impls/moab/dmmbmg.cxx

#include <petsc/private/dmmbimpl.h>
#include <petscdmmoab.h>
#include <MBTagConventions.hpp>
#include <moab/NestedRefine.hpp>

#undef __FUNCT__
#define __FUNCT__ "DMMoabGenerateHierarchy"
/*@
  DMMoabGenerateHierarchy - Generate a multi-level uniform refinement hierarchy
  by succesively refining a coarse mesh, already defined in the DM object
  provided by the user.

  Collective on MPI_Comm

  Input Parameter:
+ dmb  - The DMMoab object

  Output Parameter:
+ nlevels   - The number of levels of refinement needed to generate the hierarchy
. ldegrees  - The degree of refinement at each level in the hierarchy

  Level: beginner

.keywords: DMMoab, create, refinement
@*/
PetscErrorCode DMMoabGenerateHierarchy(DM dm,PetscInt nlevels,PetscInt *ldegrees)
{
  DM_Moab        *dmmoab;
  PetscErrorCode  ierr;
  moab::ErrorCode merr;
  PetscInt *pdegrees,i;
  std::vector<moab::EntityHandle> hsets;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);
  dmmoab = (DM_Moab*)(dm)->data;

  if (!ldegrees) {
    ierr = PetscMalloc1(nlevels,&pdegrees);CHKERRQ(ierr);
    for (i=0; i<nlevels; i++) pdegrees[i]=2; /* default = Degree 2 refinement */
  }
  else pdegrees=ldegrees;

  /* initialize set level refinement data for hierarchy */
  dmmoab->nhlevels=nlevels;

  /* Instantiate the nested refinement class */
  dmmoab->hierarchy = new moab::NestedRefine(dynamic_cast<moab::Core*>(dmmoab->mbiface), dmmoab->pcomm, dmmoab->fileset);

  ierr = PetscMalloc1(nlevels+1,&dmmoab->hsets);CHKERRQ(ierr);

  /* generate the mesh hierarchy */
  merr = dmmoab->hierarchy->generate_mesh_hierarchy(nlevels, pdegrees, hsets);MBERRNM(merr);

  if (dmmoab->pcomm->size() > 1) {
    merr = dmmoab->hierarchy->exchange_ghosts(hsets, dmmoab->nghostrings);MBERRNM(merr);
  }

  /* copy the mesh sets for nested refinement hierarchy */
  for (i=0; i<=nlevels; i++)
    dmmoab->hsets[i]=hsets[i];

  hsets.clear();
  if (!ldegrees) {
    ierr = PetscFree(pdegrees);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMRefineHierarchy_Moab"
/*@
  DMRefineHierarchy_Moab - Generate a multi-level DM hierarchy
  by succesively refining a coarse mesh.

  Collective on MPI_Comm

  Input Parameter:
+ dm  - The DMMoab object

  Output Parameter:
+ nlevels   - The number of levels of refinement needed to generate the hierarchy
. dmf  - The DM objects after successive refinement of the hierarchy

  Level: beginner

.keywords: DMMoab, generate, refinement
@*/
PetscErrorCode  DMRefineHierarchy_Moab(DM dm,PetscInt nlevels,DM dmf[])
{
  PetscErrorCode  ierr;
  PetscInt        i;

  PetscFunctionBegin;

  ierr = DMRefine(dm,PetscObjectComm((PetscObject)dm),&dmf[0]);CHKERRQ(ierr);
  for (i=1; i<nlevels; i++) {
    ierr = DMRefine(dmf[i-1],PetscObjectComm((PetscObject)dm),&dmf[i]);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMCoarsenHierarchy_Moab"
/*@
  DMCoarsenHierarchy_Moab - Generate a multi-level DM hierarchy
  by succesively coarsening a refined mesh.

  Collective on MPI_Comm

  Input Parameter:
+ dm  - The DMMoab object

  Output Parameter:
+ nlevels   - The number of levels of refinement needed to generate the hierarchy
. dmc  - The DM objects after successive coarsening of the hierarchy

  Level: beginner

.keywords: DMMoab, generate, coarsening
@*/
PetscErrorCode DMCoarsenHierarchy_Moab(DM dm,PetscInt nlevels,DM dmc[])
{
  PetscErrorCode  ierr;
  PetscInt        i;

  PetscFunctionBegin;

  ierr = DMCoarsen(dm,PetscObjectComm((PetscObject)dm),&dmc[0]);CHKERRQ(ierr);
  for (i=1; i<nlevels; i++) {
    ierr = DMCoarsen(dmc[i-1],PetscObjectComm((PetscObject)dm),&dmc[i]);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMCreateInterpolation_Moab"
/*@
  DMCreateInterpolation_Moab - Generate the interpolation operators to transform
  operators (matrices, vectors) from parent level to child level as defined by
  the DM inputs provided by the user.

