예제 #1
0
파일: virs.c 프로젝트: erdc-cm/petsc-dev
/*
     DMSetVI - Marks a DM as associated with a VI problem. This causes the interpolation/restriction operators to
               be restricted to only those variables NOT associated with active constraints.

*/
PetscErrorCode  DMSetVI(DM dm,IS inactive)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi;

  PetscFunctionBegin;
  if (!dm) PetscFunctionReturn(0);

  ierr = PetscObjectReference((PetscObject)inactive);CHKERRQ(ierr);

  ierr = PetscObjectQuery((PetscObject)dm,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) {
    ierr = PetscContainerCreate(((PetscObject)dm)->comm,&isnes);CHKERRQ(ierr);
    ierr = PetscContainerSetUserDestroy(isnes,(PetscErrorCode (*)(void*))DMDestroy_SNESVI);CHKERRQ(ierr);
    ierr = PetscNew(DM_SNESVI,&dmsnesvi);CHKERRQ(ierr);
    ierr = PetscContainerSetPointer(isnes,(void*)dmsnesvi);CHKERRQ(ierr);
    ierr = PetscObjectCompose((PetscObject)dm,"VI",(PetscObject)isnes);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&isnes);CHKERRQ(ierr);
    dmsnesvi->createinterpolation   = dm->ops->createinterpolation;
    dm->ops->createinterpolation    = DMCreateInterpolation_SNESVI;
    dmsnesvi->coarsen            = dm->ops->coarsen;
    dm->ops->coarsen             = DMCoarsen_SNESVI;
    dmsnesvi->createglobalvector = dm->ops->createglobalvector;
    dm->ops->createglobalvector  = DMCreateGlobalVector_SNESVI;
  } else {
    ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi);CHKERRQ(ierr);
    ierr = ISDestroy(&dmsnesvi->inactive);CHKERRQ(ierr);
  }
  ierr = DMClearGlobalVectors(dm);CHKERRQ(ierr);
  ierr = ISGetLocalSize(inactive,&dmsnesvi->n);CHKERRQ(ierr);
  dmsnesvi->inactive = inactive;
  dmsnesvi->dm       = dm;
  PetscFunctionReturn(0);
}
예제 #2
0
PetscErrorCode private_PetscViewerDestroy_XDMF(PetscViewer *v)
{
  PetscViewer    viewer;
  DM             dm = NULL;
  long int       *bytes;
  PetscContainer container = NULL;
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  if (!v) PetscFunctionReturn(0);
  viewer = *v;
  
  ierr = PetscObjectQuery((PetscObject)viewer,"DMSwarm",(PetscObject*)&dm);CHKERRQ(ierr);
  if (dm) {
    ierr = PetscViewerASCIIPrintf(viewer,"</Grid>\n");CHKERRQ(ierr);
    ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  }
  
  /* close xdmf header */
  ierr = PetscViewerASCIIPrintf(viewer,"</Domain>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Xdmf>\n");CHKERRQ(ierr);
  
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
    ierr = PetscFree(bytes);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&container);CHKERRQ(ierr);
  }
  
  ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
  *v = NULL;
  PetscFunctionReturn(0);
}
예제 #3
0
PetscErrorCode MatMatMultNumeric_MPIAIJ_MPIAIJ(Mat A,Mat B,Mat C)
{
  PetscErrorCode     ierr;
  Mat                *seq;
  Mat_MatMatMultMPI  *mult; 
  PetscContainer     container;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr); 
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }

  seq = &mult->B_seq;
  ierr = MatGetSubMatrices(B,1,&mult->isrowb,&mult->iscolb,MAT_REUSE_MATRIX,&seq);CHKERRQ(ierr);
  mult->B_seq = *seq;
  
  seq = &mult->A_loc;
  ierr = MatGetSubMatrices(A,1,&mult->isrowa,&mult->isrowb,MAT_REUSE_MATRIX,&seq);CHKERRQ(ierr);
  mult->A_loc = *seq;

  ierr = MatMatMult_SeqAIJ_SeqAIJ(mult->A_loc,mult->B_seq,MAT_REUSE_MATRIX,0.0,&mult->C_seq);CHKERRQ(ierr);

  ierr = PetscObjectReference((PetscObject)mult->C_seq);CHKERRQ(ierr); 
  ierr = MatMerge(((PetscObject)A)->comm,mult->C_seq,B->cmap->n,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); 
  PetscFunctionReturn(0);
}
예제 #4
0
파일: virs.c 프로젝트: erdc-cm/petsc-dev
/*
     DMCreateInterpolation_SNESVI - Modifieds the interpolation obtained from the DM by removing all rows and columns associated with active constraints.

