NEM::MSH::gmshGeoMesh Class Reference

A concrete implementation of geoMeshBase representing a Gmsh mesh. More...

Detailed Description

Definition at line 41 of file gmshGeoMesh.H.

Public Member Functions
	gmshGeoMesh ()
	Construct a gmshGeoMesh with an empty mesh. More...
	gmshGeoMesh (const std::string &gmshMesh)
	Construct a gmshGeoMesh from an existing gmsh model. More...
	~gmshGeoMesh () override
void	write (const std::string &fileName) override
	Write mesh to file. More...
void	report (std::ostream &out) const override
	Print a report about the mesh. More...
virtual void	takeGeoMesh (geoMeshBase *otherGeoMesh)
	Take the GeoMesh of another geoMeshBase. More...
virtual void	reconstructGeo ()
	Construct the geometry from the mesh alone. More...
virtual void	mergeGeoMesh (geoMeshBase *otherGeoMesh)
	Merge mesh data from a new geoMesh to an existing geoMesh. More...
const std::string &	getGeoEntArrayName () const
	Get the name of the geometric entities array. More...
void	setGeoEntArrayName (const std::string &geoEntArrayName)
	Set the name of the geometric entities array. More...
double	getAngleThreshold () const
	Get the angle threshold used for surface classification. More...
void	setAngleThreshold (double angleThreshold)
	Set the angle threshold used for surface classification. More...
nemId_t	getNumberOfPoints () const
	Get the number of points in mesh. More...
nemId_t	getNumberOfCells () const
	Get the number of cells in mesh. More...
void	getPoint (nemId_t id, std::array< double, 3 > *x) const
	Get the coordinate of a point. More...
std::array< double, 3 >	getPoint (nemId_t id) const
	Get the coordinate of a point. More...
void	getCell (nemId_t cellId, vtkGenericCell *cell) const
	Get cell. More...
vtkCell *	getCell (nemId_t cellId) const
	Get cell. More...
void	getCellBounds (nemId_t cellId, std::array< double, 6 > *bounds) const
	Get cell bounds. More...
std::array< double, 6 >	getCellBounds (nemId_t cellId) const
	Get cell bounds. More...
VTKCellType	getCellType (nemId_t cellId) const
	Get VTK cell type. More...
void	getCellPoints (nemId_t cellId, vtkIdList *ptIds) const
	Get list of point ids defining specified cell. More...
void	getPointCells (nemId_t ptId, vtkIdList *cellIds) const
	Get list of cell ids using specified point. More...
void	getCellNeighbors (nemId_t cellId, vtkIdList *ptIds, vtkIdList *cellIds) const
	Get list of cells sharing points ptIds excluding cellId. More...
int	getNumberOfPointDataArrays () const
	Get number of arrays in the point data. More...
void	getPointDataArrayCopy (const std::string &arrayName, vtkAbstractArray *array, int *arrayIdx=nullptr) const
	Get copy of point data array by name. More...
vtkSmartPointer< vtkAbstractArray >	getPointDataArrayCopy (const std::string &arrayName, int *arrayIdx=nullptr) const
	Create and return a copy of point data array by name. More...
void	getPointDataArrayCopy (int arrayIdx, vtkAbstractArray *array) const
	Get copy of point data array by index. More...
vtkSmartPointer< vtkAbstractArray >	getPointDataArrayCopy (int arrayIdx) const
	Create and return a copy of point data array by index. More...
int	getNumberOfCellDataArrays () const
	Get number of arrays in the cell data. More...
void	getCellDataArrayCopy (const std::string &arrayName, vtkAbstractArray *array, int *arrayIdx=nullptr) const
	Get copy of cell data array by name. More...
vtkSmartPointer< vtkAbstractArray >	getCellDataArrayCopy (const std::string &arrayName, int *arrayIdx=nullptr) const
	Create and return a copy of cell data array by name. More...
void	getCellDataArrayCopy (int arrayIdx, vtkAbstractArray *array) const
	Get copy of cell data array by index. More...
vtkSmartPointer< vtkAbstractArray >	getCellDataArrayCopy (int arrayIdx) const
	Create and return a copy of cell data array by index. More...
int	getNumberOfFieldDataArrays () const
	Get number of arrays in the field data. More...
void	getFieldDataArrayCopy (const std::string &arrayName, vtkAbstractArray *array, int *arrayIdx=nullptr) const
	Get copy of field data array by name. More...
vtkSmartPointer< vtkAbstractArray >	getFieldDataArrayCopy (const std::string &arrayName, int *arrayIdx=nullptr) const
	Create and return a copy of field data array by name. More...
void	getFieldDataArrayCopy (int arrayIdx, vtkAbstractArray *array) const
	Get copy of field data array by index. More...
vtkSmartPointer< vtkAbstractArray >	getFieldDataArrayCopy (int arrayIdx) const
	Create and return a copy of field data array by index. More...

Static Public Member Functions
static gmshGeoMesh *	New ()
static vtkTypeMacro(gmshGeoMesh, geoMeshBase) public VTKCellType	getVTKTypeFromGmshType (const std::string &gmshType)
	Create a gmshGeoMesh from a file. More...

