/usr/lib/petscdir/3.4.2/include/petscdmmesh_viewers.hh is in libpetsc3.4.2-dev 3.4.2.dfsg1-8.1+b1.
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#define __PETSCDMMESH_VIEWERS_HH
#include <petscdmmesh.hh>
#include <petsc-private/petscimpl.h>
#include <iomanip>
using ALE::Obj;
class VTKViewer {
public:
VTKViewer() {};
virtual ~VTKViewer() {};
#undef __FUNCT__
#define __FUNCT__ "writeHeader"
template<typename Mesh>
static PetscErrorCode writeHeader(const Obj<Mesh>& mesh, PetscViewer viewer) {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerASCIIPrintf(viewer,"# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Simplicial Mesh Example\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"ASCII\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeVertices"
template<typename Mesh>
static PetscErrorCode writeVertices(const Obj<Mesh>& mesh, PetscViewer viewer) {
Obj<typename Mesh::real_section_type> coordinates;
if (mesh->hasRealSection("coordinates_dimensioned")) {
coordinates = mesh->getRealSection("coordinates_dimensioned");
} else if (mesh->hasRealSection("coordinates")) {
coordinates = mesh->getRealSection("coordinates");
} else {
throw ALE::Exception("Missing coordinates in mesh");
}
const int embedDim = coordinates->getFiberDimension(*mesh->depthStratum(0)->begin());
Obj<typename Mesh::numbering_type> vNumbering;
PetscErrorCode ierr;
PetscFunctionBegin;
if (mesh->hasLabel("censored depth")) {
vNumbering = mesh->getFactory()->getNumbering(mesh, "censored depth", 0);
} else {
vNumbering = mesh->getFactory()->getNumbering(mesh, 0);
}
ierr = PetscViewerASCIIPrintf(viewer, "POINTS %d double\n", vNumbering->getGlobalSize());CHKERRQ(ierr);
ierr = writeSection(coordinates, embedDim, vNumbering, viewer, 3);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeField"
template<typename Section>
static PetscErrorCode writeField(const Obj<Section>& field, const std::string& name, const int fiberDim, const Obj<PETSC_MESH_TYPE::numbering_type>& numbering, PetscViewer viewer, int enforceDim = -1, int precision = 6) {
int dim = enforceDim > 0 ? enforceDim : fiberDim;
PetscErrorCode ierr;
PetscFunctionBegin;
if (enforceDim == -4) dim = 4;
if (dim == 3) {
ierr = PetscViewerASCIIPrintf(viewer, "VECTORS %s double\n", name.c_str());CHKERRQ(ierr);
} else {
if (name == "") {
ierr = PetscViewerASCIIPrintf(viewer, "SCALARS Unknown double %d\n", dim);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer, "SCALARS %s double %d\n", name.c_str(), dim);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
}
ierr = writeSection(field, fiberDim, numbering, viewer, enforceDim, precision);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeSection"
template<typename Section>
static PetscErrorCode writeSection(const Obj<Section>& field, const int fiberDim, const Obj<PETSC_MESH_TYPE::numbering_type>& numbering, PetscViewer viewer, int enforceDim = -1, int precision = 6) {
typedef typename Section::value_type value_type;
const typename Section::chart_type& chart = field->getChart();
const MPI_Datatype mpiType = ALE::New::ParallelFactory<value_type>::singleton(field->debug())->getMPIType();
const bool verify = enforceDim == -4;
const bool opt2 = enforceDim == 3 && fiberDim == 2;
const bool opt3 = std::max(fiberDim, enforceDim) == fiberDim && fiberDim == 3;
PetscErrorCode ierr;
PetscFunctionBegin;
if (verify) enforceDim = 3;
if (field->commRank() == 0) {
const typename Section::chart_type::const_iterator cEnd = chart.end();
std::ostringstream formatString;
if (opt2) {
formatString << "%." << precision << "e %." << precision << "e 0.0\n";
} else if (opt3) {
formatString << "%." << precision << "e %." << precision << "e %." << precision << "e\n";
}
for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != cEnd; ++p_iter) {
if (!numbering->hasPoint(*p_iter)) continue;
const value_type *array = field->restrictPoint(*p_iter);
const int& dim = field->getFiberDimension(*p_iter);
// Perhaps there should be a flag for excluding boundary values
if (dim != 0) {
if (opt2) {
ierr = PetscViewerASCIIPrintf(viewer, formatString.str().c_str(), array[0], array[1]);CHKERRQ(ierr);
} else if (opt3) {
ierr = PetscViewerASCIIPrintf(viewer, formatString.str().c_str(), array[0], array[1], array[2]);CHKERRQ(ierr);
} else {
ostringstream line;
line << std::resetiosflags(std::ios::fixed)
