rw::reader Namespace Reference

Collection of methods and database related to reading. More...

Data Structures
class	MshReader
	A class to read Gmsh (msh) mesh files. More...
class	VtkParticleReader
	A vtk writer for simple point data and complex fem mesh data. More...
class	VtkReader
	A class to read VTK (.vtu) mesh files. More...

Functions
CSV specific functions
void	readCsvFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, std::vector< double > *volumes)
	Reads mesh data into node file and element file.
void	readParticleCsvFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, std::vector< double > *rads, std::vector< size_t > *zones)
	Reads particles center location, radius, and zone id.
void	readParticleCsvFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, std::vector< double > *rads, const size_t &zone)
	Reads particles center location, radius, and zone id.
void	readParticleWithOrientCsvFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, std::vector< double > *rads, std::vector< double > *orients, const size_t &zone)
	Reads particles center location, radius, and zone id. In this case, file also provides initial orientation of particles.
VTU specific functions
void	readVtuFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, size_t &element_type, size_t &num_elem, std::vector< size_t > *enc, std::vector< std::vector< size_t > > *nec, std::vector< double > *volumes, bool is_fd=false)
	Reads mesh data into node file and element file.
void	readVtuFileNodes (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, bool ref_config=false)
	Reads nodal coordinates.
void	readVtuFileCells (const std::string &filename, size_t dim, size_t &element_type, size_t &num_elem, std::vector< size_t > *enc, std::vector< std::vector< size_t > > *nec)
	Reads cell data, i.e. element-node connectivity and node-element connectivity.
void	readVtuFileRestart (const std::string &filename, std::vector< util::Point > *u, std::vector< util::Point > *v, const std::vector< util::Point > *X=nullptr)
	Reads mesh data into node file and element file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< uint8_t > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< size_t > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< int > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< float > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< double > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< util::Point > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< util::SymMatrix3 > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFilePointData (const std::string &filename, const std::string &tag, std::vector< util::Matrix3 > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFileCellData (const std::string &filename, const std::string &tag, std::vector< float > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFileCellData (const std::string &filename, const std::string &tag, std::vector< double > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFileCellData (const std::string &filename, const std::string &tag, std::vector< util::Point > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFileCellData (const std::string &filename, const std::string &tag, std::vector< util::SymMatrix3 > *data)
	Reads data of specified tag from the vtu file.
bool	readVtuFileCellData (const std::string &filename, const std::string &tag, std::vector< util::Matrix3 > *data)
	Reads data of specified tag from the vtu file.
MSH specific functions
void	readMshFile (const std::string &filename, size_t dim, std::vector< util::Point > *nodes, size_t &element_type, size_t &num_elem, std::vector< size_t > *enc, std::vector< std::vector< size_t > > *nec, std::vector< double > *volumes, bool is_fd=false)
	Reads mesh data into node file and element file.
void	readMshFileRestart (const std::string &filename, std::vector< util::Point > *u, std::vector< util::Point > *v, const std::vector< util::Point > *X=nullptr)
	Reads mesh data into node file and element file.
bool	readMshFilePointData (const std::string &filename, const std::string &tag, std::vector< double > *data)
	Reads data of specified tag from the vtu file.
void	readMshFileCells (const std::string &filename, size_t dim, size_t &element_type, size_t &num_elem, std::vector< size_t > *enc, std::vector< std::vector< size_t > > *nec)
	Reads cell data, i.e. element-node connectivity and node-element connectivity.

Detailed Description

Collection of methods and database related to reading.

This namespace provides methods and data members specific to reading of the mesh data. The .csv, .vtu and .msh formats are read.

Function Documentation

readCsvFile()

void rw::reader::readCsvFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		std::vector< double > *	volumes
	)

Reads mesh data into node file and element file.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of nodes data
volumes	Vector holding volume of the nodes

Definition at line 18 of file reader.cpp.