*/
PetscErrorCode  DMCreateInterpolation_SNESVI(DM dm1,DM dm2,Mat *mat,Vec *vec)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi1,*dmsnesvi2;
  Mat                     interp;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm1,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm1)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi1);CHKERRQ(ierr);
  ierr = PetscObjectQuery((PetscObject)dm2,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm2)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi2);CHKERRQ(ierr);

  ierr = (*dmsnesvi1->createinterpolation)(dm1,dm2,&interp,PETSC_NULL);CHKERRQ(ierr);
  ierr = MatGetSubMatrix(interp,dmsnesvi2->inactive,dmsnesvi1->inactive,MAT_INITIAL_MATRIX,mat);CHKERRQ(ierr);
  ierr = MatDestroy(&interp);CHKERRQ(ierr);
  *vec = 0;
  PetscFunctionReturn(0);
}
예제 #5
0
파일: virs.c 프로젝트: erdc-cm/petsc-dev
/*
     DMCreateGlobalVector_SNESVI - Creates global vector of the size of the reduced space

*/
PetscErrorCode  DMCreateGlobalVector_SNESVI(DM dm,Vec *vec)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_PLIB,"Composed SNES is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi);CHKERRQ(ierr);
  ierr = VecCreateMPI(((PetscObject)dm)->comm,dmsnesvi->n,PETSC_DETERMINE,vec);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
예제 #6
0
파일: matrart.c 프로젝트: erdc-cm/petsc-dev
PetscErrorCode MatDestroy_SeqAIJ_RARt(Mat A)
{
  PetscErrorCode ierr;
  PetscContainer container;
  Mat_RARt       *rart=PETSC_NULL;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_RARt",(PetscObject *)&container);CHKERRQ(ierr);
  if (!container) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Container does not exit");
  ierr = PetscContainerGetPointer(container,(void **)&rart);CHKERRQ(ierr);
  A->ops->destroy   = rart->destroy;
  if (A->ops->destroy) {
    ierr = (*A->ops->destroy)(A);CHKERRQ(ierr);
  }
  ierr = PetscObjectCompose((PetscObject)A,"Mat_RARt",0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
예제 #7
0
PetscErrorCode MatDestroy_MPIAIJ_MatMatMult(Mat A)
{
  PetscErrorCode     ierr;
  PetscContainer     container;
  Mat_MatMatMultMPI  *mult=PETSC_NULL;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr);
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }
  A->ops->destroy = mult->MatDestroy;
  ierr = PetscObjectCompose((PetscObject)A,"Mat_MatMatMultMPI",0);CHKERRQ(ierr);
  ierr = (*A->ops->destroy)(A);CHKERRQ(ierr);
  ierr = PetscContainerDestroy(container);CHKERRQ(ierr); 
  PetscFunctionReturn(0);
}
예제 #8
0
파일: matrart.c 프로젝트: erdc-cm/petsc-dev
PetscErrorCode MatRARtNumeric_SeqAIJ_SeqAIJ(Mat A,Mat R,Mat C)
{
  PetscErrorCode        ierr;
  Mat_RARt              *rart;
  PetscContainer        container;
  MatTransposeColoring  matcoloring;
  Mat                   Rt,RARt;
  PetscLogDouble        Mult_sp_den=0.0,app1=0.0,app2=0.0,t0,tf;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"Mat_RARt",(PetscObject *)&container);CHKERRQ(ierr);
  if (!container) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Container does not exit");
  ierr  = PetscContainerGetPointer(container,(void **)&rart);CHKERRQ(ierr);

  /* Get dense Rt by Apply MatTransposeColoring to R */
  matcoloring = rart->matcoloring;
  Rt          = rart->Rt;
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  ierr = MatTransColoringApplySpToDen(matcoloring,R,Rt);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  app1 += tf - t0;

  /* Get dense RARt = R*A*Rt */
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  RARt = rart->RARt;
  ierr = MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense(R,A,Rt,RARt,rart->work);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  Mult_sp_den += tf - t0;

  /* Recover C from C_dense */
  ierr = PetscGetTime(&t0);CHKERRQ(ierr);
  ierr = MatTransColoringApplyDenToSp(matcoloring,RARt,C);CHKERRQ(ierr);
  ierr = PetscGetTime(&tf);CHKERRQ(ierr);
  app2 += tf - t0;