Protected Member Functions
int	setPointDataArray (vtkAbstractArray *array)
	Set point data. More...
int	setCellDataArray (vtkAbstractArray *array)
	Set cell data. More...
int	setFieldDataArray (vtkAbstractArray *array)
	Set field data. More...
void	unsetPointDataArray (int arrayIdx)
	Remove point data array by index. More...
void	unsetPointDataArray (const std::string &arrayName)
	Remove point data array by name. More...
void	unsetCellDataArray (int arrayIdx)
	Remove cell data array by index. More...
void	unsetCellDataArray (const std::string &arrayName)
	Remove cell data array by name. More...
void	unsetFieldDataArray (int arrayIdx)
	Remove field data array by index. More...
void	unsetFieldDataArray (const std::string &arrayName)
	Remove field data array by name. More...
const GeoMesh &	getGeoMesh () const
	Get the underlying geometry object. More...
void	setGeoMesh (const geoMeshBase::GeoMesh &geoMesh)
	Set the underlying geometry object. More...

Static Protected Attributes
static constexpr auto	GEO_ENT_DEFAULT_NAME = "GeoEnt"

Private Member Functions
void	resetNative () override

Static Private Member Functions
static GeoMesh	gmsh2GM (const std::string &gmshMesh)
	Convert gmshMesh (name of a gmsh model) to GeoMesh. More...
static std::string	GM2gmsh (const GeoMesh &geoMesh)
	Add the mesh from geoMesh to the gmsh model in geoMesh. More...

Private Attributes
std::string	_gmshMesh

Inherits NEM::MSH::geoMeshBase.

Constructor & Destructor Documentation

gmshGeoMesh() [1/2]

NEM::MSH::gmshGeoMesh::gmshGeoMesh

(

)

Definition at line 111 of file gmshGeoMesh.C.

Referenced by NEM::MSH::vtkStandardNewMacro().

: gmshGeoMesh(std::string()) {}

gmshGeoMesh() [2/2]

NEM::MSH::gmshGeoMesh::gmshGeoMesh ( const std::string &  gmshMesh )

explicit

Parameters

gmshMesh

name of gmsh model created from gmsh::open or gmsh::add

Definition at line 113 of file gmshGeoMesh.C.

    : geoMeshBase(gmsh2GM(gmshMesh)), _gmshMesh(gmshMesh) {
  std::cout << "gmshGeoMesh constructed" << std::endl;
}

~gmshGeoMesh()

NEM::MSH::gmshGeoMesh::~gmshGeoMesh ( )

override

Definition at line 118 of file gmshGeoMesh.C.

References NEM::MSH::GmshInterface::Finalize().

                          {
  GmshInterface::Finalize();
  std::cout << "gmshGeoMesh destructed" << std::endl;
}

Member Function Documentation

getAngleThreshold()

double NEM::MSH::geoMeshBase::getAngleThreshold ( ) const

inlineinherited

Returns

angle threshold (in radians)

Definition at line 171 of file geoMeshBase.H.

{ return _angleThreshold; }

getCell() [1/2]

void NEM::MSH::geoMeshBase::getCell ( nemId_t  cellId, vtkGenericCell *  cell  ) const

inlineinherited

Parameters

cellId	cell id
cell	cell

Definition at line 214 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

                                                           {
    _geoMesh.mesh->GetCell(cellId, cell);
  }

getCell() [2/2]

vtkCell* NEM::MSH::geoMeshBase::getCell ( nemId_t  cellId ) const

inlineinherited

Parameters

cellId

cell id

Returns

cell

Definition at line 222 of file geoMeshBase.H.

                                         {
    return _geoMesh.mesh->GetCell(cellId);
  }

getCellBounds() [1/2]

void NEM::MSH::geoMeshBase::getCellBounds ( nemId_t  cellId, std::array< double, 6 > *  bounds  ) const

inlineinherited

Parameters

cellId	cell id
bounds	array of bounds as (x_min,x_max, y_min,y_max, z_min,z_max)

Definition at line 230 of file geoMeshBase.H.

                                                                        {
    _geoMesh.mesh->GetCellBounds(cellId, bounds->data());
  }

getCellBounds() [2/2]

std::array<double, 6> NEM::MSH::geoMeshBase::getCellBounds ( nemId_t  cellId ) const

inlineinherited

Parameters

cellId

cell id

Returns

array of bounds as (x_min,x_max, y_min,y_max, z_min,z_max)

Definition at line 238 of file geoMeshBase.H.

                                                          {
    std::array<double, 6> bounds{};
    getCellBounds(cellId, &bounds);
    return bounds;
  }

getCellDataArrayCopy() [1/4]

void NEM::MSH::geoMeshBase::getCellDataArrayCopy ( const std::string &  arrayName, vtkAbstractArray *  array, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
array	cell data array
arrayIdx	array index

Definition at line 180 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

Referenced by NEM::MSH::diffMesh().

                                                            {
  getArrCopy(_geoMesh.mesh->GetCellData(), arrayName, arrayIdx, array);
}

getCellDataArrayCopy() [2/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getCellDataArrayCopy ( const std::string &  arrayName, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
arrayIdx	array index

Returns

pointer to copy of array

Definition at line 186 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                     {
  return getArrCopy(_geoMesh.mesh->GetCellData(), arrayName, arrayIdx);
}

getCellDataArrayCopy() [3/4]

void NEM::MSH::geoMeshBase::getCellDataArrayCopy ( int  arrayIdx, vtkAbstractArray *  array  ) const

inherited

Parameters

arrayIdx	array index
array	cell data array

Definition at line 191 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                                      {
  getArrCopy(_geoMesh.mesh->GetCellData(), arrayIdx, array);
}

getCellDataArrayCopy() [4/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getCellDataArrayCopy ( int  arrayIdx ) const

inherited

Parameters

arrayIdx

array index

Returns

pointer to copy of array

Definition at line 196 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                        {
  return getArrCopy(_geoMesh.mesh->GetCellData(), arrayIdx);
}

getCellNeighbors()

void NEM::MSH::geoMeshBase::getCellNeighbors ( nemId_t  cellId, vtkIdList *  ptIds, vtkIdList *  cellIds  ) const

inlineinherited

Parameters

cellId	id of cell to exclude
ptIds	point id
cellIds	list of cell ids

Definition at line 273 of file geoMeshBase.H.