                                                         {
  nodes->clear();
  volumes->clear();
  if (dim == 1) {
    io::CSVReader<3> in(filename);
    in.read_header(io::ignore_extra_column, "id", "x", "volume");
 
    double x;
    double volume;
    int id;
    while (in.read_row(id, x, volume)) {
      volumes->emplace_back(volume);
      nodes->emplace_back(util::Point(x, 0., 0.));
    }
  }
 
  if (dim == 2) {
    io::CSVReader<4> in(filename);
    in.read_header(io::ignore_extra_column, "id", "x", "y", "volume");
 
    double x, y, volume;
    int id;
    while (in.read_row(id, x, y, volume)) {
      volumes->emplace_back(volume);
      nodes->emplace_back(util::Point(x, y, 0.));
    }
  }
 
  if (dim == 3) {
    io::CSVReader<5> in(filename);
    in.read_header(io::ignore_extra_column, "id", "x", "y", "z", "volume");
 
    double x, y, z, volume;
    int id;
    while (in.read_row(id, x, y, z, volume)) {
      volumes->emplace_back(volume);
      nodes->emplace_back(util::Point(x, y, z));
    }
  }
}

Referenced by mesh::Mesh::createData().

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readMshFile()

void rw::reader::readMshFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		size_t &	element_type,
		size_t &	num_elem,
		std::vector< size_t > *	enc,
		std::vector< std::vector< size_t > > *	nec,
		std::vector< double > *	volumes,
		bool	is_fd = false
	)

Reads mesh data into node file and element file.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of nodes data
element_type	Type of element
num_elem	Number of elements
enc	Vector holding element-node connectivity
nec	Vector holding node-element connectivity
volumes	Vector holding volume of the nodes
is_fd	Flag indicating if this mesh is for finite_difference simulation

Definition at line 356 of file reader.cpp.

                                                                     {
  // call msh reader
  auto rdr = rw::reader::MshReader(filename);
  rdr.readMesh(dim, nodes, element_type, num_elem, enc, nec, volumes, is_fd);
  rdr.close();
}

Referenced by mesh::Mesh::createData().

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readMshFileCells()

void rw::reader::readMshFileCells	(	const std::string &	filename,
		size_t	dim,
		size_t &	element_type,
		size_t &	num_elem,
		std::vector< size_t > *	enc,
		std::vector< std::vector< size_t > > *	nec
	)

Reads cell data, i.e. element-node connectivity and node-element connectivity.

Parameters

filename	Name of mesh file
dim	Dimension
element_type	Type of element
num_elem	Number of elements
enc	Element-node connectivity
nec	Node-element connectivity

Definition at line 407 of file reader.cpp.

                                                                     {
  // call msh reader
  auto rdr = rw::reader::MshReader(filename);
  rdr.readCells(dim, element_type, num_elem, enc, nec);
  rdr.close();
}

Referenced by mesh::Mesh::readElementData().

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readMshFilePointData()

bool rw::reader::readMshFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< double > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 396 of file reader.cpp.

                                                               {
  // call msh reader
  auto rdr = rw::reader::MshReader(filename);
  // get velocity
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readMshFileRestart()

void rw::reader::readMshFileRestart	(	const std::string &	filename,
		std::vector< util::Point > *	u,
		std::vector< util::Point > *	v,
		const std::vector< util::Point > *	X = nullptr
	)

Reads mesh data into node file and element file.

Parameters

filename	Name of mesh file
u	Pointer to vector of nodal displacement
v	Pointer to vector of nodal velocity
X	Pointer to vector of nodal reference position (Optional)

Definition at line 368 of file reader.cpp.

                                                                   {
  // call msh reader
  auto rdr = rw::reader::MshReader(filename);
  // if displacement is not in input file, use reference coordinate to get
  // displacement
  if (!rdr.readPointData("Displacement", u)) {
    std::vector<util::Point> y;
    rdr.readNodes(&y);
    if (y.size() != X->size()) {
      throw std::runtime_error(
          util::io::Msg()
          << "Error: Number of nodes in input file = " << filename
          << " and number nodes in data X are not same.\n");
    }
 
    u->resize(y.size());
    for (size_t i = 0; i < y.size(); i++)
      (*u)[i] = y[i] - (*X)[i];
  }
 
  // get velocity
  rdr.readPointData("Velocity", v);
  rdr.close();
}

readParticleCsvFile() [1/2]

void rw::reader::readParticleCsvFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		std::vector< double > *	rads,
		const size_t &	zone
	)

Reads particles center location, radius, and zone id.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of center locations
rads	Vector of radius
zone	Only reads particle with this zone

Definition at line 82 of file reader.cpp.