<< std::setiosflags(std::ios::scientific)
<< std::setprecision(precision);
if (verify) {line << *p_iter << " ";}
for(int d = 0; d < fiberDim; d++) {
if (d > 0) {
line << " ";
}
line << array[d];
}
for(int d = fiberDim; d < enforceDim; d++) {
line << " 0.0";
}
line << std::endl;
ierr = PetscViewerASCIIPrintf(viewer, "%s", line.str().c_str());CHKERRQ(ierr);
}
}
}
for(int p = 1; p < field->commSize(); p++) {
value_type *remoteValues;
int numLocalElementsAndFiberDim[2];
int size;
MPI_Status status;
ierr = MPI_Recv(numLocalElementsAndFiberDim, 2, MPI_INT, p, 1, field->comm(), &status);CHKERRQ(ierr);
size = numLocalElementsAndFiberDim[0]*numLocalElementsAndFiberDim[1];
ierr = PetscMalloc(size * sizeof(value_type), &remoteValues);CHKERRQ(ierr);
ierr = MPI_Recv(remoteValues, size, mpiType, p, 1, field->comm(), &status);CHKERRQ(ierr);
for(int e = 0; e < numLocalElementsAndFiberDim[0]; e++) {
if (opt2) {
ierr = PetscViewerASCIIPrintf(viewer, formatString.str().c_str(), remoteValues[e*numLocalElementsAndFiberDim[1]+0], remoteValues[e*numLocalElementsAndFiberDim[1]+1]);CHKERRQ(ierr);
} else if (opt3) {
ierr = PetscViewerASCIIPrintf(viewer, formatString.str().c_str(), remoteValues[e*numLocalElementsAndFiberDim[1]+0], remoteValues[e*numLocalElementsAndFiberDim[1]+1], remoteValues[e*numLocalElementsAndFiberDim[1]+2]);CHKERRQ(ierr);
} else {
ostringstream line;
line << std::resetiosflags(std::ios::fixed)
<< std::setiosflags(std::ios::scientific)
<< std::setprecision(precision);
if (verify) {line << ((int) remoteValues[e*numLocalElementsAndFiberDim[1]+0]);}
for(int d = verify; d < numLocalElementsAndFiberDim[1]; d++) {
if (d > (int) verify) { line << " ";
}
line << remoteValues[e*numLocalElementsAndFiberDim[1]+d];
}
for(int d = numLocalElementsAndFiberDim[1]; d < enforceDim; d++) {
line << " 0.0";
}
line << std::endl;
ierr = PetscViewerASCIIPrintf(viewer, "%s", line.str().c_str());CHKERRQ(ierr);
}
}
ierr = PetscFree(remoteValues);CHKERRQ(ierr);
}
} else {
const typename Section::chart_type::const_iterator cEnd = chart.end();
int numLocalElements = numbering->getLocalSize();
const int size = numLocalElements*(fiberDim+verify);
int k = 0;
value_type *localValues;
ierr = PetscMalloc(size * sizeof(value_type), &localValues);CHKERRQ(ierr);
for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != cEnd; ++p_iter) {
if (!numbering->hasPoint(*p_iter)) continue;
if (numbering->isLocal(*p_iter)) {
const value_type *array = field->restrictPoint(*p_iter);
const int& dim = field->getFiberDimension(*p_iter);
if (verify) localValues[k++] = *p_iter;
for(int i = 0; i < dim; ++i) {
localValues[k++] = array[i];
}
}
}
if (k != size) {
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of values to send for field, %d should be %d", k, size);
}
int numLocalElementsAndFiberDim[2] = {numLocalElements, fiberDim+verify};
ierr = MPI_Send(numLocalElementsAndFiberDim, 2, MPI_INT, 0, 1, field->comm());CHKERRQ(ierr);
ierr = MPI_Send(localValues, size, mpiType, 0, 1, field->comm());CHKERRQ(ierr);
ierr = PetscFree(localValues);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
};
static int getCellType(const int dim, const int corners) {
int cellType = -1;
switch(dim) {
case 0:
switch(corners) {
case 1:
// VTK_VERTEX
cellType = 1;
break;
default:
break;
}
break;
case 1:
switch(corners) {
case 2:
// VTK_LINE
cellType = 3;
break;
case 3:
// VTJ_QUADRATIC_EDGE
cellType = 21;
break;
default:
break;
}
break;
case 2:
switch(corners) {
case 3:
// VTK_TRIANGLE
cellType = 5;
break;
case 4:
// VTK_QUAD
cellType = 9;
break;
case 6:
// VTK_QUADRATIC_TRIANGLE
cellType = 22;
break;
case 9:
// VTK_QUADRATIC_QUAD
cellType = 23;
break;
default:
break;
}
break;
case 3:
switch(corners) {
case 4:
// VTK_TETRA
cellType = 10;
break;
case 8:
// VTK_HEXAHEDRON
cellType = 12;
break;
case 10:
// VTK_QUADRATIC_TETRA
cellType = 24;
break;
case 27:
// VTK_QUADRATIC_HEXAHEDRON
cellType = 29;
break;
default:
break;
}
}
return cellType;
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, PetscViewer viewer)
{
int depth = mesh->depth();
Obj<typename Mesh::label_sequence> elements;
Obj<typename Mesh::numbering_type> cNumbering;
Obj<typename Mesh::numbering_type> vNumbering;
PetscErrorCode ierr;
/* Empty portions of the mesh can give rise to 0 for 'depth', and we need the same value */
ierr = MPI_Allreduce(&depth, &depth, 1, MPI_INT, MPI_MAX, mesh->comm());CHKERRQ(ierr);
