/usr/include/dolfin/mesh/MeshFunction.h is in libdolfin1.3-dev 1.3.0+dfsg-2.
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//
// This file is part of DOLFIN.
//
// DOLFIN is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// DOLFIN is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
// Modified by Johan Hoffman, 2007.
// Modified by Garth N. Wells, 2010-2013
//
// First added: 2006-05-22
// Last changed: 2013-05-10
#ifndef __MESH_FUNCTION_H
#define __MESH_FUNCTION_H
#include <map>
#include <vector>
#include <boost/scoped_array.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/unordered_set.hpp>
#include <dolfin/common/Hierarchical.h>
#include <dolfin/common/MPI.h>
#include <dolfin/common/NoDeleter.h>
#include <dolfin/common/Variable.h>
#include <dolfin/log/log.h>
#include <dolfin/io/File.h>
#include "LocalMeshValueCollection.h"
#include "MeshDomains.h"
#include "MeshEntity.h"
#include "Mesh.h"
#include "MeshConnectivity.h"
namespace dolfin
{
class MeshEntity;
/// A MeshFunction is a function that can be evaluated at a set of
/// mesh entities. A MeshFunction is discrete and is only defined
/// at the set of mesh entities of a fixed topological dimension.
/// A MeshFunction may for example be used to store a global
/// numbering scheme for the entities of a (parallel) mesh, marking
/// sub domains or boolean markers for mesh refinement.
template <typename T> class MeshFunction : public Variable,
public Hierarchical<MeshFunction<T> >
{
public:
/// Create empty mesh function
MeshFunction();
/// Create empty mesh function on given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
explicit MeshFunction(const Mesh& mesh);
/// Create empty mesh function on given mesh (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
explicit MeshFunction(boost::shared_ptr<const Mesh> mesh);
/// Create mesh function of given dimension on given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh function.
MeshFunction(const Mesh& mesh, std::size_t dim);
/// Create mesh function of given dimension on given mesh
/// (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh function.
MeshFunction(boost::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Create mesh of given dimension on given mesh and initialize
/// to a value
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// dim (std::size_t)
/// The mesh entity dimension.
/// value (T)
/// The value.
MeshFunction(const Mesh& mesh, std::size_t dim, const T& value);
/// Create mesh of given dimension on given mesh and initialize
/// to a value (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// dim (std::size_t)
/// The mesh entity dimension.
/// value (T)
/// The value.
MeshFunction(boost::shared_ptr<const Mesh> mesh, std::size_t dim,
const T& value);
/// Create function from data file
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// filename (std::string)
/// The filename to create mesh function from.
MeshFunction(const Mesh& mesh, const std::string filename);
/// Create function from data file (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// filename (std::string)
/// The filename to create mesh function from.
MeshFunction(boost::shared_ptr<const Mesh> mesh,
const std::string filename);
/// Create function from a MeshValueCollecion
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// value_collection (_MeshValueCollection_ <T>)
/// The mesh value collection for the mesh function data.
MeshFunction(const Mesh& mesh,
const MeshValueCollection<T>& value_collection);
/// Create function from a MeshValueCollecion (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// value_collection (_MeshValueCollection_ <T>)
/// The mesh value collection for the mesh function data.
MeshFunction(boost::shared_ptr<const Mesh> mesh,
const MeshValueCollection<T>& value_collection);
/// Create function from MeshDomains
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh to create mesh function on.
/// dim (std::size_t)
/// The dimension of the MeshFunction
/// domains (_MeshDomains)
/// The domains from which to extratc the domain markers
MeshFunction(boost::shared_ptr<const Mesh> mesh,
std::size_t dim, const MeshDomains& domains);
/// Copy constructor
///
/// *Arguments*
/// f (_MeshFunction_ <T>)
/// The object to be copied.
MeshFunction(const MeshFunction<T>& f);
/// Destructor
~MeshFunction() {}
/// Assign mesh function to other mesh function
/// Assignment operator
///
/// *Arguments*
/// f (_MeshFunction_ <T>)
/// A _MeshFunction_ object to asssign to another MeshFunction.
MeshFunction<T>& operator= (const MeshFunction<T>& f);
/// Assignment operator
///
/// *Arguments*
/// mesh (_MeshValueCollection_)
/// A _MeshValueCollection_ object used to construct a MeshFunction.
MeshFunction<T>& operator=(const MeshValueCollection<T>& mesh);
/// Return mesh associated with mesh function
///
/// *Returns*
/// _Mesh_
/// The mesh.
boost::shared_ptr<const Mesh> mesh() const;
/// Return topological dimension
///
/// *Returns*
/// std::size_t
/// The dimension.
std::size_t dim() const;
/// Return true if empty
///
/// *Returns*
/// bool
/// True if empty.
bool empty() const;
/// Return size (number of entities)
///
/// *Returns*
/// std::size_t
/// The size.
std::size_t size() const;
/// Return array of values (const. version)
///
/// *Returns*
/// T
/// The values.
const T* values() const;
/// Return array of values
///
/// *Returns*
/// T
/// The values.