  Collective on MPI_Comm

  Input Parameter:
+ dm1  - The DMMoab object
- dm2  - the second, finer DMMoab object

  Output Parameter:
+ interpl  - The interpolation operator for transferring data between the levels
- vec      - The scaling vector (optional)

  Level: developer

.keywords: DMMoab, create, refinement
@*/
PetscErrorCode DMCreateInterpolation_Moab(DM dmp,DM dmc,Mat* interpl,Vec* vec)
{
  DM_Moab         *dmbp, *dmbc;
  PetscErrorCode   ierr;
  moab::ErrorCode  merr;
  PetscInt         dim;
  PetscReal        factor;
  PetscInt         innz, *nnz, ionz, *onz;
  PetscInt         nlsizp, nlsizc, nlghsizp, ngsizp, ngsizc;
  moab::Range      eowned;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dmp,DM_CLASSID,1);
  PetscValidHeaderSpecific(dmc,DM_CLASSID,2);
  dmbp = (DM_Moab*)(dmp)->data;
  dmbc = (DM_Moab*)(dmc)->data;
  nlsizp = dmbp->nloc;// *dmb1->numFields;
  nlsizc = dmbc->nloc;// *dmb2->numFields;
  ngsizp = dmbp->n; // *dmb1->numFields;
  ngsizc = dmbc->n; // *dmb2->numFields;
  nlghsizp = (dmbp->nloc+dmbp->nghost); // *dmb1->numFields;

  // Interpolation matrix: \sum_{i=1}^P Owned(Child) * (Owned(Parent) + Ghosted(Parent))
  // Size: nlsizc * nlghsizp
  PetscInfo4(NULL,"Creating interpolation matrix %D X %D to apply transformation between levels %D -> %D.\n",ngsizc,nlghsizp,dmbp->hlevel,dmbc->hlevel);

  /* allocate the nnz, onz arrays based on block size and local nodes */
  ierr = PetscCalloc2(nlsizc,&nnz,nlsizc,&onz);CHKERRQ(ierr);

  eowned = *dmbp->elocal;
  merr = dmbp->pcomm->filter_pstatus(eowned,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
  /* Loop through the local elements and compute the relation between the current parent and the refined_level. */
  for(moab::Range::iterator iter = eowned.begin(); iter!= eowned.end(); iter++) {

    const moab::EntityHandle ehandle = *iter;
    std::vector<moab::EntityHandle> children;
    std::vector<moab::EntityHandle> connp, connc;
    moab::Range connc_owned;

    /* Get the relation between the current (coarse) parent and its corresponding (finer) children elements */
    merr = dmbp->hierarchy->parent_to_child(ehandle, dmbp->hlevel, dmbc->hlevel, children);MBERRNM(merr);

    /* Get connectivity of the parent elements */
    //merr = dmb1->mbiface->get_connectivity(ehandle,connect,vpere,false);MBERRNM(merr);
    merr = dmbp->hierarchy->get_connectivity(ehandle, dmbp->hlevel, connp);MBERRNM(merr);
    merr = dmbc->mbiface->get_connectivity(&children[0], children.size(), connc_owned);MBERRNM(merr);
    merr = dmbc->pcomm->filter_pstatus(connc_owned,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
    for (unsigned tc=0; tc<connc_owned.size(); tc++) {
      connc.push_back(connc_owned[tc]);
    }

    std::vector<int> dofsp(connp.size()), dofsc(connc.size());
    /* get DoFs for both coarse and fine scale grid */
    ierr = DMMoabGetDofsBlockedLocal(dmp, connp.size(), &connp[0], &dofsp[0]);CHKERRQ(ierr);
    ierr = DMMoabGetDofsBlockedLocal(dmc, connc.size(), &connc[0], &dofsc[0]);CHKERRQ(ierr);