if (mesh->hasLabel("censored depth")) {
elements = mesh->getLabelStratum("censored depth", depth);
cNumbering = mesh->getFactory()->getNumbering(mesh, "censored depth", depth);
vNumbering = mesh->getFactory()->getNumbering(mesh, "censored depth", 0);
} else {
elements = mesh->heightStratum(0);
cNumbering = mesh->getFactory()->getNumbering(mesh, depth);
vNumbering = mesh->getFactory()->getNumbering(mesh, 0);
}
return writeElements(mesh, elements, cNumbering, vNumbering, viewer);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, const std::string& cLabelName, const int cLabelValue, const std::string& vLabelName, const int vLabelValue, PetscViewer viewer)
{
Obj<typename Mesh::label_sequence> elements;
Obj<typename Mesh::numbering_type> cNumbering;
Obj<typename Mesh::numbering_type> vNumbering;
if (mesh->hasLabel(cLabelName)) {
elements = mesh->getLabelStratum(cLabelName, cLabelValue);
cNumbering = mesh->getFactory()->getNumbering(mesh, cLabelName, cLabelValue);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Invalid label name: %s", cLabelName.c_str());
}
if (mesh->hasLabel(vLabelName)) {
vNumbering = mesh->getFactory()->getNumbering(mesh, vLabelName, vLabelValue);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Invalid label name: %s", vLabelName.c_str());
}
return writeElements(mesh, elements, cNumbering, vNumbering, viewer);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, const Obj<typename Mesh::label_sequence>& elements, const Obj<typename Mesh::numbering_type>& cNumbering, const Obj<typename Mesh::numbering_type>& vNumbering, PetscViewer viewer)
{
typedef typename Mesh::sieve_type sieve_type;
typedef ALE::ISieveVisitor::NConeRetriever<sieve_type> visitor_type;
const Obj<sieve_type>& sieve = mesh->getSieve();
int localCorners = 0;
int corners;
int numElements;
PetscErrorCode ierr;
visitor_type ncV(*sieve, (size_t) pow((double) sieve->getMaxConeSize(), std::max(0, mesh->depth())));
PetscFunctionBegin;
if (elements->size()) localCorners = mesh->getNumCellCorners(*elements->begin());
corners = localCorners;
numElements = cNumbering->getGlobalSize();
ierr = MPI_Reduce(&localCorners, &corners, 1, MPI_INT, MPI_MAX, 0, mesh->comm());CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"CELLS %d %d\n", numElements, numElements*(corners+1));CHKERRQ(ierr);
if (mesh->commRank() == 0) {
const typename Mesh::label_sequence::iterator eEnd = elements->end();
const bool opt3 = corners == 3;
const bool opt4 = corners == 4;
for(typename Mesh::label_sequence::iterator e_iter = elements->begin(); e_iter != eEnd; ++e_iter) {
ALE::ISieveTraversal<sieve_type>::orientedClosure(*sieve, *e_iter, ncV);
const typename visitor_type::oriented_point_type *cone = ncV.getOrientedPoints();
const int coneSize = ncV.getOrientedSize();
if (coneSize != corners) {
std::ostringstream msg;
msg << "Inconsistency in topology found for mesh '"
<< mesh->getName() << "' during output.\n"
<< "Number of vertices (" << coneSize << ") in cell '"
<< *e_iter << "' does not expected number of vertices ("
<< corners << ").";
throw ALE::Exception(msg.str());
} // if
if (opt3) {
ierr = PetscViewerASCIIPrintf(viewer, "3 %d %d %d\n", vNumbering->getIndex(cone[0].first), vNumbering->getIndex(cone[1].first), vNumbering->getIndex(cone[2].first));CHKERRQ(ierr);
} else if (opt4) {
ierr = PetscViewerASCIIPrintf(viewer, "4 %d %d %d %d\n", vNumbering->getIndex(cone[0].first), vNumbering->getIndex(cone[1].first), vNumbering->getIndex(cone[2].first), vNumbering->getIndex(cone[3].first));CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer, "%d ", corners);CHKERRQ(ierr);
for(int c = 0; c < coneSize; ++c) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", vNumbering->getIndex(cone[c].first));CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
ncV.clear();
}
for(int p = 1; p < mesh->commSize(); p++) {
int numLocalElementsAndCorners[2];
int *remoteVertices;
MPI_Status status;
ierr = MPI_Recv(numLocalElementsAndCorners, 2, MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
ierr = PetscMalloc(numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1] * sizeof(int), &remoteVertices);CHKERRQ(ierr);
ierr = MPI_Recv(remoteVertices, numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1], MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