#if defined(PETSC_USE_INFO)
  ierr = PetscInfo4(C,"Num = ColorApp %g + %g + Mult_sp_den %g  = %g\n",app1,app2,Mult_sp_den,app1+app2+Mult_sp_den);CHKERRQ(ierr);
#endif
  PetscFunctionReturn(0);
}
예제 #9
0
PetscErrorCode MatDuplicate_MPIAIJ_MatMatMult(Mat A, MatDuplicateOption op, Mat *M) 
{
  PetscErrorCode     ierr;
  Mat_MatMatMultMPI  *mult; 
  PetscContainer     container;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)A,"Mat_MatMatMultMPI",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void **)&mult);CHKERRQ(ierr); 
  } else {
    SETERRQ(PETSC_ERR_PLIB,"Container does not exit");
  }
  /* Note: the container is not duplicated, because it requires deep copying of
     several large data sets (see PetscContainerDestroy_Mat_MatMatMultMPI()).
     These data sets are only used for repeated calling of MatMatMultNumeric(). 
     *M is unlikely being used in this way. Thus we create *M with pure mpiaij format */
  ierr = (*mult->MatDuplicate)(A,op,M);CHKERRQ(ierr);
  (*M)->ops->destroy   = mult->MatDestroy;   /* = MatDestroy_MPIAIJ, *M doesn't duplicate A's container! */
  (*M)->ops->duplicate = mult->MatDuplicate; /* = MatDuplicate_MPIAIJ */
  PetscFunctionReturn(0);
}
예제 #10
0
파일: zutils.c 프로젝트: erdc-cm/petsc-dev
/*
    obj - the PETSc object where the scalar pointer came from
    base - the Fortran array address
    addr - the Fortran offset from base
    N    - the amount of data

    lx   - the array space that is to be passed to XXXXRestoreArray()
*/
PetscErrorCode PetscScalarAddressFromFortran(PetscObject obj,PetscScalar *base,size_t addr,PetscInt N,PetscScalar **lx)
{
  PetscErrorCode ierr;
  PetscInt       shift;
  PetscContainer container;
  PetscScalar    *tlx;

  ierr = PetscObjectQuery(obj,"GetArrayPtr",(PetscObject *)&container);CHKERRQ(ierr);
  if (container) {
    ierr  = PetscContainerGetPointer(container,(void**)lx);CHKERRQ(ierr);
    tlx   = base + addr;

    shift = *(PetscInt*)*lx;
    ierr  = PetscMemcpy(*lx,tlx,N*sizeof(PetscScalar));CHKERRQ(ierr);
    tlx   = (PetscScalar*)(((char *)tlx) - shift);
    ierr = PetscFree(tlx);CHKERRQ(ierr);
    ierr = PetscContainerDestroy(&container);CHKERRQ(ierr);
    ierr = PetscObjectCompose(obj,"GetArrayPtr",0);CHKERRQ(ierr);
  } else {
    *lx = base + addr;
  }
  return 0;
}
예제 #11
0
파일: plexvtk.c 프로젝트: pombredanne/petsc
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
  MPI_Comm                 comm;
  PetscViewer_VTK          *vtk = (PetscViewer_VTK*) viewer->data;
  FILE                     *fp;
  PetscViewerVTKObjectLink link;
  PetscSection             coordSection, globalCoordSection;
  PetscLayout              vLayout;
  Vec                      coordinates;
  PetscReal                lengthScale;
  PetscInt                 vMax, totVertices, totCells;
  PetscBool                hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
  PetscErrorCode           ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
  /* Vertices */
  ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
  ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
  if (vMax >= 0) {
    PetscInt pStart, pEnd, p, localSize = 0;

    ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
    pEnd = PetscMin(pEnd, vMax);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt dof;

      ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
      if (dof > 0) ++localSize;
    }
    ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
    ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
    ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
    ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
  } else {
    ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
  }
  ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
  ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
  /* Cells */
  ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
  /* Vertex fields */
  for (link = vtk->link; link; link = link->next) {
    if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
    if ((link->ft == PETSC_VTK_CELL_FIELD)  || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD))  hasCell  = PETSC_TRUE;
  }
  if (hasPoint) {
    ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
    for (link = vtk->link; link; link = link->next) {
      Vec          X = (Vec) link->vec;
      DM           dmX;
      PetscSection section, globalSection, newSection = NULL;
      const char   *name;
      PetscInt     enforceDof = PETSC_DETERMINE;

      if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
      if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
      ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
      ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
      if (dmX) {
        DMLabel  subpointMap, subpointMapX;
        PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;

        ierr = DMGetDefaultSection(dmX, &section);CHKERRQ(ierr);
        /* Here is where we check whether dmX is a submesh of dm */
        ierr = DMGetDimension(dm,  &dim);CHKERRQ(ierr);
        ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
        ierr = DMPlexGetChart(dm,  &pStart, &pEnd);CHKERRQ(ierr);
        ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
        ierr = DMPlexGetSubpointMap(dm,  &subpointMap);CHKERRQ(ierr);
        ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
        if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
          const PetscInt *ind = NULL;
          IS              subpointIS;
          PetscInt        n = 0, q;

          ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
          ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
          if (subpointIS) {
            ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
            ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
          }
          ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
          ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
          for (q = qStart; q < qEnd; ++q) {
            PetscInt dof, off, p;

            ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
            if (dof) {
              ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
              if (p >= pStart) {
                ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
                ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
                ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
              }
            }
          }
          if (subpointIS) {
            ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
            ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
          }
          /* No need to setup section */
          section = newSection;
        }
      } else {
        ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &section);CHKERRQ(ierr);
        if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      }
      if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
      ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
      ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
      if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
    }
  }
  /* Cell Fields */
  ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
  if (hasCell || writePartition) {
    ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
    for (link = vtk->link; link; link = link->next) {
      Vec          X = (Vec) link->vec;
      DM           dmX;
      PetscSection section, globalSection;
      const char   *name;
      PetscInt     enforceDof = PETSC_DETERMINE;

      if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
      if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
      ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
      ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
      if (dmX) {
        ierr = DMGetDefaultSection(dmX, &section);CHKERRQ(ierr);
      } else {
        PetscContainer c;

        ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
        if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
        ierr = PetscContainerGetPointer(c, (void**) &section);CHKERRQ(ierr);
      }
      if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
      ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
      ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
      ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
    }
    if (writePartition) {
      ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
      ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
      ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
    }
  }
  /* Cleanup */
  ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
  ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
  ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
예제 #12
0
PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer)
{
  PetscBool      isswarm = PETSC_FALSE;
  const char     *viewername;
  char           datafile[PETSC_MAX_PATH_LEN];
  PetscViewer    fviewer;
  PetscInt       k,ng,dim;
  Vec            dvec;
  long int       *bytes = NULL;
  PetscContainer container = NULL;
  const char     *dmname;
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
  
  ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr);
  if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm");
  
  ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr);
  
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr);
  if (!dmname) {
    ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr);
  }
  if (!dmname) {
    ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n");CHKERRQ(ierr);
  } else {
    ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname);CHKERRQ(ierr);
  }
  
  /* create a sub-viewer for topology, geometry and all data fields */
  /* name is viewer.name + "_swarm_fields.pbin" */
  ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
  ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr);
  
  ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
  ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
  ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
  
  ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr);
  
  /* write topology header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Topology>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write topology data */
  for (k=0; k<ng; k++) {
    PetscInt pvertex[3];
    
    pvertex[0] = 1;
    pvertex[1] = 1;
    pvertex[2] = k;
    ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
  }
  bytes[0] += sizeof(PetscInt) * ng * 3;
  
  /* write geometry header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
  switch (dim) {
    case 1:
      SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D");
      break;
    case 2:
      ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n");CHKERRQ(ierr);
      break;
    case 3:
      ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n");CHKERRQ(ierr);
      break;
  }
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Geometry>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write geometry data */
  ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
  ierr = VecView(dvec,fviewer);CHKERRQ(ierr);
  ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
  bytes[0] += sizeof(PetscReal) * ng * dim;
  
  ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
  
  PetscFunctionReturn(0);
}
예제 #13
0
PetscErrorCode private_ISView_Swarm_XDMF(IS is,PetscViewer viewer)
{
  long int       *bytes = NULL;
  PetscContainer container = NULL;
  const char     *viewername;
  char           datafile[PETSC_MAX_PATH_LEN];
  PetscViewer    fviewer;
  PetscInt       N,bs;
  const char     *vecname;
  char           fieldname[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;
  
  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
  if (container) {
    ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
  } else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
  
  ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
  ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
  