                                                         {
 
  nodes->clear();
  rads->clear();
 
  io::CSVReader<5> in(filename);
  in.read_header(io::ignore_extra_column, "i", "x", "y", "z", "r");
 
  double x, y, z, r;
  int id;
  while (in.read_row(id, x, y, z, r)) {
    if (id == zone) {
      rads->emplace_back(r);
      nodes->emplace_back(util::Point(x, y, z));
    }
  }
}

readParticleCsvFile() [2/2]

void rw::reader::readParticleCsvFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		std::vector< double > *	rads,
		std::vector< size_t > *	zones
	)

Reads particles center location, radius, and zone id.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of center locations
rads	Vector of radius
zones	Vector zone ids

Definition at line 61 of file reader.cpp.

                                                               {
 
  nodes->clear();
  zones->clear();
  rads->clear();
 
  io::CSVReader<5> in(filename);
  in.read_header(io::ignore_extra_column, "i", "x", "y", "z", "r");
 
  double x, y, z, r;
  int id;
  while (in.read_row(id, x, y, z, r)) {
    rads->emplace_back(r);
    nodes->emplace_back(util::Point(x, y, z));
    zones->emplace_back(id);
  }
}

readParticleWithOrientCsvFile()

void rw::reader::readParticleWithOrientCsvFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		std::vector< double > *	rads,
		std::vector< double > *	orients,
		const size_t &	zone
	)

Reads particles center location, radius, and zone id. In this case, file also provides initial orientation of particles.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of center locations
rads	Vector of radius
orients	Vector of orientation of particles
zone	Only reads particle with this zone

Definition at line 103 of file reader.cpp.

                                                         {
 
  nodes->clear();
  rads->clear();
  orients->clear();
 
  io::CSVReader<6> in(filename);
  in.read_header(io::ignore_extra_column, "i", "x", "y", "z", "r", "o");
 
  double x, y, z, r, o;
  int id;
  while (in.read_row(id, x, y, z, r, o)) {
    if (id == zone) {
      rads->emplace_back(r);
      nodes->emplace_back(util::Point(x, y, z));
      orients->emplace_back(o);
    }
  }
}

readVtuFile()

void rw::reader::readVtuFile	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		size_t &	element_type,
		size_t &	num_elem,
		std::vector< size_t > *	enc,
		std::vector< std::vector< size_t > > *	nec,
		std::vector< double > *	volumes,
		bool	is_fd = false
	)

Reads mesh data into node file and element file.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of nodes data
element_type	Type of element
num_elem	Number of elements
enc	Vector holding element-node connectivity
nec	Vector holding node-element connectivity
volumes	Vector holding volume of the nodes
is_fd	Flag indicating if this mesh is for finite_difference simulation

Definition at line 127 of file reader.cpp.

                                                                     {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  rdr.readMesh(dim, nodes, element_type, num_elem, enc, nec, volumes, is_fd);
  rdr.close();
}

readVtuFileCellData() [1/5]

bool rw::reader::readVtuFileCellData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< double > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 312 of file reader.cpp.

                                                              {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readCellData(tag, data);
  rdr.close();
  return st;
}

readVtuFileCellData() [2/5]

bool rw::reader::readVtuFileCellData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< float > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 301 of file reader.cpp.

                                                             {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readCellData(tag, data);
  rdr.close();
  return st;
}

readVtuFileCellData() [3/5]

bool rw::reader::readVtuFileCellData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::Matrix3 > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 345 of file reader.cpp.

                                                                   {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readCellData(tag, data);
  rdr.close();
  return st;
}

readVtuFileCellData() [4/5]

bool rw::reader::readVtuFileCellData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::Point > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 323 of file reader.cpp.

                                                                 {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readCellData(tag, data);
  rdr.close();
  return st;
}

readVtuFileCellData() [5/5]

bool rw::reader::readVtuFileCellData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::SymMatrix3 > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 334 of file reader.cpp.

                                                                      {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readCellData(tag, data);
  rdr.close();
  return st;
}

readVtuFileCells()

void rw::reader::readVtuFileCells	(	const std::string &	filename,
		size_t	dim,
		size_t &	element_type,
		size_t &	num_elem,
		std::vector< size_t > *	enc,
		std::vector< std::vector< size_t > > *	nec
	)

Reads cell data, i.e. element-node connectivity and node-element connectivity.