    for (unsigned tp=0;tp<connp.size(); tp++) {
      if (dmbp->vowned->find(connp[tp]) != dmbp->vowned->end()) {
        for (unsigned tc=0;tc<connc.size(); tc++) {
          if (dmbc->vowned->find(connc[tc]) != dmbc->vowned->end()) {
            /* FIXME: This will over-allocate since we multi-count shared nodes.
               Disadvantage of using element traversal for nnz computation. */
            nnz[dofsc[tc]]++;
          }
        }
      }
      else if (dmbp->vghost->find(connp[tp]) != dmbp->vghost->end()) {
        for (unsigned tc=0;tc<connc.size(); tc++) {
          if (dmbc->vowned->find(connc[tc]) != dmbc->vowned->end()) {
            /* FIXME: This will over-allocate since we multi-count shared nodes.
               Disadvantage of using element traversal for nnz computation. */
            onz[dofsc[tc]]++;
          }
        }
      }
      else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Invalid entity in child level %D\n", connp[tp]);
    }
  }

  ionz=onz[0];
  innz=nnz[0];
  for (int tc=0; tc < nlsizc; tc++) {
    // check for maximum allowed sparsity = fully dense
    nnz[tc] = std::min(nlsizp,nnz[tc]);
    onz[tc] = std::min(nlghsizp-nlsizp,onz[tc]);

    innz = (innz < nnz[tc] ? nnz[tc] : innz);
    ionz = (ionz < onz[tc] ? onz[tc] : ionz);
  }

  /* create interpolation matrix */
  ierr = MatCreate(PetscObjectComm((PetscObject)dmc), interpl);CHKERRQ(ierr);
  ierr = MatSetSizes(*interpl, nlsizc, nlsizp, ngsizc, ngsizp);CHKERRQ(ierr);
  //ierr = MatSetType(*interpl, dm1->mattype);CHKERRQ(ierr);
  ierr = MatSetType(*interpl,MATAIJ);CHKERRQ(ierr);
  ierr = MatSetFromOptions(*interpl);CHKERRQ(ierr);

  ierr = MatSeqAIJSetPreallocation(*interpl,innz,nnz);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(*interpl,innz,nnz,ionz,onz);CHKERRQ(ierr);

  /* clean up temporary memory */
  ierr = PetscFree2(nnz,onz);CHKERRQ(ierr);

  /* set up internal matrix data-structures */
  ierr = MatSetUp(*interpl);CHKERRQ(ierr);

  /* TODO: Decipher the correct non-zero pattern. There is still some issue with onz allocation */
  // ierr = MatSetOption(*interpl, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr);

  ierr = DMGetDimension(dmp, &dim);CHKERRQ(ierr);

  factor = std::pow(2.0 /*degree_P_for_refinement*/,(dmbc->hlevel-dmbp->hlevel)*dmbp->dim*1.0);

  /* Loop through the remaining vertices. These vertices appear only on the current refined_level. */
  for(moab::Range::iterator iter = eowned.begin(); iter!= eowned.end(); iter++) {

    const moab::EntityHandle ehandle = *iter;
    std::vector<moab::EntityHandle> children;
    std::vector<moab::EntityHandle> connp, connc;
    moab::Range connc_owned;

    /* Get the relation between the current (coarse) parent and its corresponding (finer) children elements */
    merr = dmbp->hierarchy->parent_to_child(ehandle, dmbp->hlevel, dmbc->hlevel, children);MBERRNM(merr);

    /* Get connectivity and coordinates of the parent vertices */
    merr = dmbp->hierarchy->get_connectivity(ehandle, dmbp->hlevel, connp);MBERRNM(merr);
    merr = dmbc->mbiface->get_connectivity(&children[0], children.size(), connc_owned);MBERRNM(merr);
    merr = dmbc->pcomm->filter_pstatus(connc_owned,PSTATUS_NOT_OWNED,PSTATUS_NOT);MBERRNM(merr);
    for (unsigned tc=0; tc<connc_owned.size(); tc++) {
      connc.push_back(connc_owned[tc]);
    }

    std::vector<double> pcoords(connp.size()*3), ccoords(connc.size()*3), values_phi(connc.size());
    /* Get coordinates for connectivity entities in canonical order for both coarse and finer levels */
    merr = dmbp->hierarchy->get_coordinates(&connp[0], connp.size(), dmbp->hlevel, &pcoords[0]);MBERRNM(merr);
    merr = dmbc->hierarchy->get_coordinates(&connc[0], connc.size(), dmbc->hlevel, &ccoords[0]);MBERRNM(merr);

    std::vector<int> dofsp(connp.size()), dofsc(connc.size());
    /* TODO: specific to scalar system - use GetDofs */
    ierr = DMMoabGetDofsBlocked(dmp, connp.size(), &connp[0], &dofsp[0]);CHKERRQ(ierr);
    ierr = DMMoabGetDofsBlocked(dmc, connc.size(), &connc[0], &dofsc[0]);CHKERRQ(ierr);