for(int e = 0; e < numLocalElementsAndCorners[0]; e++) {
ierr = PetscViewerASCIIPrintf(viewer, "%d ", numLocalElementsAndCorners[1]);CHKERRQ(ierr);
for(int c = 0; c < numLocalElementsAndCorners[1]; c++) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", remoteVertices[e*numLocalElementsAndCorners[1]+c]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
ierr = PetscFree(remoteVertices);CHKERRQ(ierr);
}
} else {
const typename Mesh::label_sequence::iterator eEnd = elements->end();
int numLocalElements = cNumbering->getLocalSize();
int *localVertices;
int k = 0;
ierr = PetscMalloc(numLocalElements*corners * sizeof(int), &localVertices);CHKERRQ(ierr);
for(typename Mesh::label_sequence::iterator e_iter = elements->begin(); e_iter != eEnd; ++e_iter) {
if (cNumbering->isLocal(*e_iter)) {
ALE::ISieveTraversal<sieve_type>::orientedClosure(*sieve, *e_iter, ncV);
const typename visitor_type::oriented_point_type *cone = ncV.getOrientedPoints();
for(int c = 0; c < ncV.getOrientedSize(); ++c) {
localVertices[k++] = vNumbering->getIndex(cone[c].first);
}
ncV.clear();
}
}
if (k != numLocalElements*corners) {
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numLocalElements*corners);
}
int numLocalElementsAndCorners[2] = {numLocalElements, corners};
ierr = MPI_Send(numLocalElementsAndCorners, 2, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
ierr = MPI_Send(localVertices, numLocalElements*corners, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
ierr = PetscFree(localVertices);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "CELL_TYPES %d\n", numElements);CHKERRQ(ierr);
const int cellType = getCellType(mesh->getDimension(), corners);
for(int e = 0; e < numElements; e++) {
ierr = PetscViewerASCIIPrintf(viewer, "%d\n", cellType);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
static PetscErrorCode writeElements(const Obj<PETSC_MESH_TYPE>& mesh, const Obj<PETSC_MESH_TYPE::label_sequence>& elements, const Obj<PETSC_MESH_TYPE::numbering_type>& cNumbering, const Obj<PETSC_MESH_TYPE::numbering_type>& vNumbering, PetscViewer viewer)
{
typedef ALE::SieveAlg<PETSC_MESH_TYPE> sieve_alg_type;
const Obj<PETSC_MESH_TYPE::sieve_type>& sieve = mesh->getSieve();
int depth = mesh->depth();
int localCorners = 0;
int corners;
int numElements;
PetscErrorCode ierr;
PetscFunctionBegin;
if (elements->size()) localCorners = mesh->getNumCellCorners();
corners = localCorners;
numElements = cNumbering->getGlobalSize();
ierr = MPI_Reduce(&localCorners, &corners, 1, MPI_INT, MPI_MAX, 0, mesh->comm());CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"CELLS %d %d\n", numElements, numElements*(corners+1));CHKERRQ(ierr);
if (mesh->commRank() == 0) {
#ifdef PETSC_OPT_SIEVE
ALE::ISieveVisitor::NConeRetriever<PETSC_MESH_TYPE::sieve_type> ncV(*sieve, (size_t) pow((double) sieve->getMaxConeSize(), std::max(0, depth)));
#endif
const PETSC_MESH_TYPE::label_sequence::iterator eEnd = elements->end();
for(PETSC_MESH_TYPE::label_sequence::iterator e_iter = elements->begin(); e_iter != eEnd; ++e_iter) {
ierr = PetscViewerASCIIPrintf(viewer, "%d ", corners);CHKERRQ(ierr);
#ifdef PETSC_OPT_SIEVE
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*sieve, *e_iter, ncV);
const int coneSize = ncV.getSize();
const PETSC_MESH_TYPE::point_type *cone = ncV.getPoints();
for(int v = 0; v < coneSize; ++v) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", vNumbering->getIndex(cone[v]));CHKERRQ(ierr);
}
ncV.clear();
#else
const Obj<sieve_alg_type::coneArray>& cone = sieve_alg_type::nCone(mesh, *e_iter, depth);
const sieve_alg_type::coneArray::iterator cEnd = cone->end();
for(sieve_alg_type::coneArray::iterator c_iter = cone->begin(); c_iter != cEnd; ++c_iter) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", vNumbering->getIndex(*c_iter));CHKERRQ(ierr);
}
#endif
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
for(int p = 1; p < mesh->commSize(); p++) {
int numLocalElementsAndCorners[2];
int *remoteVertices;
MPI_Status status;
ierr = MPI_Recv(numLocalElementsAndCorners, 2, MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
ierr = PetscMalloc(numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1] * sizeof(int), &remoteVertices);CHKERRQ(ierr);
ierr = MPI_Recv(remoteVertices, numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1], MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
