Ejemplo n.º 1
0
static PetscErrorCode BuildGradientReconstruction(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom)
{
  DMLabel        ghostLabel;
  PetscScalar   *dx, *grad, **gref;
  PetscInt       dim, cStart, cEnd, c, cEndInterior, maxNumFaces;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
  ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr);
  ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr);
  ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
  ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr);
  for (c = cStart; c < cEndInterior; c++) {
    const PetscInt *faces;
    PetscInt        numFaces, usedFaces, f, d;
    const CellGeom *cg;
    PetscBool       boundary;
    PetscInt        ghost;

    ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
    ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr);
    ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr);
    if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces);
    for (f = 0, usedFaces = 0; f < numFaces; ++f) {
      const CellGeom *cg1;
      FaceGeom       *fg;
      const PetscInt *fcells;
      PetscInt        ncell, side;

      ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
      ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
      if ((ghost >= 0) || boundary) continue;
      ierr  = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr);
      side  = (c != fcells[0]); /* c is on left=0 or right=1 of face */
      ncell = fcells[!side];    /* the neighbor */
      ierr  = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr);
      ierr  = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr);
      for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d];
      gref[usedFaces++] = fg->grad[side];  /* Gradient reconstruction term will go here */
    }
    if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?");
    ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr);
    for (f = 0, usedFaces = 0; f < numFaces; ++f) {
      ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
      ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
      if ((ghost >= 0) || boundary) continue;
      for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d];
      ++usedFaces;
    }
  }
  ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 2
0
PetscErrorCode TestSetup(DMLabel label, AppCtx *user)
{
  PetscRandom    r;
  PetscInt       n = (PetscInt) (user->fill*(user->pEnd - user->pStart)), i;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);/* -random_type <> */
  ierr = PetscRandomSetInterval(r, user->pStart, user->pEnd);CHKERRQ(ierr);
  ierr = PetscRandomSetSeed(r, 123456789L);CHKERRQ(ierr);
  ierr = PetscRandomSeed(r);CHKERRQ(ierr);
  user->size = 0;
  for(i = 0; i < n; ++i) {
    PetscReal p;
    PetscInt  val;

    ierr = PetscRandomGetValueReal(r, &p);CHKERRQ(ierr);
    ierr = DMLabelGetValue(label, (PetscInt) p, &val);CHKERRQ(ierr);
    if (val < 0) {
      ++user->size;
      ierr = DMLabelSetValue(label, (PetscInt) p, i % user->numStrata);CHKERRQ(ierr);
    }
  }
  ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
  ierr = DMLabelCreateIndex(label, user->pStart, user->pEnd);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_SELF, "Created label with chart [%D, %D) and set %D values\n", user->pStart, user->pEnd, user->size);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 3
0
/*@C
  DMPlexGetLabelValue - Get the value in a Sieve Label for the given point, with 0 as the default

  Not Collective

  Input Parameters:
+ dm   - The DMPlex object
. name - The label name
- point - The mesh point

  Output Parameter:
. value - The label value for this point, or -1 if the point is not in the label

  Level: beginner

.keywords: mesh
.seealso: DMLabelGetValue(), DMPlexSetLabelValue(), DMPlexGetStratumIS()
@*/
PetscErrorCode DMPlexGetLabelValue(DM dm, const char name[], PetscInt point, PetscInt *value)
{
  DMLabel        label;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidCharPointer(name, 2);
  ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr);
  if (!label) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No label named %s was found", name);CHKERRQ(ierr);
  ierr = DMLabelGetValue(label, point, value);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 4
0
PetscErrorCode TestClear(DMLabel label, AppCtx *user)
{
  PetscInt       pStart = user->pStart, pEnd = user->pEnd, p;
  PetscInt       defaultValue;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMLabelGetDefaultValue(label,&defaultValue);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; p++) {
    PetscInt  val;
    PetscBool hasPoint;

    ierr = DMLabelGetValue(label,p,&val);CHKERRQ(ierr);
    if (val != defaultValue) {
      ierr = DMLabelClearValue(label,p,val);CHKERRQ(ierr);
    }
    ierr = DMLabelGetValue(label,p,&val);CHKERRQ(ierr);
    ierr = DMLabelHasPoint(label,p,&hasPoint);CHKERRQ(ierr);
    if (val != defaultValue) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Expected default value %D after clearing point %D, got %D",defaultValue,p,val);
    if (hasPoint) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Label contains %D after clearing",p);
  }
  PetscFunctionReturn(0);
}
Ejemplo n.º 5
0
static PetscErrorCode CreateAdaptivityLabel(DM forest,DMLabel *adaptLabel)
{
  DMLabel        identLabel;
  PetscInt       cStart, cEnd, c;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMLabelCreate("adapt",adaptLabel);CHKERRQ(ierr);
  ierr = DMLabelSetDefaultValue(*adaptLabel,DM_ADAPT_COARSEN);CHKERRQ(ierr);
  ierr = DMGetLabel(forest,"identity",&identLabel);CHKERRQ(ierr);
  ierr = DMForestGetCellChart(forest,&cStart,&cEnd);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; c++) {
    PetscInt basePoint;