                                                  {
    _geoMesh.mesh->GetCellNeighbors(cellId, ptIds, cellIds);
  }

getCellPoints()

void NEM::MSH::geoMeshBase::getCellPoints ( nemId_t  cellId, vtkIdList *  ptIds  ) const

inlineinherited

Parameters

cellId	cell id
ptIds	list of point ids

Definition at line 256 of file geoMeshBase.H.

                                                             {
    _geoMesh.mesh->GetCellPoints(cellId, ptIds);
  }

getCellType()

VTKCellType NEM::MSH::geoMeshBase::getCellType ( nemId_t  cellId ) const

inlineinherited

Parameters

cellId

cell id

Returns

VTK cell type (see vtk documentation for specifics)

Definition at line 248 of file geoMeshBase.H.

                                                {
    return static_cast<VTKCellType>(_geoMesh.mesh->GetCellType(cellId));
  }

getFieldDataArrayCopy() [1/4]

void NEM::MSH::geoMeshBase::getFieldDataArrayCopy ( const std::string &  arrayName, vtkAbstractArray *  array, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
array	field data array
arrayIdx	array index

Definition at line 201 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                             {
  getArrCopy(_geoMesh.mesh->GetFieldData(), arrayName, arrayIdx, array);
}

getFieldDataArrayCopy() [2/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getFieldDataArrayCopy ( const std::string &  arrayName, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
arrayIdx	array index

Returns

pointer to copy of array

Definition at line 207 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                     {
  return getArrCopy(_geoMesh.mesh->GetFieldData(), arrayName, arrayIdx);
}

getFieldDataArrayCopy() [3/4]

void NEM::MSH::geoMeshBase::getFieldDataArrayCopy ( int  arrayIdx, vtkAbstractArray *  array  ) const

inherited

Parameters

arrayIdx	array index
array	field data array

Definition at line 212 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                                       {
  getArrCopy(_geoMesh.mesh->GetFieldData(), arrayIdx, array);
}

getFieldDataArrayCopy() [4/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getFieldDataArrayCopy ( int  arrayIdx ) const

inherited

Parameters

arrayIdx

array index

Returns

pointer to copy of array

Definition at line 217 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                        {
  return getArrCopy(_geoMesh.mesh->GetFieldData(), arrayIdx);
}

getGeoEntArrayName()

const std::string& NEM::MSH::geoMeshBase::getGeoEntArrayName ( ) const

inlineinherited

Returns

name of geometric entities array

Definition at line 157 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

{ return _geoMesh.link; }

getGeoMesh()

const GeoMesh& NEM::MSH::geoMeshBase::getGeoMesh ( ) const

inlineprotectedinherited

Note

This is not a copy; Gmsh does not support cloning a model.

Definition at line 533 of file geoMeshBase.H.

Referenced by NEM::MSH::exoGeoMesh::addCellsToBlock(), NEM::MSH::exoGeoMesh::addElemBlock(), NEM::MSH::exoGeoMesh::addElemBlockProperty(), NEM::MSH::exoGeoMesh::addNodeSet(), NEM::MSH::exoGeoMesh::addSideSet(), NEM::MSH::exoGeoMesh::exoGeoMesh(), NEM::MSH::exoGeoMesh::getElemBlock(), NEM::MSH::exoGeoMesh::getElemBlockId(), NEM::MSH::exoGeoMesh::getSideSet(), NEM::MSH::vtkGeoMesh::getVtkMesh(), NEM::MSH::inpGeoMesh::inpGeoMesh(), NEM::MSH::exoGeoMesh::reassignCells(), NEM::MSH::oshGeoMesh::reconstructGeo(), NEM::MSH::exoGeoMesh::reconstructGeo(), NEM::MSH::geoMeshBase::report(), NEM::MSH::exoGeoMesh::resetElemBlocks(), NEM::MSH::smeshGeoMesh::resetNative(), resetNative(), NEM::MSH::inpGeoMesh::resetNative(), NEM::MSH::foamGeoMesh::resetNative(), NEM::MSH::oshGeoMesh::resetNative(), NEM::MSH::exoGeoMesh::resetNative(), NEM::MSH::exoGeoMesh::scaleNodes(), NEM::MSH::oshGeoMesh::setOshMesh(), NEM::MSH::exoGeoMesh::setPhysGrpPropertyName(), NEM::MSH::exoGeoMesh::setSideSetObjId(), NEM::MSH::exoGeoMesh::stitch(), write(), NEM::MSH::vtkGeoMesh::write(), and NEM::MSH::exoGeoMesh::write().