  /* re-open a sub-viewer for all data fields */
  /* name is viewer.name + "_swarm_fields.pbin" */
  ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
  ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
  ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr);
  ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
  
  ierr = ISGetSize(is,&N);CHKERRQ(ierr);
  ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
  N = N/bs;
  ierr = PetscObjectGetName((PetscObject)is,&vecname);CHKERRQ(ierr);
  if (!vecname) {
    ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)is)->tag);CHKERRQ(ierr);
  } else {
    ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr);
  }
  
  /* write data header */
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  if (bs == 1) {
    ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);CHKERRQ(ierr);
  } else {
    ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);CHKERRQ(ierr);
  }
  ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  ierr = PetscViewerASCIIPrintf(viewer,"</Attribute>\n");CHKERRQ(ierr);
  ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
  
  /* write data */
  ierr = ISView(is,fviewer);CHKERRQ(ierr);
  bytes[0] += sizeof(PetscInt) * N * bs;
  
  ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
  
  PetscFunctionReturn(0);
}
예제 #14
0
파일: virs.c 프로젝트: erdc-cm/petsc-dev
/*
     DMCoarsen_SNESVI - Computes the regular coarsened DM then computes additional information about its inactive set

*/
PetscErrorCode  DMCoarsen_SNESVI(DM dm1,MPI_Comm comm,DM *dm2)
{
  PetscErrorCode          ierr;
  PetscContainer          isnes;
  DM_SNESVI               *dmsnesvi1;
  Vec                     finemarked,coarsemarked;
  IS                      inactive;
  VecScatter              inject;
  const PetscInt          *index;
  PetscInt                n,k,cnt = 0,rstart,*coarseindex;
  PetscScalar             *marked;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)dm1,"VI",(PetscObject *)&isnes);CHKERRQ(ierr);
  if (!isnes) SETERRQ(((PetscObject)dm1)->comm,PETSC_ERR_PLIB,"Composed VI data structure is missing");
  ierr = PetscContainerGetPointer(isnes,(void**)&dmsnesvi1);CHKERRQ(ierr);

  /* get the original coarsen */
  ierr = (*dmsnesvi1->coarsen)(dm1,comm,dm2);CHKERRQ(ierr);

  /* not sure why this extra reference is needed, but without the dm2 disappears too early */
  ierr = PetscObjectReference((PetscObject)*dm2);CHKERRQ(ierr);

  /* need to set back global vectors in order to use the original injection */
  ierr = DMClearGlobalVectors(dm1);CHKERRQ(ierr);
  dm1->ops->createglobalvector = dmsnesvi1->createglobalvector;
  ierr = DMCreateGlobalVector(dm1,&finemarked);CHKERRQ(ierr);
  ierr = DMCreateGlobalVector(*dm2,&coarsemarked);CHKERRQ(ierr);

  /*
     fill finemarked with locations of inactive points
  */
  ierr = ISGetIndices(dmsnesvi1->inactive,&index);CHKERRQ(ierr);
  ierr = ISGetLocalSize(dmsnesvi1->inactive,&n);CHKERRQ(ierr);
  ierr = VecSet(finemarked,0.0);CHKERRQ(ierr);
  for (k=0;k<n;k++){
      ierr = VecSetValue(finemarked,index[k],1.0,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = VecAssemblyBegin(finemarked);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(finemarked);CHKERRQ(ierr);

  ierr = DMCreateInjection(*dm2,dm1,&inject);CHKERRQ(ierr);
  ierr = VecScatterBegin(inject,finemarked,coarsemarked,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(inject,finemarked,coarsemarked,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&inject);CHKERRQ(ierr);

  /*
     create index set list of coarse inactive points from coarsemarked
  */
  ierr = VecGetLocalSize(coarsemarked,&n);CHKERRQ(ierr);
  ierr = VecGetOwnershipRange(coarsemarked,&rstart,PETSC_NULL);CHKERRQ(ierr);
  ierr = VecGetArray(coarsemarked,&marked);CHKERRQ(ierr);
  for (k=0; k<n; k++) {
    if (marked[k] != 0.0) cnt++;
  }
  ierr = PetscMalloc(cnt*sizeof(PetscInt),&coarseindex);CHKERRQ(ierr);
  cnt  = 0;
  for (k=0; k<n; k++) {
    if (marked[k] != 0.0) coarseindex[cnt++] = k + rstart;
  }
  ierr = VecRestoreArray(coarsemarked,&marked);CHKERRQ(ierr);
  ierr = ISCreateGeneral(((PetscObject)coarsemarked)->comm,cnt,coarseindex,PETSC_OWN_POINTER,&inactive);CHKERRQ(ierr);