for(int e = 0; e < numLocalElementsAndCorners[0]; e++) {
ierr = PetscViewerASCIIPrintf(viewer, "%d ", numLocalElementsAndCorners[1]);CHKERRQ(ierr);
for(int c = 0; c < numLocalElementsAndCorners[1]; c++) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", remoteVertices[e*numLocalElementsAndCorners[1]+c]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
ierr = PetscFree(remoteVertices);CHKERRQ(ierr);
}
} else {
int numLocalElements = cNumbering->getLocalSize();
int *localVertices;
int k = 0;
#ifdef PETSC_OPT_SIEVE
ALE::ISieveVisitor::NConeRetriever<PETSC_MESH_TYPE::sieve_type> ncV(*sieve, (size_t) pow((double) sieve->getMaxConeSize(), std::max(0, depth)));
#endif
const PETSC_MESH_TYPE::label_sequence::iterator eEnd = elements->end();
ierr = PetscMalloc(numLocalElements*corners * sizeof(int), &localVertices);CHKERRQ(ierr);
for(PETSC_MESH_TYPE::label_sequence::iterator e_iter = elements->begin(); e_iter != eEnd; ++e_iter) {
#ifdef PETSC_OPT_SIEVE
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*sieve, *e_iter, ncV);
const int coneSize = ncV.getSize();
const PETSC_MESH_TYPE::point_type *cone = ncV.getPoints();
if (cNumbering->isLocal(*e_iter)) {
for(int v = 0; v < coneSize; ++v) {
localVertices[k++] = vNumbering->getIndex(cone[v]);
}
}
ncV.clear();
#else
const Obj<sieve_alg_type::coneArray>& cone = sieve_alg_type::nCone(mesh, *e_iter, depth);
if (cNumbering->isLocal(*e_iter)) {
const PETSC_MESH_TYPE::sieve_type::coneArray::iterator cEnd = cone->end();
for(PETSC_MESH_TYPE::sieve_type::coneArray::iterator c_iter = cone->begin(); c_iter != cEnd; ++c_iter) {
localVertices[k++] = vNumbering->getIndex(*c_iter);
}
}
#endif
}
if (k != numLocalElements*corners) {
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numLocalElements*corners);
}
int numLocalElementsAndCorners[2] = {numLocalElements, corners};
ierr = MPI_Send(numLocalElementsAndCorners, 2, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
ierr = MPI_Send(localVertices, numLocalElements*corners, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
ierr = PetscFree(localVertices);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "CELL_TYPES %d\n", numElements);CHKERRQ(ierr);
const int cellType = getCellType(mesh->getDimension(), corners);
for(int e = 0; e < numElements; e++) {
ierr = PetscViewerASCIIPrintf(viewer, "%d\n", cellType);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
};
};
class VTKXMLViewer {
public:
VTKXMLViewer() {};
virtual ~VTKXMLViewer() {};
#undef __FUNCT__
#define __FUNCT__ "getVertexNumbering"
template<typename Mesh>
static Obj<typename Mesh::numbering_type> getVertexNumbering(const Obj<Mesh>& mesh) {
if (mesh->hasLabel("censored depth")) {
return mesh->getFactory()->getNumbering(mesh, "censored depth", 0);
}
return mesh->getFactory()->getNumbering(mesh, 0);
};
#undef __FUNCT__
#define __FUNCT__ "getCellNumbering"
template<typename Mesh>
static Obj<typename Mesh::numbering_type> getCellNumbering(const Obj<Mesh>& mesh) {
const int depth = mesh->depth();
if (mesh->hasLabel("censored depth")) {
return mesh->getFactory()->getNumbering(mesh, "censored depth", depth);
}
return mesh->getFactory()->getNumbering(mesh, depth);
};
#undef __FUNCT__
#define __FUNCT__ "getCells"
template<typename Mesh>
static Obj<typename Mesh::label_sequence> getCells(const Obj<Mesh>& mesh) {
const int depth = mesh->depth();
if (mesh->hasLabel("censored depth")) {
return mesh->getLabelStratum("censored depth", depth);
}
return mesh->heightStratum(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeHeader"
template<typename Mesh>
static PetscErrorCode writeHeader(const Obj<Mesh>& mesh, PetscViewer viewer) {
Obj<typename Mesh::numbering_type> vNumbering = getVertexNumbering(mesh);
Obj<typename Mesh::numbering_type> cNumbering = getCellNumbering(mesh);
PetscErrorCode ierr;
PetscFunctionBegin;
#ifdef PETSC_WORDS_BIGENDIAN
ierr = PetscViewerASCIIPrintf(viewer,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"BigEndian\">\n");CHKERRQ(ierr);
#else
ierr = PetscViewerASCIIPrintf(viewer,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");CHKERRQ(ierr);
#endif
ierr = PetscViewerASCIIPrintf(viewer," <UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," <Piece NumberOfPoints=\"%d\" NumberOfCells=\"%d\">\n", vNumbering->getGlobalSize(), cNumbering->getGlobalSize());CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeVertices"