    /* Compute the interpolation weights by determining distance of 1-ring
       neighbor vertices from current vertex

       TODO: This needs to be replaced with a consistent interface to compute
       the basis function interpolation between the levels evaluated correctly.
       RBF basis will be terrible for any unsmooth problems..
       -- NEEDS TO BE REMOVED --
    */
    values_phi.resize(connp.size());
    for (unsigned tc=0;tc<connc.size(); tc++) {

      double normsum=0.0;
      for (unsigned tp=0;tp<connp.size(); tp++) {
        values_phi[tp] = 0.0;
        for (unsigned k=0;k<3; k++)
          values_phi[tp] += std::pow(pcoords[tp*3+k]-ccoords[k+tc*3], dim);
        if (values_phi[tp] < 1e-12) {
          values_phi[tp] = 1e12;
        }
        else {
          //values_phi[tp] = std::pow(values_phi[tp], -1.0/dim);
          values_phi[tp] = std::pow(values_phi[tp], -1.0);
          normsum += values_phi[tp];
        }
      }
      for (unsigned tp=0;tp<connp.size(); tp++) {
        if (values_phi[tp] > 1e11)
          values_phi[tp] = factor*0.5/connp.size();
        else
          values_phi[tp] = factor*values_phi[tp]*0.5/(connp.size()*normsum);
      }
      ierr = MatSetValues(*interpl, 1, &dofsc[tc], connp.size(), &dofsp[0], &values_phi[0], ADD_VALUES);CHKERRQ(ierr);
    }

    //get interpolation weights
    //ierr = Compute_Quad4_Basis(pcoords, 1, coord, values_phi);CHKERRQ(ierr);
    // for (int j=0;j<dofs_per_element; j++)
    //  std::cout<<"values "<<values_phi[j]<<std::endl;

  }

  ierr = MatAssemblyBegin(*interpl,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(*interpl,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMCreateInjection_Moab"
/*@
  DMCreateInjection_Moab - Generate a multi-level uniform refinement hierarchy
  by succesively refining a coarse mesh, already defined in the DM object
  provided by the user.

  Collective on MPI_Comm

  Input Parameter:
. dmb  - The DMMoab object

  Output Parameter:
. nlevels   - The number of levels of refinement needed to generate the hierarchy
+ ldegrees  - The degree of refinement at each level in the hierarchy

  Level: beginner

.keywords: DMMoab, create, refinement
@*/
PetscErrorCode DMCreateInjection_Moab(DM dm1,DM dm2,VecScatter* ctx)
{
  //DM_Moab        *dmmoab;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm1,DM_CLASSID,1);
  PetscValidHeaderSpecific(dm2,DM_CLASSID,2);
  //dmmoab = (DM_Moab*)(dm1)->data;

  PetscPrintf(PETSC_COMM_WORLD, "[DMCreateInjection_Moab] :: Placeholder\n");
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DM_UMR_Moab_Private"
PetscErrorCode  DM_UMR_Moab_Private(DM dm,MPI_Comm comm,PetscBool refine,DM *dmref)
{
  PetscErrorCode  ierr;
  PetscInt        i,dim;
  DM              dm2;
  moab::ErrorCode merr;
  DM_Moab        *dmb = (DM_Moab*)dm->data,*dd2;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);
  PetscValidPointer(dmref,4);

  if ( (dmb->hlevel == dmb->nhlevels && refine) || (dmb->hlevel == 0 && !refine) ) {
    if (dmb->hlevel+1 > dmb->nhlevels && refine) PetscInfo2(NULL,"Invalid multigrid refinement hierarchy level specified (%D). MOAB UMR max levels = %D. Creating a NULL object.\n",dmb->hlevel+1,dmb->nhlevels);
    if (dmb->hlevel-1 < 0 && !refine) PetscInfo1(NULL,"Invalid multigrid coarsen hierarchy level specified (%D). Creating a NULL object.\n",dmb->hlevel-1);
    *dmref = PETSC_NULL;
    PetscFunctionReturn(0);
  }

  ierr = DMMoabCreate(PetscObjectComm((PetscObject)dm), &dm2);CHKERRQ(ierr);
  dd2 = (DM_Moab*)dm2->data;

  dd2->mbiface = dmb->mbiface;
  dd2->pcomm = dmb->pcomm;
  dd2->icreatedinstance = PETSC_FALSE;
  dd2->nghostrings=dmb->nghostrings;