{ return _geoMesh; }

getNumberOfCellDataArrays()

int NEM::MSH::geoMeshBase::getNumberOfCellDataArrays ( ) const

inlineinherited

Returns

number of arrays in the cell data

Definition at line 318 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

                                        {
    return _geoMesh.mesh->GetCellData()->GetNumberOfArrays();
  }

getNumberOfCells()

nemId_t NEM::MSH::geoMeshBase::getNumberOfCells ( ) const

inlineinherited

Returns

number of cells in mesh

Definition at line 190 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

{ return _geoMesh.mesh->GetNumberOfCells(); }

getNumberOfFieldDataArrays()

int NEM::MSH::geoMeshBase::getNumberOfFieldDataArrays ( ) const

inlineinherited

Returns

number of arrays in the field data

Definition at line 355 of file geoMeshBase.H.

                                         {
    return _geoMesh.mesh->GetFieldData()->GetNumberOfArrays();
  }

getNumberOfPointDataArrays()

int NEM::MSH::geoMeshBase::getNumberOfPointDataArrays ( ) const

inlineinherited

Returns

number of arrays in the point data

Definition at line 281 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

                                         {
    return _geoMesh.mesh->GetPointData()->GetNumberOfArrays();
  }

getNumberOfPoints()

nemId_t NEM::MSH::geoMeshBase::getNumberOfPoints ( ) const

inlineinherited

Returns

number of points in mesh

Definition at line 183 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

                                    {
    return _geoMesh.mesh->GetNumberOfPoints();
  }

getPoint() [1/2]

void NEM::MSH::geoMeshBase::getPoint ( nemId_t  id, std::array< double, 3 > *  x  ) const

inlineinherited

Parameters

id	point id
x	array of coordinates as (x,y,z)

Definition at line 196 of file geoMeshBase.H.

Referenced by NEM::MSH::diffMesh().

                                                          {
    _geoMesh.mesh->GetPoint(id, x->data());
  }

getPoint() [2/2]

std::array<double, 3> NEM::MSH::geoMeshBase::getPoint ( nemId_t  id ) const

inlineinherited

Parameters

id

point id

Returns

array of coordinates as (x,y,z)

Definition at line 204 of file geoMeshBase.H.

                                                 {
    std::array<double, 3> x{};
    getPoint(id, &x);
    return x;
  }

getPointCells()

void NEM::MSH::geoMeshBase::getPointCells ( nemId_t  ptId, vtkIdList *  cellIds  ) const

inlineinherited

Parameters

ptId	point id
cellIds	list of cell ids

Definition at line 264 of file geoMeshBase.H.

                                                             {
    _geoMesh.mesh->GetPointCells(ptId, cellIds);
  }

getPointDataArrayCopy() [1/4]

void NEM::MSH::geoMeshBase::getPointDataArrayCopy ( const std::string &  arrayName, vtkAbstractArray *  array, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
array	point data array
arrayIdx	array index

Definition at line 159 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

Referenced by NEM::MSH::diffMesh().

                                                             {
  getArrCopy(_geoMesh.mesh->GetPointData(), arrayName, arrayIdx, array);
}

getPointDataArrayCopy() [2/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getPointDataArrayCopy ( const std::string &  arrayName, int *  arrayIdx = nullptr  ) const

inherited

Optionally, get array index.

Parameters

arrayName	array name
arrayIdx	array index

Returns

pointer to copy of array

Definition at line 165 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                     {
  return getArrCopy(_geoMesh.mesh->GetPointData(), arrayName, arrayIdx);
}

getPointDataArrayCopy() [3/4]

void NEM::MSH::geoMeshBase::getPointDataArrayCopy ( int  arrayIdx, vtkAbstractArray *  array  ) const

inherited

Parameters

arrayIdx	array index
array	point data array

Definition at line 170 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                                                                       {
  getArrCopy(_geoMesh.mesh->GetPointData(), arrayIdx, array);
}

getPointDataArrayCopy() [4/4]

vtkSmartPointer< vtkAbstractArray > NEM::MSH::geoMeshBase::getPointDataArrayCopy ( int  arrayIdx ) const

inherited

Parameters

arrayIdx

array index

Returns

pointer to copy of array

Definition at line 175 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, and NEM::MSH::geoMeshBase::GeoMesh::mesh.

                        {
  return getArrCopy(_geoMesh.mesh->GetPointData(), arrayIdx);
}

getVTKTypeFromGmshType()

VTKCellType NEM::MSH::gmshGeoMesh::getVTKTypeFromGmshType ( const std::string &  gmshType )

static

Parameters

fileName

file name that gmsh can read

Returns

new gmshGeoMesh object Convert gmsh cell type to VTK cell type

Parameters

gmshType

gmsh cell type

Returns

VTK cell type

Definition at line 131 of file gmshGeoMesh.C.

References nemAux::findFromStr(), and nemAux::findToStr().

                                                                         {
  std::string name = nemAux::findToStr(gmshType, " ");
  int numV;
  if (name == "Point") {
    numV = 1;
  } else {
    numV = std::stoi(nemAux::findFromStr(gmshType, " "));
  }