    ierr = DMLabelGetValue(identLabel,c,&basePoint);CHKERRQ(ierr);
    if (!basePoint) {ierr = DMLabelSetValue(*adaptLabel,c,DM_ADAPT_REFINE);CHKERRQ(ierr);}
  }
  PetscFunctionReturn(0);
}
Ejemplo n.º 6
0
PetscErrorCode TestLookup(DMLabel label, AppCtx *user)
{
  const PetscInt pStart = user->pStart;
  const PetscInt pEnd   = user->pEnd;
  PetscInt       p, n = 0;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  for(p = pStart; p < pEnd; ++p) {
    PetscInt  val;
    PetscBool has;

    ierr = DMLabelGetValue(label, p, &val);CHKERRQ(ierr);
    ierr = DMLabelHasPoint(label, p, &has);CHKERRQ(ierr);
    if (((val >= 0) && !has) || ((val < 0) && has)) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Label value %D does not match contains check %D for point %D", val, (PetscInt) has, p);
    if (has) ++n;
  }
  if (n != user->size) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of label points detected %D does not match number set %D", n, user->size);
  /* Also put in timing code */
  PetscFunctionReturn(0);
}
Ejemplo n.º 7
0
/*@
  DMPlexGetOrdering - Calculate a reordering of the mesh

  Collective on DM

  Input Parameter:
+ dm - The DMPlex object
. otype - type of reordering, one of the following:
$     MATORDERINGNATURAL - Natural
$     MATORDERINGND - Nested Dissection
$     MATORDERING1WD - One-way Dissection
$     MATORDERINGRCM - Reverse Cuthill-McKee
$     MATORDERINGQMD - Quotient Minimum Degree
- label - [Optional] Label used to segregate ordering into sets, or NULL


  Output Parameter:
. perm - The point permutation as an IS, perm[old point number] = new point number

  Note: The label is used to group sets of points together by label value. This makes it easy to reorder a mesh which
  has different types of cells, and then loop over each set of reordered cells for assembly.

  Level: intermediate

.keywords: mesh
.seealso: MatGetOrdering()
@*/
PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, DMLabel label, IS *perm)
{
  PetscInt       numCells = 0;
  PetscInt      *start = NULL, *adjacency = NULL, *cperm, *clperm, *invclperm, *mask, *xls, pStart, pEnd, c, i;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidPointer(perm, 3);
  ierr = DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency);CHKERRQ(ierr);
  ierr = PetscMalloc3(numCells,&cperm,numCells,&mask,numCells*2,&xls);CHKERRQ(ierr);
  if (numCells) {
    /* Shift for Fortran numbering */
    for (i = 0; i < start[numCells]; ++i) ++adjacency[i];
    for (i = 0; i <= numCells; ++i)       ++start[i];
    ierr = SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls);CHKERRQ(ierr);
  }
  ierr = PetscFree(start);CHKERRQ(ierr);
  ierr = PetscFree(adjacency);CHKERRQ(ierr);
  /* Shift for Fortran numbering */
  for (c = 0; c < numCells; ++c) --cperm[c];
  /* Segregate */
  if (label) {
    IS              valueIS;
    const PetscInt *values;
    PetscInt        numValues, numPoints = 0;
    PetscInt       *sperm, *vsize, *voff, v;

    ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr);
    ierr = ISSort(valueIS);CHKERRQ(ierr);
    ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr);
    ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr);
    ierr = PetscCalloc3(numCells,&sperm,numValues,&vsize,numValues+1,&voff);CHKERRQ(ierr);
    for (v = 0; v < numValues; ++v) {
      ierr = DMLabelGetStratumSize(label, values[v], &vsize[v]);CHKERRQ(ierr);
      if (v < numValues-1) voff[v+2] += vsize[v] + voff[v+1];
      numPoints += vsize[v];
    }
    if (numPoints != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label only covers %D cells < %D total", numPoints, numCells);
    for (c = 0; c < numCells; ++c) {
      const PetscInt oldc = cperm[c];
      PetscInt       val, vloc;

      ierr = DMLabelGetValue(label, oldc, &val);CHKERRQ(ierr);
      if (val == -1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %D not present in label", oldc);
      ierr = PetscFindInt(val, numValues, values, &vloc);CHKERRQ(ierr);
      if (vloc < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Value %D not present label", val);
      sperm[voff[vloc+1]++] = oldc;
    }
    for (v = 0; v < numValues; ++v) {
      if (voff[v+1] - voff[v] != vsize[v]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of %D values found is %D != %D", values[v], voff[v+1] - voff[v], vsize[v]);
    }
    ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr);
    ierr = ISDestroy(&valueIS);CHKERRQ(ierr);
    ierr = PetscMemcpy(cperm, sperm, numCells * sizeof(PetscInt));CHKERRQ(ierr);
    ierr = PetscFree3(sperm, vsize, voff);CHKERRQ(ierr);
  }
  /* Construct closure */
  ierr = DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm);CHKERRQ(ierr);
  ierr = PetscFree3(cperm,mask,xls);CHKERRQ(ierr);
  ierr = PetscFree(clperm);CHKERRQ(ierr);
  /* Invert permutation */
  ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
  ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd-pStart, invclperm, PETSC_OWN_POINTER, perm);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 8
0
PetscErrorCode DMPlexVTKWriteCells_ASCII(DM dm, FILE *fp, PetscInt *totalCells)
{
  MPI_Comm       comm;
  DMLabel        label;
  IS             globalVertexNumbers = NULL;
  const PetscInt *gvertex;
  PetscInt       dim;
  PetscInt       numCorners = 0, totCorners = 0, maxCorners, *corners;
  PetscInt       numCells   = 0, totCells   = 0, maxCells, cellHeight;
  PetscInt       numLabelCells, maxLabelCells, cMax, cStart, cEnd, c, vStart, vEnd, v;
  PetscMPIInt    numProcs, rank, proc, tag;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
  if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
  ierr = DMPlexGetLabel(dm, "vtk", &label);CHKERRQ(ierr);
  ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
  ierr = MPI_Allreduce(&numLabelCells, &maxLabelCells, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
  if (!maxLabelCells) label = NULL;
  for (c = cStart; c < cEnd; ++c) {
    PetscInt *closure = NULL;
    PetscInt closureSize, value;

