On Wed, Mar 6, 2024 at 5:44 PM Adrian Croucher <a.crouc...@auckland.ac.nz> wrote:
> hi Matt, > On 7/03/24 2:55 am, Matthew Knepley wrote: > > Let's do this. Can you send me a dual porosity mesh, and I will figure out > why the stratification > algorithm does not work? I think you can just output the Plex as binary or > HDF5, but you could > also give me code that makes one. > > OK, I've attached an example dual porosity / MINC DM, output before the > attempted redistribution. > > The original mesh is a vertical column of 11 hexahedral cells. Six of the > cells (2 - 7) have two levels of interior MINC cells added (i.e. an > interior cell, and then another interior cell inside that). So there are a > total of 11 + 2*6 = 23 cells. The DM was distributed over two processes. > > For each extra interior face I also create one interior edge and one > interior vertex. I give the interior vertices arbitrary (0,0,0) locations. > I assign all the extra interior DM points (cells, vertices, faces, edges) > cell type DM_POLYTOPE_INTERIOR_GHOST. > > Okay, here are my first steps 1. I fixed the problem with repeated stratification knepley/fix-da-periodicity *$:/PETSc3/petsc/petsc-dev$ git diff diff --git a/src/dm/impls/plex/plex.c b/src/dm/impls/plex/plex.c index 0ffc372ea08..9d27d308538 100644 --- a/src/dm/impls/plex/plex.c +++ b/src/dm/impls/plex/plex.c @@ -4439,6 +4439,7 @@ PetscErrorCode DMPlexStratify(DM dm) PetscCall(PetscLogEventBegin(DMPLEX_Stratify, dm, 0, 0, 0)); // Create depth label + PetscCall(DMRemoveLabel(dm, "depth", NULL)); PetscCall(DMCreateLabel(dm, "depth")); PetscCall(DMPlexGetDepthLabel(dm, &label)); I put it in an MR: https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7347__;!!G_uCfscf7eWS!akE1sOGj7q57_P3AdMmPLRvCeEmgzsdIGxognMBQWmrcCwBpjPGdMYH9Z9FEokIWKyOyOXJH7cBRBon3iXCi$ 2. I wrote a small program to load the mesh, and then restratify it. It is attached. 3. I ran stratification on this mesh, but I did not get an error: master *:~/Downloads/tmp/Adrian$ ./minc -dm_plex_filename minc_dm.h5 -dm_view DM Object: 1 MPI process type: plex DM_0x84000000_0 in 3 dimensions: Number of 0-cells per rank: 60 (12) Number of 1-cells per rank: 104 (12) Number of 2-cells per rank: 68 (12) Number of 3-cells per rank: 23 (12) Labels: depth: 4 strata with value/size (0 (60), 1 (104), 2 (68), 3 (23)) Cell Sets: 1 strata with value/size (0 (11)) boundary: 1 strata with value/size (1 (46)) celltype: 5 strata with value/size (0 (48), 1 (92), 13 (48), 4 (56), 7 (11)) ghost: 1 strata with value/size (1 (46)) minc_level: 3 strata with value/size (0 (6), 1 (6), 2 (6)) minc_rocktype_zone: 1 strata with value/size (1 (6)) minc_zone: 1 strata with value/size (1 (6)) open_boundary: 1 strata with value/size (1 (1)) rock_type: 2 strata with value/size (1 (5), 3 (6)) source: 2 strata with value/size (0 (1), 1 (1)) vtk: 1 strata with value/size (1 (11)) zone_minc: 1 strata with value/size (1 (6)) DM Object: DM_0x84000000_0 1 MPI process type: plex DM_0x84000000_0 in 3 dimensions: Number of 0-cells per rank: 60 (12) Number of 1-cells per rank: 104 (12) Number of 2-cells per rank: 68 (12) Number of 3-cells per rank: 23 (12) Labels: Cell Sets: 1 strata with value/size (0 (11)) boundary: 1 strata with value/size (1 (46)) celltype: 5 strata with value/size (0 (48), 1 (92), 13 (48), 4 (56), 7 (11)) ghost: 1 strata with value/size (1 (46)) minc_level: 3 strata with value/size (0 (6), 1 (6), 2 (6)) minc_rocktype_zone: 1 strata with value/size (1 (6)) minc_zone: 1 strata with value/size (1 (6)) open_boundary: 1 strata with value/size (1 (1)) rock_type: 2 strata with value/size (1 (5), 3 (6)) source: 2 strata with value/size (0 (1), 1 (1)) vtk: 1 strata with value/size (1 (11)) zone_minc: 1 strata with value/size (1 (6)) depth: 4 strata with value/size (0 (60), 1 (104), 2 (68), 3 (23)) > - Adrian > > -- > Dr Adrian Croucher > Senior Research Fellow > Department of Engineering Science > Waipapa Taumata Rau / University of Auckland, New Zealand > email: a.crouc...@auckland.ac.nz > tel: +64 (0)9 923 4611 > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!akE1sOGj7q57_P3AdMmPLRvCeEmgzsdIGxognMBQWmrcCwBpjPGdMYH9Z9FEokIWKyOyOXJH7cBRBlTTBnv2$ <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!akE1sOGj7q57_P3AdMmPLRvCeEmgzsdIGxognMBQWmrcCwBpjPGdMYH9Z9FEokIWKyOyOXJH7cBRBjxEQXbi$ >
minc.c
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