  if (name == "Point") {
    return VTK_VERTEX;
  } else if (name == "Line") {
    switch (numV) {
      case 3: return VTK_QUADRATIC_EDGE;
      default: return VTK_LINE;
    }
  } else if (name == "Triangle") {
    switch (numV) {
      case 6: return VTK_QUADRATIC_TRIANGLE;
      default: return VTK_TRIANGLE;
    }
  } else if (name == "Quadrilateral") {
    switch (numV) {
      case 8: return VTK_QUADRATIC_QUAD;
      case 9: return VTK_BIQUADRATIC_QUAD;
      default: return VTK_QUAD;
    }
  } else if (name == "Polygon") {
    return VTK_POLYGON;
  } else if (name == "Tetrahedron") {
    switch (numV) {
      case 10: return VTK_QUADRATIC_TETRA;
      default: return VTK_TETRA;
    }
  } else if (name == "Hexahedron") {
    switch (numV) {
      case 20: return VTK_QUADRATIC_HEXAHEDRON;
      case 27: return VTK_TRIQUADRATIC_HEXAHEDRON;
      default: return VTK_HEXAHEDRON;
    }
  } else if (name == "Prism") {
    return VTK_WEDGE;
  } else if (name == "Pyramid") {
    return VTK_PYRAMID;
  } else if (name == "Trihedron" ||  // Flat Quad + 2 Tris.
             name == "Polyhedron")   // Occurs in MElementCuts
  {
    std::cerr << "ERROR in Gmsh to VTK element conversion: Gmsh element \""
              << name << "\" is not supported by VTK." << std::endl;
  } else {
    std::cerr << "ERROR in Gmsh to VTK element conversion: Gmsh element \""
              << name << "\" is not recognized." << std::endl;
  }
  throw;
}

GM2gmsh()

std::string NEM::MSH::gmshGeoMesh::GM2gmsh ( const GeoMesh &  geoMesh )

staticprivate

Definition at line 271 of file gmshGeoMesh.C.

References NEM::MSH::geoMeshBase::GeoMesh::geo, NEM::MSH::geoMeshBase::SideSet::getGeoEntArr(), NEM::MSH::geoMeshBase::GeoMesh::link, NEM::MSH::geoMeshBase::GeoMesh::mesh, NEM::MSH::geoMeshBase::SideSet::sides, and NEM::MSH::geoMeshBase::GeoMesh::sideSet.

Referenced by write().

                                                     {
  gmsh::model::setCurrent(geoMesh.geo);

  if (geoMesh.mesh->GetNumberOfPoints() > 0) {  // Add points
    std::vector<std::size_t> nodeTags;
    std::vector<double> coord;

    vtkSmartPointer<vtkPoints> dataSetPoints = geoMesh.mesh->GetPoints();
    coord.resize(3 * dataSetPoints->GetNumberOfPoints());
    nodeTags.resize(dataSetPoints->GetNumberOfPoints());
    for (vtkIdType ptId = 0; ptId < dataSetPoints->GetNumberOfPoints();
         ++ptId) {
      nodeTags[ptId] = ptId + 1;
      dataSetPoints->GetPoint(ptId, &coord[3 * ptId]);
    }

    gmsh::vectorpair dimTags;
    gmsh::model::getEntities(dimTags);
    gmsh::model::mesh::addNodes(dimTags[0].first, dimTags[0].second, nodeTags,
                                coord);
  }

  if (geoMesh.mesh->GetNumberOfCells() > 0) {  // Add elements
    // Sort all cells by entity and element type
    auto it =
        vtkSmartPointer<vtkCellIterator>::Take(geoMesh.mesh->NewCellIterator());
    vtkSmartPointer<vtkIntArray> geoEntArray = vtkIntArray::FastDownCast(
        geoMesh.mesh->GetCellData()->GetArray(geoMesh.link.c_str()));
    for (it->InitTraversal(); !it->IsDoneWithTraversal(); it->GoToNextCell()) {
      int geoEnt = geoEntArray->GetTypedComponent(it->GetCellId(), 0);

      vtkSmartPointer<vtkIdList> ptIds = it->GetPointIds();
      std::vector<std::size_t> nodeTag;
      for (vtkIdType pt = 0; pt < it->GetNumberOfPoints(); ++pt) {
        nodeTag.emplace_back(ptIds->GetId(pt) + 1);
      }

      gmsh::model::mesh::addElementsByType(
          geoEnt, getGmshTypeFromVTKType(it->GetCellType()),
          {static_cast<std::size_t>(it->GetCellId() + 1)}, nodeTag);
    }
  }

  if (geoMesh.sideSet.sides && geoMesh.sideSet.sides->GetNumberOfCells() > 0) {
    auto it = vtkSmartPointer<vtkCellIterator>::Take(
        geoMesh.sideSet.sides->NewCellIterator());
    auto geoEntArray = geoMesh.sideSet.getGeoEntArr();
    for (it->InitTraversal(); !it->IsDoneWithTraversal(); it->GoToNextCell()) {
      int geoEnt = geoEntArray->GetTypedComponent(it->GetCellId(), 0);

      vtkSmartPointer<vtkIdList> ptIds = it->GetPointIds();
      std::vector<std::size_t> nodeTag;
      for (vtkIdType pt = 0; pt < it->GetNumberOfPoints(); ++pt) {
        nodeTag.emplace_back(ptIds->GetId(pt) + 1);
      }

      gmsh::model::mesh::addElementsByType(
          geoEnt, getGmshTypeFromVTKType(it->GetCellType()),
          {static_cast<std::size_t>(it->GetCellId() + 1)}, nodeTag);
    }
  }

  gmsh::model::mesh::reclassifyNodes();

  return geoMesh.geo;
}

gmsh2GM()

geoMeshBase::GeoMesh NEM::MSH::gmshGeoMesh::gmsh2GM ( const std::string &  gmshMesh )

staticprivate

Definition at line 187 of file gmshGeoMesh.C.

References NEM::MSH::geoMeshBase::GEO_ENT_DEFAULT_NAME, NEM::MSH::New(), and points.