template<typename Mesh>
static PetscErrorCode writeVertices(const Obj<Mesh>& mesh, PetscViewer viewer) {
Obj<typename Mesh::real_section_type> coordinates;
if (mesh->hasRealSection("coordinates_dimensioned")) {
coordinates = mesh->getRealSection("coordinates_dimensioned");
} else if (mesh->hasRealSection("coordinates")) {
coordinates = mesh->getRealSection("coordinates");
} else {
throw ALE::Exception("Missing coordinates in mesh");
}
const int embedDim = coordinates->getFiberDimension(*mesh->depthStratum(0)->begin());
Obj<typename Mesh::numbering_type> vNumbering = getVertexNumbering(mesh);
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerASCIIPrintf(viewer, "<Points>\n");CHKERRQ(ierr);
ierr = writeSection(coordinates, embedDim, vNumbering, viewer, 3);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, "</Points>\n");CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeSection"
template<typename Section>
static PetscErrorCode writeSection(const Obj<Section>& field, const int fiberDim, const Obj<PETSC_MESH_TYPE::numbering_type>& numbering, PetscViewer viewer, int enforceDim = -1, int precision = 6) {
typedef typename Section::value_type value_type;
const typename Section::chart_type& chart = field->getChart();
const typename Section::chart_type::const_iterator cEnd = chart.end();
const MPI_Datatype mpiType = ALE::New::ParallelFactory<value_type>::singleton(field->debug())->getMPIType();
PetscErrorCode ierr;
PetscFunctionBegin;
int numLocalElements = numbering->getLocalSize();
const int size = numLocalElements*std::max(fiberDim, enforceDim);
int k = 0;
value_type *localValues;
ierr = PetscMalloc(size * sizeof(value_type), &localValues);CHKERRQ(ierr);
for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != cEnd; ++p_iter) {
if (!numbering->hasPoint(*p_iter)) continue;
if (numbering->isLocal(*p_iter)) {
const value_type *array = field->restrictPoint(*p_iter);
const int& dim = field->getFiberDimension(*p_iter);
for(int i = 0; i < dim; ++i) {
localValues[k++] = array[i];
}
for(int d = dim; d < enforceDim; d++) {
localValues[k++] = 0.0;
}
}
}
if (k != size) {
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of values to send for field, %d should be %d", k, size);
}
if (field->commRank() == 0) {
ierr = PetscViewerASCIIPrintf(viewer, "<DataArray type=\"Float32\" Name=\"%s\" format=\"binary\" Number of Components=\"%d\">\n", field->getName());CHKERRQ(ierr);
// Encode and write data
for(int p = 1; p < field->commSize(); p++) {
value_type *remoteValues;
int numLocalElementsAndFiberDim[2];
int remoteSize;
MPI_Status status;
ierr = MPI_Recv(numLocalElementsAndFiberDim, 2, MPI_INT, p, 1, field->comm(), &status);CHKERRQ(ierr);
remoteSize = numLocalElementsAndFiberDim[0]*numLocalElementsAndFiberDim[1];
ierr = PetscMalloc(remoteSize * sizeof(value_type), &remoteValues);CHKERRQ(ierr);
ierr = MPI_Recv(remoteValues, remoteSize, mpiType, p, 1, field->comm(), &status);CHKERRQ(ierr);
// Encode and write data
ierr = PetscFree(remoteValues);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "</DataArray>\n");CHKERRQ(ierr);
} else {
int numLocalElementsAndFiberDim[2] = {numLocalElements, fiberDim};
ierr = MPI_Send(numLocalElementsAndFiberDim, 2, MPI_INT, 0, 1, field->comm());CHKERRQ(ierr);
ierr = MPI_Send(localValues, size, mpiType, 0, 1, field->comm());CHKERRQ(ierr);
}
ierr = PetscFree(localValues);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, PetscViewer viewer)
{
Obj<typename Mesh::label_sequence> elements = getCells(mesh);
Obj<typename Mesh::numbering_type> cNumbering = getCellNumbering(mesh);
Obj<typename Mesh::numbering_type> vNumbering = getVertexNumbering(mesh);
return writeElements(mesh, elements, cNumbering, vNumbering, viewer);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, const std::string& cLabelName, const int cLabelValue, const std::string& vLabelName, const int vLabelValue, PetscViewer viewer)
{
Obj<typename Mesh::label_sequence> elements;
Obj<typename Mesh::numbering_type> cNumbering;
Obj<typename Mesh::numbering_type> vNumbering;
if (mesh->hasLabel(cLabelName)) {
elements = mesh->getLabelStratum(cLabelName, cLabelValue);
cNumbering = mesh->getFactory()->getNumbering(mesh, cLabelName, cLabelValue);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Invalid label name: %s", cLabelName.c_str());
