[petsc-users] Periodic BC with AMR

[Daniil Svyatsky]

Dear petsc developers and users,

I'm trying to set up a periodic BC on a mesh obtained by AMR  technique.
I have a problem accessing the real coordinates of nodes on the periodic
boundary.

First, I generated a box mesh and apply periodic BC:

 bc_cond[0] = DM_BOUNDARY_PERIODIC;

 bc_cond[1] = DM_BOUNDARY_PERIODIC;

 bc_cond[2] = DM_BOUNDARY_PERIODIC;


 DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_FALSE,

                      num_faces, lower_cor, top_cor, bc_cond, interpolate,
&(dm));

  DM               baseParallel;

  PetscPartitioner part;


  ierr = DMPlexGetPartitioner(dm,&part);CHKERRQ(ierr);

  ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);

  ierr = DMPlexDistribute(dm,0,NULL,&baseParallel);CHKERRQ(ierr);

  if (baseParallel) {

    ierr = DMDestroy(&(dm));CHKERRQ(ierr);

    dm = baseParallel;

  }



 After this step I can access coordinates of boundary nodes correctly.
Then I applied AMR on this mesh:

    DM   preForest, postForest;

    DMLabel adaptLabel = NULL;


    ierr = DMCreate(PETSC_COMM_SELF, &preForest);CHKERRQ(ierr);

    ierr = DMSetType(preForest,(dim == 2) ? DMP4EST :
DMP8EST);CHKERRQ(ierr);

    ierr = DMForestSetBaseDM(preForest,env->dstruct->dm);CHKERRQ(ierr);

    ierr = DMForestSetMinimumRefinement(preForest,0);CHKERRQ(ierr);

    ierr = DMForestSetInitialRefinement(preForest,0);CHKERRQ(ierr);

    ierr = DMSetFromOptions(preForest);CHKERRQ(ierr);

    ierr = DMSetUp(preForest);CHKERRQ(ierr);


    ierr = CreateAdaptivityLabel(env,preForest,&adaptLabel);CHKERRQ(ierr);

    ierr = DMForestTemplate(preForest,PETSC_COMM_SELF,
&postForest);CHKERRQ(ierr);

    ierr = DMForestSetAdaptivityLabel(postForest,adaptLabel);CHKERRQ(ierr);

    ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr);

    ierr = DMSetUp(postForest);CHKERRQ(ierr);


    DM dmConv;

    ierr = DMConvert(postForest,DMPLEX,&dmConv);CHKERRQ(ierr);



    if (dmConv){

      DMDestroy(&dm);

      dm = dmConv;

    }

In my example,  boundary cells were also refined. After AMR I have a
problem accessing the coordinates of nodes.
To access node coordinates I do the following:

  DMGetCoordinatesLocal(dm, &coordinates);

  DMGetCoordinateDM(dm, &cdm);

  DMGetSection(cdm, &cs);


  for (cell = cStart; cell < cEnd; ++cell) {

    PetscInt numFaces;

    const PetscInt *faces;

    ierr = DMPlexGetConeSize(dm, cell, &numFaces);

    ierr = DMPlexGetCone(dm, cell, &faces);

    for (int f = 0; f<numFaces; f++){

      temp_f = NULL;

      DMPlexVecGetClosure(dm, cs, coordinates, faces[f], &fsize, &temp_f);

      for (p=0; p<fsize;p+=dim){

         DMLocalizeCoordinate(dm, temp_f+p, PETSC_FALSE, coord_p)

      }

    }

  }


coord_p has wrong coordinates either I used PETSC_TRUE or PETSC_FALSE
in DMLocalizeCoordinate.

What am I doing wrong? I'm using petsc-3.14.1 version.
Thank you for your help in advance.

Best regards,
Daniil Svyatsky.
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