                                                                 {
  auto vtkMesh = vtkSmartPointer<vtkUnstructuredGrid>::New();

  if (gmshMesh.empty()) return {vtkMesh, gmshMesh, "", {}};

  std::string geoEntArrayName = GEO_ENT_DEFAULT_NAME;

  gmsh::model::setCurrent(gmshMesh);

  // Track GMSH node ids and VTK point ids.
  std::map<std::size_t, vtkIdType> gmshNodeNum2vtkId;

  {  // Add points
    vtkSmartPointer<vtkPoints> points =
        vtkSmartPointer<vtkPoints>::Take(vtkPoints::New(VTK_DOUBLE));

    // Get GMSH nodes
    std::vector<std::size_t> nodeTags;
    std::vector<double> coord;
    std::vector<double> parametricCoord;
    gmsh::model::mesh::getNodes(nodeTags, coord, parametricCoord);

    // Allocate
    points->Allocate(nodeTags.size());

    // Convert GMSH nodes to VTK points
    for (std::size_t i = 0; i < nodeTags.size(); ++i) {
      gmshNodeNum2vtkId[nodeTags[i]] = points->GetNumberOfPoints();
      points->InsertNextPoint(coord[i * 3 + 0], coord[i * 3 + 1],
                              coord[i * 3 + 2]);
    }

    vtkMesh->SetPoints(points);
  }

  {  // Add elements and geometric entities
    // Note: Cannot pre-allocate cells since GMSH does not provide an API to get
    // total number of elements

    gmsh::vectorpair dimTags;
    gmsh::model::getEntities(dimTags, gmsh::model::getDimension());

    // geoEnt: Track entities to place as cell data
    vtkSmartPointer<vtkIntArray> vtkEntities =
        vtkSmartPointer<vtkIntArray>::New();
    vtkEntities->Initialize();  // Cannot allocate
    vtkEntities->SetName(geoEntArrayName.c_str());

    addGmshEntitiesToDataSet(dimTags, gmshNodeNum2vtkId, vtkMesh, vtkEntities);

    // geoEnt: Add geometric entity data to VTK
    vtkMesh->GetCellData()->AddArray(vtkEntities);

    // Since could not allocate elements/cells, we have to squeeze
    vtkMesh->Squeeze();
  }

  SideSet sideSet{};
  {  // sideSet
    gmsh::vectorpair dimTags;
    gmsh::model::getEntities(dimTags, gmsh::model::getDimension() - 1);
    if (!dimTags.empty()) {
      auto sideSetPD = vtkSmartPointer<vtkPolyData>::New();
      sideSetPD->SetPoints(vtkMesh->GetPoints());
      sideSetPD->Allocate();
      vtkNew<vtkIntArray> vtkEntities{};

      addGmshEntitiesToDataSet(dimTags, gmshNodeNum2vtkId, sideSetPD,
                               vtkEntities);
      if (sideSetPD->GetNumberOfCells() > 0) {
        sideSetPD->Squeeze();
        sideSet = SideSet(sideSetPD, vtkEntities);
      }
    }
  }

  // TODO: Add point, cell data

  // Only keep the geometry in the gmshMesh
  gmsh::model::mesh::clear();

  return {vtkMesh, gmshMesh, geoEntArrayName, sideSet};
}

mergeGeoMesh()

void NEM::MSH::geoMeshBase::mergeGeoMesh ( geoMeshBase *  otherGeoMesh )

virtualinherited

Deletes the data from the new geoMesh pointer

Parameters

otherGeoMesh

A new geoMesh data to merge

Definition at line 113 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, NEM::MSH::geoMeshBase::GeoMesh::mesh, NEM::MSH::New(), and NEM::MSH::geoMeshBase::resetNative().

                                                        {
  vtkSmartPointer<vtkAppendFilter> appendFilter =
      vtkSmartPointer<vtkAppendFilter>::New();
  appendFilter->AddInputData(_geoMesh.mesh);
  appendFilter->AddInputData(otherGeoMesh->_geoMesh.mesh);
  appendFilter->MergePointsOn();
  appendFilter->Update();
  _geoMesh.mesh = appendFilter->GetOutput();
  otherGeoMesh->_geoMesh = {
      vtkSmartPointer<vtkUnstructuredGrid>::New(), {}, {}, {}};
  otherGeoMesh->resetNative();
}

New()

static gmshGeoMesh* NEM::MSH::gmshGeoMesh::New ( )

static

Referenced by NEM::MSH::New(), and NEM::SRV::srvBase::RequestDataObject().

reconstructGeo()

void NEM::MSH::geoMeshBase::reconstructGeo ( )

virtualinherited

Sets geometry, link, and side set. Does not alter the mesh.

Reimplemented in NEM::MSH::exoGeoMesh, NEM::MSH::oshGeoMesh, and NEM::MSH::inpGeoMesh.

Definition at line 466 of file geoMeshBaseReconstructGeo.C.

References NEM::MSH::geoMeshBase::_angleThreshold, NEM::MSH::geoMeshBase::_geoMesh, NEM::MSH::geoMeshBase::GeoMesh::geo, NEM::MSH::geoMeshBase::GEO_ENT_DEFAULT_NAME, nemAux::getRandomString(), NEM::MSH::geoMeshBase::GeoMesh::link, NEM::MSH::geoMeshBase::GeoMesh::mesh, NEM::MSH::geoMeshBase::SideSet::sides, and NEM::MSH::geoMeshBase::GeoMesh::sideSet.