    if (label) {
      ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
      if (value != 1) continue;
    }
    ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    for (v = 0; v < closureSize*2; v += 2) {
      if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++numCorners;
    }
    ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    ++numCells;
  }
  maxCells = numCells;
  ierr     = MPI_Reduce(&numCells, &totCells, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
  ierr     = MPI_Reduce(&numCells, &maxCells, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
  ierr     = MPI_Reduce(&numCorners, &totCorners, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
  ierr     = MPI_Reduce(&numCorners, &maxCorners, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
  ierr     = DMPlexGetVertexNumbering(dm, &globalVertexNumbers);CHKERRQ(ierr);
  ierr     = ISGetIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
  ierr     = PetscMalloc1(maxCells, &corners);CHKERRQ(ierr);
  ierr     = PetscFPrintf(comm, fp, "CELLS %d %d\n", totCells, totCorners+totCells);CHKERRQ(ierr);
  if (!rank) {
    PetscInt *remoteVertices;
    int      *vertices;

    ierr = PetscMalloc1(maxCorners, &vertices);CHKERRQ(ierr);
    for (c = cStart, numCells = 0; c < cEnd; ++c) {
      PetscInt *closure = NULL;
      PetscInt closureSize, value, nC = 0;

      if (label) {
        ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
        if (value != 1) continue;
      }
      ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      for (v = 0; v < closureSize*2; v += 2) {
        if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
          const PetscInt gv = gvertex[closure[v] - vStart];
          vertices[nC++] = gv < 0 ? -(gv+1) : gv;
        }
      }
      ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      corners[numCells++] = nC;
      ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
      ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
      for (v = 0; v < nC; ++v) {
        ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
      }
      ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
    }
    if (numProcs > 1) {ierr = PetscMalloc1(maxCorners+maxCells, &remoteVertices);CHKERRQ(ierr);}
    for (proc = 1; proc < numProcs; ++proc) {
      MPI_Status status;

      ierr = MPI_Recv(&numCorners, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
      ierr = MPI_Recv(remoteVertices, numCorners, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
      for (c = 0; c < numCorners;) {
        PetscInt nC = remoteVertices[c++];

        for (v = 0; v < nC; ++v, ++c) {
          vertices[v] = remoteVertices[c];
        }
        ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
        ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
        for (v = 0; v < nC; ++v) {
          ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
        }
        ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
      }
    }
    if (numProcs > 1) {ierr = PetscFree(remoteVertices);CHKERRQ(ierr);}
    ierr = PetscFree(vertices);CHKERRQ(ierr);
  } else {
    PetscInt *localVertices, numSend = numCells+numCorners, k = 0;

    ierr = PetscMalloc1(numSend, &localVertices);CHKERRQ(ierr);
    for (c = cStart, numCells = 0; c < cEnd; ++c) {
      PetscInt *closure = NULL;
      PetscInt closureSize, value, nC = 0;

      if (label) {
        ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
        if (value != 1) continue;
      }
      ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      for (v = 0; v < closureSize*2; v += 2) {
        if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
          const PetscInt gv = gvertex[closure[v] - vStart];
          closure[nC++] = gv < 0 ? -(gv+1) : gv;
        }
      }
      corners[numCells++] = nC;
      localVertices[k++]  = nC;
      for (v = 0; v < nC; ++v, ++k) {
        localVertices[k] = closure[v];
      }
      ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    }
    if (k != numSend) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numSend);
    ierr = MPI_Send(&numSend, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
    ierr = MPI_Send(localVertices, numSend, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
    ierr = PetscFree(localVertices);CHKERRQ(ierr);
  }
  ierr = ISRestoreIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
  ierr = PetscFPrintf(comm, fp, "CELL_TYPES %d\n", totCells);CHKERRQ(ierr);
  if (!rank) {
    PetscInt cellType;

    for (c = 0; c < numCells; ++c) {
      ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
      ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
    }
    for (proc = 1; proc < numProcs; ++proc) {
      MPI_Status status;

      ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
      ierr = MPI_Recv(corners, numCells, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
      for (c = 0; c < numCells; ++c) {
        ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
        ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
      }
    }
  } else {
    ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
    ierr = MPI_Send(corners, numCells, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
  }
  ierr        = PetscFree(corners);CHKERRQ(ierr);
  *totalCells = totCells;
  PetscFunctionReturn(0);
}
Ejemplo n.º 9
0
/*@C
  PetscSectionCreateGlobalSectionLabel - Create a section describing the global field layout using
  the local section and an SF describing the section point overlap.