}
if (mesh->hasLabel(vLabelName)) {
vNumbering = mesh->getFactory()->getNumbering(mesh, vLabelName, vLabelValue);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Invalid label name: %s", vLabelName.c_str());
}
return writeElements(mesh, elements, cNumbering, vNumbering, viewer);
};
#undef __FUNCT__
#define __FUNCT__ "writeElements"
template<typename Mesh>
static PetscErrorCode writeElements(const Obj<Mesh>& mesh, const Obj<typename Mesh::label_sequence>& elements, const Obj<typename Mesh::numbering_type>& cNumbering, const Obj<typename Mesh::numbering_type>& vNumbering, PetscViewer viewer)
{
typedef typename Mesh::sieve_type sieve_type;
typedef ALE::ISieveVisitor::NConeRetriever<sieve_type> visitor_type;
const Obj<sieve_type>& sieve = mesh->getSieve();
const typename Mesh::label_sequence::iterator eEnd = elements->end();
int localCorners = elements->size() ? mesh->getNumCellCorners(*elements->begin()) : 0;
int corners = localCorners;
int numElements = cNumbering->getGlobalSize();
int numLocalElements = cNumbering->getLocalSize();
int k = 0;
int *localVertices;
PetscErrorCode ierr;
visitor_type ncV(*sieve, (size_t) pow((double) sieve->getMaxConeSize(), std::max(0, mesh->depth())));
PetscFunctionBegin;
ierr = MPI_Reduce(&localCorners, &corners, 1, MPI_INT, MPI_MAX, 0, mesh->comm());CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," <Cells>\n");CHKERRQ(ierr);
ierr = PetscMalloc(numLocalElements*corners * sizeof(int), &localVertices);CHKERRQ(ierr);
for(typename Mesh::label_sequence::iterator e_iter = elements->begin(); e_iter != eEnd; ++e_iter) {
if (cNumbering->isLocal(*e_iter)) {
ALE::ISieveTraversal<sieve_type>::orientedClosure(*sieve, *e_iter, ncV);
const typename visitor_type::oriented_point_type *cone = ncV.getOrientedPoints();
for(int c = 0; c < ncV.getOrientedSize(); ++c) {
localVertices[k++] = vNumbering->getIndex(cone[c].first);
}
ncV.clear();
}
}
if (k != numLocalElements*corners) {
SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numLocalElements*corners);
}
if (mesh->commRank() == 0) {
ierr = PetscViewerASCIIPrintf(viewer, " <DataArray type=\"Int32\" Name=\"connectivity\" format=\"ascii\">\n");CHKERRQ(ierr);
for(int e = 0; e < numLocalElements; e++) {
for(int c = 0; c < corners; c++) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", localVertices[e*corners+c]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
for(int p = 1; p < mesh->commSize(); p++) {
int numLocalElementsAndCorners[2];
int *remoteVertices;
MPI_Status status;
ierr = MPI_Recv(numLocalElementsAndCorners, 2, MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
ierr = PetscMalloc(numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1] * sizeof(int), &remoteVertices);CHKERRQ(ierr);
ierr = MPI_Recv(remoteVertices, numLocalElementsAndCorners[0]*numLocalElementsAndCorners[1], MPI_INT, p, 1, mesh->comm(), &status);CHKERRQ(ierr);
for(int e = 0; e < numLocalElementsAndCorners[0]; e++) {
for(int c = 0; c < numLocalElementsAndCorners[1]; c++) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", remoteVertices[e*numLocalElementsAndCorners[1]+c]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, "\n");CHKERRQ(ierr);
}
ierr = PetscFree(remoteVertices);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, " </DataArray>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, " <DataArray type=\"Int32\" Name=\"offsets\" format=\"ascii\">\n");CHKERRQ(ierr);
for(int e = 0; e < numElements*corners; e += corners) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", e);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, " </DataArray>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer, " <DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n");CHKERRQ(ierr);
const int cellType = getCellType(mesh->getDimension(), corners);
for(int e = 0; e < numElements; e++) {
ierr = PetscViewerASCIIPrintf(viewer, " %d", cellType);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, " </DataArray>\n");CHKERRQ(ierr);
} else {
int numLocalElementsAndCorners[2] = {numLocalElements, corners};
ierr = MPI_Send(numLocalElementsAndCorners, 2, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
ierr = MPI_Send(localVertices, numLocalElements*corners, MPI_INT, 0, 1, mesh->comm());CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPrintf(viewer, " </Cells>\n");CHKERRQ(ierr);