Referenced by NEM::MSH::inpGeoMesh::reconstructGeo(), NEM::MSH::oshGeoMesh::reconstructGeo(), and NEM::MSH::exoGeoMesh::reconstructGeo().

                                 {
#ifdef HAVE_GMSH
  if (_geoMesh.geo.empty()) {
    _geoMesh.geo = "geoMesh_" + nemAux::getRandomString(6);
  } else {
    gmsh::model::setCurrent(_geoMesh.geo);
    gmsh::model::remove();
  }
  gmsh::model::add(_geoMesh.geo);
  gmsh::model::setCurrent(_geoMesh.geo);
#endif
  if (_geoMesh.link.empty()) {
    _geoMesh.link = GEO_ENT_DEFAULT_NAME;
  }
  _geoMesh.sideSet = SideSet{
      computeDiscreteGeoFromMsh(_geoMesh.mesh, _geoMesh.link, _angleThreshold)};
  assert(_geoMesh.mesh->GetPoints() == _geoMesh.sideSet.sides->GetPoints());
}

report()

void NEM::MSH::gmshGeoMesh::report ( std::ostream &  out ) const

overridevirtual

Parameters

out

stream

Implements NEM::MSH::geoMeshBase.

Definition at line 129 of file gmshGeoMesh.C.

References NEM::MSH::geoMeshBase::report().

{ geoMeshBase::report(out); }

resetNative()

void NEM::MSH::gmshGeoMesh::resetNative ( )

overrideprivatevirtual

Implements NEM::MSH::geoMeshBase.

Definition at line 338 of file gmshGeoMesh.C.

References _gmshMesh, NEM::MSH::geoMeshBase::GEO_ENT_DEFAULT_NAME, NEM::MSH::geoMeshBase::getGeoMesh(), nemAux::getRandomString(), mesh, NEM::MSH::geoMeshBase::GeoMesh::mesh, NEM::MSH::New(), and NEM::MSH::geoMeshBase::setGeoMesh().

                              {
  auto gm = getGeoMesh();
  if (gm.geo.empty()) {
    gm.geo = "geoMesh_" + nemAux::getRandomString(6);
    gmsh::model::add(gm.geo);
  }
  if (gm.link.empty()) {
    gm.link = GEO_ENT_DEFAULT_NAME;
    auto linkArr = vtkSmartPointer<vtkIntArray>::New();
    linkArr->SetName(gm.link.c_str());
    linkArr->SetNumberOfTuples(getGeoMesh().mesh->GetNumberOfCells());
    linkArr->FillComponent(0, 1);
    getGeoMesh().mesh->GetCellData()->AddArray(linkArr);
  }
  setGeoMesh(gm);
  _gmshMesh = gm.geo;
}

setAngleThreshold()

void NEM::MSH::geoMeshBase::setAngleThreshold ( double  angleThreshold )

inlineinherited

Parameters

angleThreshold

(in radians)

Definition at line 176 of file geoMeshBase.H.

                                                {
    _angleThreshold = angleThreshold;
  }

setCellDataArray()

int NEM::MSH::geoMeshBase::setCellDataArray ( vtkAbstractArray *  array )

inlineprotectedinherited

Parameters

array

array pointer

Returns

array index

Definition at line 473 of file geoMeshBase.H.

                                                {
    return _geoMesh.mesh->GetCellData()->AddArray(array);
  }

setFieldDataArray()

int NEM::MSH::geoMeshBase::setFieldDataArray ( vtkAbstractArray *  array )

inlineprotectedinherited

Parameters

array

array pointer

Returns

array index

Definition at line 481 of file geoMeshBase.H.

                                                 {
    return _geoMesh.mesh->GetFieldData()->AddArray(array);
  }

setGeoEntArrayName()

void NEM::MSH::geoMeshBase::setGeoEntArrayName ( const std::string &  geoEntArrayName )

inlineinherited

Parameters

geoEntArrayName

name of geometric entities array

Definition at line 162 of file geoMeshBase.H.

                                                            {
    auto a = _geoMesh.mesh->GetCellData()->GetArray(_geoMesh.link.c_str());
    if (a) a->SetName(geoEntArrayName.c_str());
    _geoMesh.link = geoEntArrayName;
  }

setGeoMesh()

void NEM::MSH::geoMeshBase::setGeoMesh ( const geoMeshBase::GeoMesh &  geoMesh )

inlineprotectedinherited

Parameters

geoMesh

a mesh and geometry

Definition at line 538 of file geoMeshBase.H.

References NEM::MSH::geoMeshBase::GeoMesh::mesh, NEM::MSH::geoMeshBase::SideSet::sides, and NEM::MSH::geoMeshBase::GeoMesh::sideSet.

Referenced by NEM::MSH::exoGeoMesh::addCellsToBlock(), NEM::MSH::exoGeoMesh::addElemBlock(), NEM::MSH::exoGeoMesh::addSideSet(), NEM::MSH::exoGeoMesh::reassignCells(), NEM::MSH::exoGeoMesh::reconstructGeo(), resetNative(), NEM::MSH::exoGeoMesh::resetNative(), NEM::MSH::exoGeoMesh::scaleNodes(), NEM::MSH::foamGeoMesh::setFoamMesh(), NEM::MSH::oshGeoMesh::setOshMesh(), NEM::MSH::smeshGeoMesh::setSMeshMesh(), NEM::MSH::vtkGeoMesh::setVtkMesh(), NEM::MSH::exoGeoMesh::stitch(), NEM::MSH::oshGeoMesh::takeGeoMesh(), and NEM::MSH::exoGeoMesh::takeGeoMesh().