  /* set the new level based on refinement/coarsening */
  if (refine) {
    dd2->hlevel=dmb->hlevel+1;
  }
  else {
    dd2->hlevel=dmb->hlevel-1;
  }

  /* Copy the multilevel hierarchy pointers in MOAB */
  dd2->hierarchy = dmb->hierarchy;
  dd2->nhlevels = dmb->nhlevels;
  ierr = PetscMalloc1(dd2->nhlevels+1,&dd2->hsets);CHKERRQ(ierr);
  for (i=0; i<=dd2->nhlevels; i++) {
    dd2->hsets[i]=dmb->hsets[i];
  }
  dd2->fileset = dd2->hsets[dd2->hlevel];

  /* do the remaining initializations for DMMoab */
  dd2->bs = dmb->bs;
  dd2->numFields = dmb->numFields;
  dd2->rw_dbglevel = dmb->rw_dbglevel;
  dd2->partition_by_rank = dmb->partition_by_rank;
  ierr = PetscStrcpy(dd2->extra_read_options, dmb->extra_read_options);CHKERRQ(ierr);
  ierr = PetscStrcpy(dd2->extra_write_options, dmb->extra_write_options);CHKERRQ(ierr);
  dd2->read_mode = dmb->read_mode;
  dd2->write_mode = dmb->write_mode;

  /* set global ID tag handle */
  ierr = DMMoabSetLocalToGlobalTag(dm2, dmb->ltog_tag);CHKERRQ(ierr);

  merr = dd2->mbiface->tag_get_handle(MATERIAL_SET_TAG_NAME, dd2->material_tag);MBERRNM(merr);

  ierr = DMSetOptionsPrefix(dm2,((PetscObject)dm)->prefix);CHKERRQ(ierr);
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMSetDimension(dm2,dim);CHKERRQ(ierr);

  /* allow overloaded (user replaced) operations to be inherited by refinement clones */
  dm2->ops->creatematrix = dm->ops->creatematrix;

  /* copy fill information if given */
  ierr = DMMoabSetBlockFills(dm2, dmb->dfill, dmb->ofill);CHKERRQ(ierr);

  /* copy vector type information */
  ierr = DMSetMatType(dm2,dm->mattype);CHKERRQ(ierr);
  ierr = DMSetVecType(dm2,dm->vectype);CHKERRQ(ierr);
  dd2->numFields = dmb->numFields;
  if (dmb->numFields) {
    ierr = DMMoabSetFieldNames(dm2,dmb->numFields,dmb->fieldNames);CHKERRQ(ierr);
  }

  ierr = DMSetFromOptions(dm2);CHKERRQ(ierr);

  /* recreate Dof numbering for the refined DM and make sure the distribution is correctly populated */
  ierr = DMSetUp(dm2);CHKERRQ(ierr);

  *dmref = dm2;
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMRefine_Moab"
/*@
  DMRefine_Moab - Generate a multi-level uniform refinement hierarchy
  by succesively refining a coarse mesh, already defined in the DM object
  provided by the user.

  Collective on DM

  Input Parameter:
+ dm  - The DMMoab object
- comm - the communicator to contain the new DM object (or MPI_COMM_NULL)

  Output Parameter:
. dmf - the refined DM, or NULL

  Note: If no refinement was done, the return value is NULL

  Level: developer

.keywords: DMMoab, create, refinement
@*/
PetscErrorCode DMRefine_Moab(DM dm,MPI_Comm comm,DM* dmf)
{
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);

  ierr = DM_UMR_Moab_Private(dm,comm,PETSC_TRUE,dmf);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMCoarsen_Moab"
/*@
  DMCoarsen_Moab - Generate a multi-level uniform refinement hierarchy
  by succesively refining a coarse mesh, already defined in the DM object
  provided by the user.

  Collective on DM

  Input Parameter:
. dm  - The DMMoab object
- comm - the communicator to contain the new DM object (or MPI_COMM_NULL)

  Output Parameter:
. dmf - the coarsened DM, or NULL

  Note: If no coarsening was done, the return value is NULL

  Level: developer

.keywords: DMMoab, create, coarsening
@*/
PetscErrorCode DMCoarsen_Moab(DM dm,MPI_Comm comm,DM* dmc)
{
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm,DM_CLASSID,1);

  ierr = DM_UMR_Moab_Private(dm,comm,PETSC_FALSE,dmc);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}