Parameters

filename	Name of mesh file
dim	Dimension
element_type	Type of element
num_elem	Number of elements
enc	Element-node connectivity
nec	Node-element connectivity

Definition at line 172 of file reader.cpp.

                                                                     {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
 
  // below will read the current position of nodes
  rdr.readCells(dim, element_type, num_elem, enc, nec);
 
  rdr.close();
}

Referenced by mesh::Mesh::createData(), and mesh::Mesh::readElementData().

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readVtuFileNodes()

void rw::reader::readVtuFileNodes	(	const std::string &	filename,
		size_t	dim,
		std::vector< util::Point > *	nodes,
		bool	ref_config = false
	)

Reads nodal coordinates.

Parameters

filename	Name of mesh file
dim	Dimension
nodes	Vector of nodes data
ref_config	Flag which specifies if we need to subtract the displacement from nodes obtained from vtu file to get reference position of nodes

Definition at line 139 of file reader.cpp.

                                                   {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
 
  // below will read the current position of nodes
  rdr.readNodes(nodes);
 
  // need to subtract the displacement to get reference configuration of nodes
  if (ref_config) {
    std::vector<util::Point> u;
    if (rdr.readPointData("Displacement", &u)) {
      throw std::runtime_error(
          util::io::Msg()
          << "Error: Did not find displacement in the vtu file."
          << std::endl);
    }
 
    if (u.size() != nodes->size()) {
      throw std::runtime_error(
          util::io::Msg()
          << "Error: Displacement data and node data size do not match."
          << std::endl);
    }
 
    for (size_t i = 0; i < u.size(); i++)
      (*nodes)[i] -= u[i];
  }
 
  rdr.close();
}

Referenced by mesh::Mesh::createData().

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readVtuFilePointData() [1/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< double > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 257 of file reader.cpp.

                                                               {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [2/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< float > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 246 of file reader.cpp.

                                                              {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [3/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< int > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 235 of file reader.cpp.

                                                            {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [4/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< size_t > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 224 of file reader.cpp.

                                                               {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [5/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< uint8_t > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 213 of file reader.cpp.

                                                                {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

Referenced by mesh::Mesh::createData().

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readVtuFilePointData() [6/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::Matrix3 > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 290 of file reader.cpp.

                                                                    {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [7/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::Point > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 268 of file reader.cpp.

                                                                  {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFilePointData() [8/8]

bool rw::reader::readVtuFilePointData	(	const std::string &	filename,
		const std::string &	tag,
		std::vector< util::SymMatrix3 > *	data
	)

Reads data of specified tag from the vtu file.

Parameters

filename	Name of mesh file
tag	Name of point data to be read from .vtu file
data	Pointer to vector of point data

Returns

bool True if found the data in file

Definition at line 279 of file reader.cpp.

                                                                       {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // read data
  auto st = rdr.readPointData(tag, data);
  rdr.close();
  return st;
}

readVtuFileRestart()

void rw::reader::readVtuFileRestart	(	const std::string &	filename,
		std::vector< util::Point > *	u,
		std::vector< util::Point > *	v,
		const std::vector< util::Point > *	X = nullptr
	)

Reads mesh data into node file and element file.

Parameters

filename	Name of mesh file
u	Pointer to vector of nodal displacement
v	Pointer to vector of nodal velocity
X	Pointer to vector of nodal reference position (Optional)

Definition at line 185 of file reader.cpp.

                                                                   {
  // call vtk reader
  auto rdr = rw::reader::VtkReader(filename);
  // if displacement is not in input file, use reference coordinate to get
  // displacement
  if (!rdr.readPointData("Displacement", u)) {
    std::vector<util::Point> y;
    rdr.readNodes(&y);
    if (y.size() != X->size()) {
      throw std::runtime_error(
          util::io::Msg()
          << "Error: Number of nodes in input file = " << filename
          << " and number nodes in data X are not same.\n");
    }
 
    u->resize(y.size());
    for (size_t i = 0; i < y.size(); i++)
      (*u)[i] = y[i] - (*X)[i];
  }
 
  // get velocity
  rdr.readPointData("Velocity", v);
  rdr.close();
}