                                                     {
    assert(geoMesh.mesh->GetNumberOfCells() == 0 ||
           geoMesh.mesh->GetNumberOfPoints() == 0 ||
           geoMesh.sideSet.sides == nullptr ||
           geoMesh.sideSet.sides->GetPoints() == geoMesh.mesh->GetPoints());
    _geoMesh = geoMesh;
  }

setPointDataArray()

int NEM::MSH::geoMeshBase::setPointDataArray ( vtkAbstractArray *  array )

inlineprotectedinherited

Parameters

array

array pointer

Returns

array index

Definition at line 465 of file geoMeshBase.H.

                                                 {
    return _geoMesh.mesh->GetPointData()->AddArray(array);
  }

takeGeoMesh()

void NEM::MSH::geoMeshBase::takeGeoMesh ( geoMeshBase *  otherGeoMesh )

virtualinherited

Note that otherGeoMesh will be left with an empty mesh.

Parameters

otherGeoMesh

other geoMeshBase object; mesh will be left empty

Reimplemented in NEM::MSH::exoGeoMesh, and NEM::MSH::oshGeoMesh.

Definition at line 104 of file geoMeshBase.C.

References NEM::MSH::geoMeshBase::_geoMesh, NEM::MSH::New(), and NEM::MSH::geoMeshBase::resetNative().

Referenced by NEM::MSH::oshGeoMesh::takeGeoMesh(), and NEM::MSH::exoGeoMesh::takeGeoMesh().

                                                       {
  _geoMesh = std::move(otherGeoMesh->_geoMesh);
  otherGeoMesh->_geoMesh = {
      vtkSmartPointer<vtkUnstructuredGrid>::New(), {}, {}, {}};
  otherGeoMesh->resetNative();
  resetNative();
}

unsetCellDataArray() [1/2]

void NEM::MSH::geoMeshBase::unsetCellDataArray ( int  arrayIdx )

inlineprotectedinherited

Parameters

arrayIdx

array index

Definition at line 503 of file geoMeshBase.H.

                                        {
    _geoMesh.mesh->GetCellData()->RemoveArray(arrayIdx);
  }

unsetCellDataArray() [2/2]

void NEM::MSH::geoMeshBase::unsetCellDataArray ( const std::string &  arrayName )

inlineprotectedinherited

Parameters

arrayName

array name

Definition at line 510 of file geoMeshBase.H.

                                                      {
    _geoMesh.mesh->GetCellData()->RemoveArray(arrayName.c_str());
  }

unsetFieldDataArray() [1/2]

void NEM::MSH::geoMeshBase::unsetFieldDataArray ( int  arrayIdx )

inlineprotectedinherited

Parameters

arrayIdx

array index

Definition at line 517 of file geoMeshBase.H.

                                         {
    _geoMesh.mesh->GetFieldData()->RemoveArray(arrayIdx);
  }

unsetFieldDataArray() [2/2]

void NEM::MSH::geoMeshBase::unsetFieldDataArray ( const std::string &  arrayName )

inlineprotectedinherited

Parameters

arrayName

array name

Definition at line 524 of file geoMeshBase.H.

                                                       {
    _geoMesh.mesh->GetFieldData()->RemoveArray(arrayName.c_str());
  }

unsetPointDataArray() [1/2]

void NEM::MSH::geoMeshBase::unsetPointDataArray ( int  arrayIdx )

inlineprotectedinherited

Parameters

arrayIdx

array index

Definition at line 489 of file geoMeshBase.H.

                                         {
    _geoMesh.mesh->GetPointData()->RemoveArray(arrayIdx);
  }

unsetPointDataArray() [2/2]

void NEM::MSH::geoMeshBase::unsetPointDataArray ( const std::string &  arrayName )

inlineprotectedinherited

Parameters

arrayName

array name

Definition at line 496 of file geoMeshBase.H.

                                                       {
    _geoMesh.mesh->GetPointData()->RemoveArray(arrayName.c_str());
  }

write()

void NEM::MSH::gmshGeoMesh::write ( const std::string &  fileName )

overridevirtual

Parameters

fileName

file name

Implements NEM::MSH::geoMeshBase.

Definition at line 123 of file gmshGeoMesh.C.

References _gmshMesh, NEM::MSH::geoMeshBase::getGeoMesh(), and GM2gmsh().

                                                 {
  _gmshMesh = GM2gmsh(this->getGeoMesh());
  gmsh::write(fileName);
  gmsh::model::mesh::clear();
}

Member Data Documentation

_gmshMesh

std::string NEM::MSH::gmshGeoMesh::_gmshMesh

private

Definition at line 92 of file gmshGeoMesh.H.

Referenced by resetNative(), and write().

GEO_ENT_DEFAULT_NAME

constexpr auto NEM::MSH::geoMeshBase::GEO_ENT_DEFAULT_NAME = "GeoEnt"

staticprotectedinherited

Definition at line 446 of file geoMeshBase.H.

Referenced by gmsh2GM(), NEM::MSH::inpGeoMesh::inp2GM(), NEM::MSH::oshGeoMesh::osh2GM(), NEM::MSH::exoGeoMesh::reconstructGeo(), NEM::MSH::geoMeshBase::reconstructGeo(), and resetNative().

---

The documentation for this class was generated from the following files:

• gmshGeoMesh.H
• gmshGeoMesh.C