Wolfgang, Thanks! I did end up getting it all working and I have now submitted a pull request to dealii.
Thanks again for all the hard work you all have put into this! Best, Sean Johnson On Tuesday, December 10, 2024 at 6:30:14 AM UTC-7 Wolfgang Bangerth wrote: > > 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 > > > > -- > > The deal.II project is located at http://www.dealii.org/ <https:// > > nam10.safelinks.protection.outlook.com/? > > url=http%3A%2F%2Fwww.dealii.org%2F&data=05%7C02%7CWolfgang.Bangerth% > 40colostate.edu > %7C98c10b8299c94e8832dc08dd18a341f1%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638693811665413564%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=oAjy4MZnaqM%2FCKOxcpuTnaJzwWDiSaICKcldkqNcicI%3D&reserved=0> > > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii? > > hl=en <https://nam10.safelinks.protection.outlook.com/? > > url=https%3A%2F%2Fgroups.google.com > %2Fd%2Fforum%2Fdealii%3Fhl%3Den&data=05%7C02%7CWolfgang.Bangerth% > 40colostate.edu > %7C98c10b8299c94e8832dc08dd18a341f1%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638693811665439568%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hgFwYYkb54lIVcVqvK98Zl%2BlTQnfSopvDU01J6f2n60%3D&reserved=0> > > --- > > You received this message because you are subscribed to the Google > Groups > > "deal.II User Group" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to dealii+un...@googlegroups.com > > <mailto:dealii+un...@googlegroups.com>. > > To view this discussion visit https://groups.google.com/d/msgid/dealii/ > > e28280cc-0893-481d-bafa-f5e9c7fac310n%40googlegroups.com <https:// > > nam10.safelinks.protection.outlook.com/? > > url=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fdealii%2Fe28280cc-0893-481d- > > > > > bafa- > > f5e9c7fac310n%2540googlegroups.com > %3Futm_medium%3Demail%26utm_source%3Dfooter&data=05%7C02%7CWolfgang.Bangerth% > 40colostate.edu > %7C98c10b8299c94e8832dc08dd18a341f1%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638693811665457012%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=txgCCeeoByPKMB6JcnE3PzH2fgibyycWVWb4SUXmvDU%3D&reserved=0>. > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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