,12,14,16.
>
> Again, feel free to correct me if I made a dumb mistake
somewhere, but I
> did try the code in 2D and there were no problems there.
The code is
> super simplistic and will not give you enough information
about
> coordinates if you step up to 3D.
Sean:
I don't know much about the matrix-fee framework, and so can't
say much
about whether it does what it's supposed to -- someone else
will have to
chime in here.
But can you describe what the code you attach outputs, and how
that
differs from what you *expect* it to output? It's often
difficult for
those who didn't write the code to say what is expected, and
how what
you get differs from the expectation.
Best
WB
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