  ierr = DMClearGlobalVectors(dm1);CHKERRQ(ierr);
  dm1->ops->createglobalvector = DMCreateGlobalVector_SNESVI;
  ierr = DMSetVI(*dm2,inactive);CHKERRQ(ierr);

  ierr = VecDestroy(&finemarked);CHKERRQ(ierr);
  ierr = VecDestroy(&coarsemarked);CHKERRQ(ierr);
  ierr = ISDestroy(&inactive);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
예제 #15
0
/*
    Performs an efficient scatter on the rows of B needed by this process; this is
    a modification of the VecScatterBegin_() routines.
*/
PetscErrorCode MatMPIDenseScatter(Mat A,Mat B,Mat C,Mat *outworkB)
{
  Mat_MPIAIJ             *aij = (Mat_MPIAIJ*)A->data;
  PetscErrorCode         ierr;
  PetscScalar            *b,*w,*svalues,*rvalues;
  VecScatter             ctx = aij->Mvctx; 
  VecScatter_MPI_General *from = (VecScatter_MPI_General*) ctx->fromdata;
  VecScatter_MPI_General *to   = ( VecScatter_MPI_General*) ctx->todata;
  PetscInt               i,j,k;
  PetscInt               *sindices,*sstarts,*rindices,*rstarts;
  PetscMPIInt            *sprocs,*rprocs,nrecvs;
  MPI_Request            *swaits,*rwaits;
  MPI_Comm               comm = ((PetscObject)A)->comm;
  PetscMPIInt            tag = ((PetscObject)ctx)->tag,ncols = B->cmap->N, nrows = aij->B->cmap->n,imdex,nrowsB = B->rmap->n;
  MPI_Status             status;
  MPIAIJ_MPIDense        *contents;
  PetscContainer         cont;
  Mat                    workB;

  PetscFunctionBegin;
  ierr = PetscObjectQuery((PetscObject)C,"workB",(PetscObject*)&cont);CHKERRQ(ierr);
  ierr = PetscContainerGetPointer(cont,(void**)&contents);CHKERRQ(ierr);

  workB = *outworkB = contents->workB;
  if (nrows != workB->rmap->n) SETERRQ2(PETSC_ERR_PLIB,"Number of rows of workB %D not equal to columns of aij->B %D",nrows,workB->cmap->n);
  sindices  = to->indices;
  sstarts   = to->starts;
  sprocs    = to->procs;
  swaits    = contents->swaits;
  svalues   = contents->svalues;

  rindices  = from->indices;
  rstarts   = from->starts;
  rprocs    = from->procs;
  rwaits    = contents->rwaits;
  rvalues   = contents->rvalues;

  ierr = MatGetArray(B,&b);CHKERRQ(ierr);
  ierr = MatGetArray(workB,&w);CHKERRQ(ierr);

  for (i=0; i<from->n; i++) {
    ierr = MPI_Irecv(rvalues+ncols*rstarts[i],ncols*(rstarts[i+1]-rstarts[i]),MPIU_SCALAR,rprocs[i],tag,comm,rwaits+i);CHKERRQ(ierr);
  } 

  for (i=0; i<to->n; i++) {
    /* pack a message at a time */
    CHKMEMQ;
    for (j=0; j<sstarts[i+1]-sstarts[i]; j++){
      for (k=0; k<ncols; k++) {
        svalues[ncols*(sstarts[i] + j) + k] = b[sindices[sstarts[i]+j] + nrowsB*k];
      }
    }
    CHKMEMQ;
    ierr = MPI_Isend(svalues+ncols*sstarts[i],ncols*(sstarts[i+1]-sstarts[i]),MPIU_SCALAR,sprocs[i],tag,comm,swaits+i);CHKERRQ(ierr);
  }

  nrecvs = from->n;
  while (nrecvs) {
    ierr = MPI_Waitany(from->n,rwaits,&imdex,&status);CHKERRQ(ierr);
    nrecvs--;
    /* unpack a message at a time */
    CHKMEMQ;
    for (j=0; j<rstarts[imdex+1]-rstarts[imdex]; j++){
      for (k=0; k<ncols; k++) {
        w[rindices[rstarts[imdex]+j] + nrows*k] = rvalues[ncols*(rstarts[imdex] + j) + k];
      }
    }
    CHKMEMQ;
  }
  if (to->n) {ierr = MPI_Waitall(to->n,swaits,to->sstatus);CHKERRQ(ierr)}