  Input Parameters:
  + s - The PetscSection for the local field layout
  . sf - The SF describing parallel layout of the section points
  . includeConstraints - By default this is PETSC_FALSE, meaning that the global field vector will not possess constrained dofs
  . label - The label specifying the points
  - labelValue - The label stratum specifying the points

  Output Parameter:
  . gsection - The PetscSection for the global field layout

  Note: This gives negative sizes and offsets to points not owned by this process

  Level: developer

.seealso: PetscSectionCreate()
@*/
PetscErrorCode PetscSectionCreateGlobalSectionLabel(PetscSection s, PetscSF sf, PetscBool includeConstraints, DMLabel label, PetscInt labelValue, PetscSection *gsection)
{
  PetscInt      *neg = NULL, *tmpOff = NULL;
  PetscInt       pStart, pEnd, p, dof, cdof, off, globalOff = 0, nroots;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) s), gsection);CHKERRQ(ierr);
  ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(*gsection, pStart, pEnd);CHKERRQ(ierr);
  ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr);
  if (nroots >= 0) {
    if (nroots < pEnd-pStart) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "PetscSF nroots %d < %d section size", nroots, pEnd-pStart);
    ierr = PetscCalloc1(nroots, &neg);CHKERRQ(ierr);
    if (nroots > pEnd-pStart) {
      ierr = PetscCalloc1(nroots, &tmpOff);CHKERRQ(ierr);
    } else {
      tmpOff = &(*gsection)->atlasDof[-pStart];
    }
  }
  /* Mark ghost points with negative dof */
  for (p = pStart; p < pEnd; ++p) {
    PetscInt value;

    ierr = DMLabelGetValue(label, p, &value);CHKERRQ(ierr);
    if (value != labelValue) continue;
    ierr = PetscSectionGetDof(s, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionSetDof(*gsection, p, dof);CHKERRQ(ierr);
    ierr = PetscSectionGetConstraintDof(s, p, &cdof);CHKERRQ(ierr);
    if (!includeConstraints && cdof > 0) {ierr = PetscSectionSetConstraintDof(*gsection, p, cdof);CHKERRQ(ierr);}
    if (neg) neg[p] = -(dof+1);
  }
  ierr = PetscSectionSetUpBC(*gsection);CHKERRQ(ierr);
  if (nroots >= 0) {
    ierr = PetscSFBcastBegin(sf, MPIU_INT, neg, tmpOff);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(sf, MPIU_INT, neg, tmpOff);CHKERRQ(ierr);
    if (nroots > pEnd-pStart) {
      for (p = pStart; p < pEnd; ++p) {if (tmpOff[p] < 0) (*gsection)->atlasDof[p-pStart] = tmpOff[p];}
    }
  }
  /* Calculate new sizes, get proccess offset, and calculate point offsets */
  for (p = 0, off = 0; p < pEnd-pStart; ++p) {
    cdof = (!includeConstraints && s->bc) ? s->bc->atlasDof[p] : 0;
    (*gsection)->atlasOff[p] = off;
    off += (*gsection)->atlasDof[p] > 0 ? (*gsection)->atlasDof[p]-cdof : 0;
  }
  ierr       = MPI_Scan(&off, &globalOff, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject) s));CHKERRQ(ierr);
  globalOff -= off;
  for (p = 0, off = 0; p < pEnd-pStart; ++p) {
    (*gsection)->atlasOff[p] += globalOff;
    if (neg) neg[p] = -((*gsection)->atlasOff[p]+1);
  }
  /* Put in negative offsets for ghost points */
  if (nroots >= 0) {
    ierr = PetscSFBcastBegin(sf, MPIU_INT, neg, tmpOff);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(sf, MPIU_INT, neg, tmpOff);CHKERRQ(ierr);
    if (nroots > pEnd-pStart) {
      for (p = pStart; p < pEnd; ++p) {if (tmpOff[p] < 0) (*gsection)->atlasOff[p-pStart] = tmpOff[p];}
    }
  }
  if (nroots >= 0 && nroots > pEnd-pStart) {ierr = PetscFree(tmpOff);CHKERRQ(ierr);}
  ierr = PetscFree(neg);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 10
0
static PetscErrorCode DMPlexTSSetupGeometry(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
  DM             dmFace, dmCell;
  DMLabel        ghostLabel;
  PetscSection   sectionFace, sectionCell;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscReal      minradius;
  PetscScalar   *fgeom, *cgeom;
  PetscInt       dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (dmplexts->setupGeom) PetscFunctionReturn(0);
  ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
  /* Make cell centroids and volumes */
  ierr = DMClone(dm, &dmCell);CHKERRQ(ierr);
  ierr = DMSetCoordinateSection(dmCell, coordSection);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr);
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &sectionCell);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, sizeof(CellGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
  ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr);
  ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&sectionCell);CHKERRQ(ierr);
  ierr = DMCreateLocalVector(dmCell, &dmplexts->cellgeom);CHKERRQ(ierr);
  ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
  for (c = cStart; c < cEndInterior; ++c) {
    CellGeom *cg;

    ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
    ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr);
    ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr);
  }
  /* Compute face normals and minimum cell radius */
  ierr = DMClone(dm, &dmFace);CHKERRQ(ierr);
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &sectionFace);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr);
  for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, sizeof(FaceGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
  ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr);
  ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&sectionFace);CHKERRQ(ierr);
  ierr = DMCreateLocalVector(dmFace, &dmplexts->facegeom);CHKERRQ(ierr);
  ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
  ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
  minradius = PETSC_MAX_REAL;
  for (f = fStart; f < fEnd; ++f) {
    FaceGeom *fg;
    PetscReal area;
    PetscInt  ghost, d;

    ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);
    if (ghost >= 0) continue;
    ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr);
    ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr);
    for (d = 0; d < dim; ++d) fg->normal[d] *= area;
    /* Flip face orientation if necessary to match ordering in support, and Update minimum radius */
    {
      CellGeom       *cL, *cR;
      const PetscInt *cells;
      PetscReal      *lcentroid, *rcentroid;
      PetscReal       v[3];

      ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr);
      ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr);
      ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr);
      lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid;
      rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid;
      WaxpyD(dim, -1, lcentroid, rcentroid, v);
      if (DotRealD(dim, fg->normal, v) < 0) {
        for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d];
      }
      if (DotRealD(dim, fg->normal, v) <= 0) {
        if (dim == 2) SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g) v (%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) v[0], (double) v[1]);
        if (dim == 3) SETERRQ7(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g,%g) v (%g,%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) fg->normal[2], (double) v[0], (double) v[1], (double) v[2]);
        SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f);
      }
      if (cells[0] < cEndInterior) {
        WaxpyD(dim, -1, fg->centroid, cL->centroid, v);
        minradius = PetscMin(minradius, NormD(dim, v));
      }
      if (cells[1] < cEndInterior) {
        WaxpyD(dim, -1, fg->centroid, cR->centroid, v);
        minradius = PetscMin(minradius, NormD(dim, v));
      }
    }
  }
  ierr = MPI_Allreduce(&minradius, &dmplexts->minradius, 1, MPIU_REAL, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
  /* Compute centroids of ghost cells */
  for (c = cEndInterior; c < cEnd; ++c) {
    FaceGeom       *fg;
    const PetscInt *cone,    *support;
    PetscInt        coneSize, supportSize, s;

    ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr);
    if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize);
    ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr);
    ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr);
    if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 1", cone[0], supportSize);
    ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr);
    for (s = 0; s < 2; ++s) {
      /* Reflect ghost centroid across plane of face */
      if (support[s] == c) {
        const CellGeom *ci;
        CellGeom       *cg;
        PetscReal       c2f[3], a;

        ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr);
        WaxpyD(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */
        a    = DotRealD(dim, c2f, fg->normal)/DotRealD(dim, fg->normal, fg->normal);
        ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr);
        WaxpyD(dim, 2*a, fg->normal, ci->centroid, cg->centroid);
        cg->volume = ci->volume;
      }
    }
  }
  ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
  ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
  ierr = DMDestroy(&dmCell);CHKERRQ(ierr);
  ierr = DMDestroy(&dmFace);CHKERRQ(ierr);
  dmplexts->setupGeom = PETSC_TRUE;
  PetscFunctionReturn(0);
}
Ejemplo n.º 11
0
static PetscErrorCode TSComputeRHSFunction_DMPlex(TS ts, PetscReal time, Vec X, Vec F, void *ctx)
{
  DM                 dm;
  DMTS_Plex         *dmplexts = (DMTS_Plex *) ctx;
  void             (*riemann)(const PetscReal[], const PetscReal[], const PetscScalar[], const PetscScalar[], PetscScalar[], void *) = dmplexts->riemann;
  PetscFV            fvm;
  PetscLimiter       lim;
  Vec                faceGeometry = dmplexts->facegeom;
  Vec                cellGeometry = dmplexts->cellgeom;
  Vec                Grad = NULL, locGrad, locX;
  DM                 dmFace, dmCell;
  DMLabel            ghostLabel;
  PetscCellGeometry  fgeom, cgeom;
  const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
  PetscScalar       *grad, *f, *uL, *uR, *fluxL, *fluxR;
  PetscReal         *centroid, *normal, *vol, *cellPhi;
  PetscBool          computeGradients;
  PetscInt           Nf, dim, pdim, fStart, fEnd, numFaces = 0, face, iface, cell, cStart, cEnd, cEndInterior;
  PetscErrorCode     ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(ts,TS_CLASSID,1);
  PetscValidHeaderSpecific(X,VEC_CLASSID,3);
  PetscValidHeaderSpecific(F,VEC_CLASSID,5);
  ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
  ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
  ierr = VecZeroEntries(locX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
  ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
  ierr = VecZeroEntries(F);CHKERRQ(ierr);
  ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
  ierr = DMGetField(dm, 0, (PetscObject *) &fvm);CHKERRQ(ierr);
  ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr);
  ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
  ierr = PetscFVGetComputeGradients(fvm, &computeGradients);CHKERRQ(ierr);
  if (computeGradients) {
    ierr = DMGetGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
    ierr = VecZeroEntries(Grad);CHKERRQ(ierr);
    ierr = VecGetArray(Grad, &grad);CHKERRQ(ierr);
  }
  ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
  ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr);
  ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr);
  ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
  ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
  ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr);
  /* Count faces and reconstruct gradients */
  for (face = fStart; face < fEnd; ++face) {
    const PetscInt    *cells;
    const FaceGeom    *fg;
    const PetscScalar *cx[2];
    PetscScalar       *cgrad[2];
    PetscBool          boundary;
    PetscInt           ghost, c, pd, d;

    ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
    if (ghost >= 0) continue;
    ++numFaces;
    if (!computeGradients) continue;
    ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
    if (boundary) continue;
    ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
    for (c = 0; c < 2; ++c) {
      ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr);
      ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cells[c], grad, &cgrad[c]);CHKERRQ(ierr);
    }
    for (pd = 0; pd < pdim; ++pd) {
      PetscScalar delta = cx[1][pd] - cx[0][pd];

      for (d = 0; d < dim; ++d) {
        if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta;
        if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta;
      }
    }
  }
  /* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */
  ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
  ierr = DMGetWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
  for (cell = computeGradients && lim ? cStart : cEnd; cell < cEndInterior; ++cell) {
    const PetscInt    *faces;
    const PetscScalar *cx;
    const CellGeom    *cg;
    PetscScalar       *cgrad;
    PetscInt           coneSize, f, pd, d;

    ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr);
    ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr);
    ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cell, grad, &cgrad);CHKERRQ(ierr);
    if (!cgrad) continue; /* Unowned overlap cell, we do not compute */
    /* Limiter will be minimum value over all neighbors */
    for (d = 0; d < pdim; ++d) cellPhi[d] = PETSC_MAX_REAL;
    for (f = 0; f < coneSize; ++f) {
      const PetscScalar *ncx;
      const CellGeom    *ncg;
      const PetscInt    *fcells;
      PetscInt           face = faces[f], ncell, ghost;
      PetscReal          v[3];
      PetscBool          boundary;

      ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
      ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
      if ((ghost >= 0) || boundary) continue;
      ierr  = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr);
      ncell = cell == fcells[0] ? fcells[1] : fcells[0];
      ierr  = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr);
      ierr  = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr);
      WaxpyD(dim, -1, cg->centroid, ncg->centroid, v);
      for (d = 0; d < pdim; ++d) {
        /* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */
        PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DotD(dim, &cgrad[d*dim], v);

        ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr);
        cellPhi[d] = PetscMin(cellPhi[d], phi);
      }
    }
    /* Apply limiter to gradient */
    for (pd = 0; pd < pdim; ++pd)
      /* Scalar limiter applied to each component separately */
      for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd];
  }
  ierr = DMRestoreWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
  ierr = DMPlexInsertBoundaryValuesFVM_Static(dm, fvm, time, locX, Grad, dmplexts);CHKERRQ(ierr);
  if (computeGradients) {
    ierr = VecRestoreArray(Grad, &grad);CHKERRQ(ierr);
    ierr = DMGetLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
    ierr = DMGlobalToLocalBegin(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
    ierr = DMGlobalToLocalEnd(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
    ierr = DMRestoreGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
    ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr);
  }
  ierr = PetscMalloc7(numFaces*dim,&centroid,numFaces*dim,&normal,numFaces*2,&vol,numFaces*pdim,&uL,numFaces*pdim,&uR,numFaces*pdim,&fluxL,numFaces*pdim,&fluxR);CHKERRQ(ierr);
  /* Read out values */
  for (face = fStart, iface = 0; face < fEnd; ++face) {
    const PetscInt    *cells;
    const FaceGeom    *fg;
    const CellGeom    *cgL, *cgR;
    const PetscScalar *xL, *xR, *gL, *gR;
    PetscInt           ghost, d;

    ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
    if (ghost >= 0) continue;
    ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
    ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dm, cells[0], x, &xL);CHKERRQ(ierr);
    ierr = DMPlexPointLocalRead(dm, cells[1], x, &xR);CHKERRQ(ierr);
    if (computeGradients) {
      PetscReal dxL[3], dxR[3];

      ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr);
      ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr);
      WaxpyD(dim, -1, cgL->centroid, fg->centroid, dxL);
      WaxpyD(dim, -1, cgR->centroid, fg->centroid, dxR);
      for (d = 0; d < pdim; ++d) {
        uL[iface*pdim+d] = xL[d] + DotD(dim, &gL[d*dim], dxL);
        uR[iface*pdim+d] = xR[d] + DotD(dim, &gR[d*dim], dxR);
      }
    } else {
      for (d = 0; d < pdim; ++d) {
        uL[iface*pdim+d] = xL[d];
        uR[iface*pdim+d] = xR[d];
      }
    }
    for (d = 0; d < dim; ++d) {
      centroid[iface*dim+d] = fg->centroid[d];
      normal[iface*dim+d]   = fg->normal[d];
    }
    vol[iface*2+0] = cgL->volume;
    vol[iface*2+1] = cgR->volume;
    ++iface;
  }
  if (computeGradients) {
    ierr = VecRestoreArrayRead(locGrad,&lgrad);CHKERRQ(ierr);
    ierr = DMRestoreLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
  }
  ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
  fgeom.v0  = centroid;
  fgeom.n   = normal;
  cgeom.vol = vol;
  /* Riemann solve */
  ierr = PetscFVIntegrateRHSFunction(fvm, numFaces, Nf, &fvm, 0, fgeom, cgeom, uL, uR, riemann, fluxL, fluxR, dmplexts->rhsfunctionlocalctx);CHKERRQ(ierr);
  /* Insert fluxes */
  ierr = VecGetArray(F, &f);CHKERRQ(ierr);
  for (face = fStart, iface = 0; face < fEnd; ++face) {
    const PetscInt *cells;
    PetscScalar    *fL, *fR;
    PetscInt        ghost, d;

    ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
    if (ghost >= 0) continue;
    ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
    ierr = DMPlexPointGlobalRef(dm, cells[0], f, &fL);CHKERRQ(ierr);
    ierr = DMPlexPointGlobalRef(dm, cells[1], f, &fR);CHKERRQ(ierr);
    for (d = 0; d < pdim; ++d) {
      if (fL) fL[d] -= fluxL[iface*pdim+d];
      if (fR) fR[d] += fluxR[iface*pdim+d];
    }
    ++iface;
  }
  ierr = VecRestoreArray(F, &f);CHKERRQ(ierr);
  ierr = PetscFree7(centroid,normal,vol,uL,uR,fluxL,fluxR);CHKERRQ(ierr);
  ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 12
0
PETSC_EXTERN PetscErrorCode DMPlexRefine_CTetgen(DM dm, PetscReal *maxVolumes, DM *dmRefined)
{
  MPI_Comm       comm;
  const PetscInt dim       = 3;
  const char    *labelName = "marker";
  PLC           *in, *out;
  DMLabel        label;
  PetscInt       verbose = 0, vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,((PetscObject) dm)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
  ierr = MPIU_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMGetLabel(dm, labelName, &label);CHKERRQ(ierr);
  ierr = PLCCreate(&in);CHKERRQ(ierr);
  ierr = PLCCreate(&out);CHKERRQ(ierr);

  in->numberofpoints = vEnd - vStart;
  if (in->numberofpoints > 0) {
    PetscSection coordSection;
    Vec          coordinates;
    PetscScalar *array;

    ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberofpoints, &in->pointmarkerlist);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
    ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
    ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, m = -1;

      ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
      for (d = 0; d < dim; ++d) {
        in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
      }
      if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}

      in->pointmarkerlist[idx] = (int) m;
    }
    ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
  }
  ierr  = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);

  in->numberofcorners       = 4;
  in->numberoftetrahedra    = cEnd - cStart;
  in->tetrahedronvolumelist = maxVolumes;
  if (in->numberoftetrahedra > 0) {
    ierr = PetscMalloc1(in->numberoftetrahedra*in->numberofcorners, &in->tetrahedronlist);CHKERRQ(ierr);
    for (c = cStart; c < cEnd; ++c) {
      const PetscInt idx      = c - cStart;
      PetscInt      *closure = NULL;
      PetscInt       closureSize;

      ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      if ((closureSize != 5) && (closureSize != 15)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %D vertices in closure", closureSize);
      for (v = 0; v < 4; ++v) {
        in->tetrahedronlist[idx*in->numberofcorners + v] = closure[(v+closureSize-4)*2] - vStart;
      }
      ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    }
  }
  if (!rank) {
    TetGenOpts t;

    ierr = TetGenOptsInitialize(&t);CHKERRQ(ierr);

    t.in        = dm; /* Should go away */
    t.refine    = 1;
    t.varvolume = 1;
    t.quality   = 1;
    t.edgesout  = 1;
    t.zeroindex = 1;
    t.quiet     = 1;
    t.verbose   = verbose; /* Change this */

    ierr = TetGenCheckOpts(&t);CHKERRQ(ierr);
    ierr = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
  }
  in->tetrahedronvolumelist = NULL;
  {
    DMLabel        rlabel      = NULL;
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out->numberoftetrahedra;
    const PetscInt numVertices = out->numberofpoints;
    double         *meshCoords;
    int            *cells      = out->tetrahedronlist;
    PetscBool      interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;

    if (sizeof (PetscReal) == sizeof (double)) {
      meshCoords = (double *) out->pointlist;
    }
    else {
      PetscInt i;

      ierr = PetscMalloc1(3 * numVertices,&meshCoords);CHKERRQ(ierr);
      for (i = 0; i < 3 * numVertices; i++) {
        meshCoords[i] = (PetscReal) out->pointlist[i];
      }
    }

    ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
    ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
    if (sizeof (PetscReal) != sizeof (double)) {
      ierr = PetscFree(meshCoords);CHKERRQ(ierr);
    }
    if (label) {ierr = DMCreateLabel(*dmRefined, labelName); ierr = DMGetLabel(*dmRefined, labelName, &rlabel);}
    /* Set labels */
    for (v = 0; v < numVertices; ++v) {
      if (out->pointmarkerlist[v]) {
        if (rlabel) {ierr = DMLabelSetValue(rlabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
      }
    }
    if (interpolate) {
      PetscInt e, f;

      for (e = 0; e < out->numberofedges; e++) {
        if (out->edgemarkerlist[e]) {
          const PetscInt  vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
          const PetscInt *edges;
          PetscInt        numEdges;

          ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
          if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
          if (rlabel) {ierr = DMLabelSetValue(rlabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
        }
      }
      for (f = 0; f < out->numberoftrifaces; f++) {
        if (out->trifacemarkerlist[f]) {
          const PetscInt  vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
          const PetscInt *faces;
          PetscInt        numFaces;

          ierr = DMPlexGetFullJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
          if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
          if (rlabel) {ierr = DMLabelSetValue(rlabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
        }
      }
    }
    ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
  }
  ierr = PLCDestroy(&in);CHKERRQ(ierr);
  ierr = PLCDestroy(&out);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Ejemplo n.º 13
0
PETSC_EXTERN PetscErrorCode DMPlexGenerate_CTetgen(DM boundary, PetscBool interpolate, DM *dm)
{
  MPI_Comm       comm;
  const PetscInt dim       = 3;
  const char    *labelName = "marker";
  PLC           *in, *out;
  DMLabel        label;
  PetscInt       verbose = 0, vStart, vEnd, v, fStart, fEnd, f;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,((PetscObject) boundary)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMGetLabel(boundary, labelName, &label);CHKERRQ(ierr);
  ierr = PLCCreate(&in);CHKERRQ(ierr);
  ierr = PLCCreate(&out);CHKERRQ(ierr);

  in->numberofpoints = vEnd - vStart;
  if (in->numberofpoints > 0) {
    PetscSection coordSection;
    Vec          coordinates;
    PetscScalar *array;

    ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberofpoints,       &in->pointmarkerlist);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
    ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
    ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, m = -1;

      ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
      for (d = 0; d < dim; ++d) {
        in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
      }
      if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}

      in->pointmarkerlist[idx] = (int) m;
    }
    ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
  }
  ierr  = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr);

  in->numberoffacets = fEnd - fStart;
  if (in->numberoffacets > 0) {
    ierr = PetscMalloc1(in->numberoffacets, &in->facetlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberoffacets,   &in->facetmarkerlist);CHKERRQ(ierr);
    for (f = fStart; f < fEnd; ++f) {
      const PetscInt idx     = f - fStart;
      PetscInt      *points = NULL, numPoints, p, numVertices = 0, v, m = -1;
      polygon       *poly;

      in->facetlist[idx].numberofpolygons = 1;

      ierr = PetscMalloc1(in->facetlist[idx].numberofpolygons, &in->facetlist[idx].polygonlist);CHKERRQ(ierr);

      in->facetlist[idx].numberofholes    = 0;
      in->facetlist[idx].holelist         = NULL;

      ierr = DMPlexGetTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
      for (p = 0; p < numPoints*2; p += 2) {
        const PetscInt point = points[p];
        if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
      }

      poly                   = in->facetlist[idx].polygonlist;
      poly->numberofvertices = numVertices;
      ierr                   = PetscMalloc1(poly->numberofvertices, &poly->vertexlist);CHKERRQ(ierr);
      for (v = 0; v < numVertices; ++v) {
        const PetscInt vIdx = points[v] - vStart;
        poly->vertexlist[v] = vIdx;
      }
      if (label) {ierr = DMLabelGetValue(label, f, &m);CHKERRQ(ierr);}
      in->facetmarkerlist[idx] = (int) m;
      ierr = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
    }
  }
  if (!rank) {
    TetGenOpts t;

    ierr        = TetGenOptsInitialize(&t);CHKERRQ(ierr);
    t.in        = boundary; /* Should go away */
    t.plc       = 1;
    t.quality   = 1;
    t.edgesout  = 1;
    t.zeroindex = 1;
    t.quiet     = 1;
    t.verbose   = verbose;
    ierr        = TetGenCheckOpts(&t);CHKERRQ(ierr);
    ierr        = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
  }
  {
    DMLabel        glabel      = NULL;
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out->numberoftetrahedra;
    const PetscInt numVertices = out->numberofpoints;
    double         *meshCoords;
    int            *cells      = out->tetrahedronlist;

    if (sizeof (PetscReal) == sizeof (double)) {
      meshCoords = (double *) out->pointlist;
    }
    else {
      PetscInt i;

      ierr = PetscMalloc1(3 * numVertices,&meshCoords);CHKERRQ(ierr);
      for (i = 0; i < 3 * numVertices; i++) {
        meshCoords[i] = (PetscReal) out->pointlist[i];
      }
    }

    ierr = DMPlexInvertCells_Internal(dim, numCells, numCorners, cells);CHKERRQ(ierr);
    ierr = DMPlexCreateFromCellList(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
    if (sizeof (PetscReal) != sizeof (double)) {
      ierr = PetscFree(meshCoords);CHKERRQ(ierr);
    }
    if (label) {ierr = DMCreateLabel(*dm, labelName); ierr = DMGetLabel(*dm, labelName, &glabel);}
    /* Set labels */
    for (v = 0; v < numVertices; ++v) {
      if (out->pointmarkerlist[v]) {
        if (glabel) {ierr = DMLabelSetValue(glabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
      }
    }
    if (interpolate) {
      PetscInt e;

      for (e = 0; e < out->numberofedges; e++) {
        if (out->edgemarkerlist[e]) {
          const PetscInt  vertices[2] = {out->edgelist[e*2+0]+numCells, out->edgelist[e*2+1]+numCells};
          const PetscInt *edges;
          PetscInt        numEdges;

          ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
          if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
          if (glabel) {ierr = DMLabelSetValue(glabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
        }
      }
      for (f = 0; f < out->numberoftrifaces; f++) {
        if (out->trifacemarkerlist[f]) {
          const PetscInt  vertices[3] = {out->trifacelist[f*3+0]+numCells, out->trifacelist[f*3+1]+numCells, out->trifacelist[f*3+2]+numCells};
          const PetscInt *faces;
          PetscInt        numFaces;

          ierr = DMPlexGetFullJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
          if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
          if (glabel) {ierr = DMLabelSetValue(glabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
        }
      }
    }
    ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
  }

  ierr = PLCDestroy(&in);CHKERRQ(ierr);
  ierr = PLCDestroy(&out);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}