ierr = PetscFree(localVertices);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "writeFooter"
static PetscErrorCode writeFooter(PetscViewer viewer) {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerASCIIPrintf(viewer," </Piece>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer," </UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</VTKFile>\n");CHKERRQ(ierr);
PetscFunctionReturn(0);
};
};
#undef __FUNCT__
#define __FUNCT__ "SectionView_Sieve_Ascii"
template<typename Bundle, typename Section>
PetscErrorCode SectionView_Sieve_Ascii(const Obj<Bundle>& bundle, const Obj<Section>& s, const char name[], PetscViewer viewer, int enforceDim = -1)
{
// state 0: No header has been output
// state 1: Only POINT_DATA has been output
// state 2: Only CELL_DATA has been output
// state 3: Output both, POINT_DATA last
// state 4: Output both, CELL_DATA last
PetscViewerFormat format;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerGetFormat(viewer, &format);CHKERRQ(ierr);
if (format == PETSC_VIEWER_ASCII_VTK || format == PETSC_VIEWER_ASCII_VTK_CELL) {
static PetscInt stateId = -1;
PetscInt doOutput = 0;
PetscInt outputState = 0;
PetscBool hasState;
if (stateId < 0) {
ierr = PetscObjectComposedDataRegister(&stateId);CHKERRQ(ierr);
ierr = PetscObjectComposedDataSetInt((PetscObject) viewer, stateId, 0);CHKERRQ(ierr);
}
ierr = PetscObjectComposedDataGetInt((PetscObject) viewer, stateId, outputState, hasState);CHKERRQ(ierr);
if (format == PETSC_VIEWER_ASCII_VTK) {
if (outputState == 0) {
outputState = 1;
doOutput = 1;
} else if (outputState == 1) {
doOutput = 0;
} else if (outputState == 2) {
outputState = 3;
doOutput = 1;
} else if (outputState == 3) {
doOutput = 0;
} else if (outputState == 4) {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Tried to output POINT_DATA again after intervening CELL_DATA");
}
const ALE::Obj<PETSC_MESH_TYPE::numbering_type>& numbering = bundle->getFactory()->getNumbering(bundle, 0);
PetscInt fiberDim = std::abs(s->getFiberDimension(*bundle->depthStratum(0)->begin()));
if (doOutput) {
ierr = PetscViewerASCIIPrintf(viewer, "POINT_DATA %d\n", numbering->getGlobalSize());CHKERRQ(ierr);
}
VTKViewer::writeField(s, std::string(name), fiberDim, numbering, viewer, enforceDim);
} else {
if (outputState == 0) {
outputState = 2;
doOutput = 1;
} else if (outputState == 1) {
outputState = 4;
doOutput = 1;
} else if (outputState == 2) {
doOutput = 0;
} else if (outputState == 3) {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE, "Tried to output CELL_DATA again after intervening POINT_DATA");
} else if (outputState == 4) {
doOutput = 0;
}
const ALE::Obj<PETSC_MESH_TYPE::numbering_type>& numbering = bundle->getFactory()->getNumbering(bundle, bundle->depth());
PetscInt fiberDim = s->getFiberDimension(*bundle->heightStratum(0)->begin());
if (doOutput) {
ierr = PetscViewerASCIIPrintf(viewer, "CELL_DATA %d\n", numbering->getGlobalSize());CHKERRQ(ierr);
}
VTKViewer::writeField(s, std::string(name), fiberDim, numbering, viewer, enforceDim);
}
ierr = PetscObjectComposedDataSetInt((PetscObject) viewer, stateId, outputState);CHKERRQ(ierr);
} else {
s->view(name);
}
PetscFunctionReturn(0);
}
#undef __FUNCT__
#define __FUNCT__ "DMMeshView_Sieve_Ascii"
template<typename Mesh, typename Section>
PetscErrorCode DMMeshView_Sieve_Ascii(const Obj<Mesh>& mesh, const Obj<Section>& partition, PetscViewer viewer)
{
typedef ALE::IUniformSection<typename Mesh::point_type, typename Section::point_type> partitionMap_type;
const int numLocalPoints = partition->size();
int numPoints;
PetscErrorCode ierr;
ierr = MPI_Allreduce((void *) &numLocalPoints, (void *) &numPoints, 1, MPI_INT, MPI_SUM, partition->comm());CHKERRQ(ierr);
Obj<partitionMap_type> partitionMap = new partitionMap_type(mesh->comm(), 0, numPoints, mesh->debug());
PetscFunctionBegin;
ALE::Partitioner<>::createPartitionMap(partition, partitionMap);
ierr = VTKViewer::writeHeader(mesh, viewer);CHKERRQ(ierr);
ierr = VTKViewer::writeVertices(mesh, viewer);CHKERRQ(ierr);
ierr = VTKViewer::writeElements(mesh, viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK_CELL);CHKERRQ(ierr);
ierr = SectionView_Sieve_Ascii(mesh, partitionMap, "Partition", viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
#endif // __PETSCDMMESH_VIEWERS_HH
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