T* values();
/// Return value at given mesh entity
///
/// *Arguments*
/// entity (_MeshEntity_)
/// The mesh entity.
///
/// *Returns*
/// T
/// The value at the given entity.
T& operator[] (const MeshEntity& entity);
/// Return value at given mesh entity (const version)
///
/// *Arguments*
/// entity (_MeshEntity_)
/// The mesh entity.
///
/// *Returns*
/// T
/// The value at the given entity.
const T& operator[] (const MeshEntity& entity) const;
/// Return value at given index
///
/// *Arguments*
/// index (std::size_t)
/// The index.
///
/// *Returns*
/// T
/// The value at the given index.
T& operator[] (std::size_t index);
/// Return value at given index (const version)
///
/// *Arguments*
/// index (std::size_t)
/// The index.
///
/// *Returns*
/// T
/// The value at the given index.
const T& operator[] (std::size_t index) const;
/// Set all values to given value
const MeshFunction<T>& operator= (const T& value);
/// Initialize mesh function for given topological dimension
///
/// *Arguments*
/// dim (std::size_t)
/// The dimension.
void init(std::size_t dim);
/// Initialize mesh function for given topological dimension of
/// given size
///
/// *Arguments*
/// dim (std::size_t)
/// The dimension.
/// size (std::size_t)
/// The size.
void init(std::size_t dim, std::size_t size);
/// Initialize mesh function for given topological dimension
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
/// dim (std::size_t)
/// The dimension.
void init(const Mesh& mesh, std::size_t dim);
/// Initialize mesh function for given topological dimension
/// (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
/// dim (std::size_t)
/// The dimension.
void init(boost::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Initialize mesh function for given topological dimension of
/// given size
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
/// dim (std::size_t)
/// The dimension.
/// size (std::size_t)
/// The size.
void init(const Mesh& mesh, std::size_t dim, std::size_t size);
/// Initialize mesh function for given topological dimension of
/// given size (shared_ptr version)
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
/// dim (std::size_t)
/// The dimension.
/// size (std::size_t)
/// The size.
void init(boost::shared_ptr<const Mesh> mesh, std::size_t dim,
std::size_t size);
/// Set value at given index
///
/// *Arguments*
/// index (std::size_t)
/// The index.
/// value (T)
/// The value.
void set_value(std::size_t index, const T& value);
/// Compatibility function for use in SubDomains
void set_value(std::size_t index, const T& value, const Mesh& mesh)
{ set_value(index, value); }
/// Set values
///
/// *Arguments*
/// values (std::vector<T>)
/// The values.
void set_values(const std::vector<T>& values);
/// Set all values to given value
///
/// *Arguments*
/// value (T)
/// The value to set all values to.
void set_all(const T& value);
/// Return informal string representation (pretty-print)
///
/// *Arguments*
/// verbose (bool)
/// Flag to turn on additional output.
///
/// *Returns*
/// std::string
/// An informal representation.
std::string str(bool verbose) const;
private:
// Values at the set of mesh entities. We don't use a std::vector<T>
// here because it has trouble with bool, which C++ specialises.
boost::scoped_array<T> _values;
// The mesh
boost::shared_ptr<const Mesh> _mesh;
// Topological dimension
std::size_t _dim;
// Number of mesh entities
std::size_t _size;
};
template<> std::string MeshFunction<double>::str(bool verbose) const;
template<> std::string MeshFunction<std::size_t>::str(bool verbose) const;
//---------------------------------------------------------------------------
// Implementation of MeshFunction
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction() : Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _values(0), _dim(0),
_size(0)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const Mesh& mesh)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this),
_mesh(reference_to_no_delete_pointer(mesh)), _dim(0), _size(0)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh), _dim(0), _size(0)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const Mesh& mesh, std::size_t dim)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this),
_mesh(reference_to_no_delete_pointer(mesh)) , _dim(0), _size(0)
{
init(dim);
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh,
std::size_t dim)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh), _dim(0), _size(0)
{
init(dim);
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const Mesh& mesh, std::size_t dim,
const T& value)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this),
_mesh(reference_to_no_delete_pointer(mesh)), _dim(0), _size(0)
{
init(dim);
set_all(value);
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh,
std::size_t dim, const T& value)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh), _dim(0), _size(0)
{
init(dim);
set_all(value);
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const Mesh& mesh, const std::string filename)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this),
_mesh(reference_to_no_delete_pointer(mesh)), _dim(0), _size(0)
{
File file(filename);
file >> *this;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh,
const std::string filename)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh), _dim(0), _size(0)
{
File file(filename);
file >> *this;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const Mesh& mesh,
const MeshValueCollection<T>& value_collection) :
Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this),
_mesh(reference_to_no_delete_pointer(mesh)),
_dim(value_collection.dim()), _size(0)
{
*this = value_collection;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh,
const MeshValueCollection<T>& value_collection)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh),
_dim(value_collection.dim()), _size(0)
{
*this = value_collection;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(boost::shared_ptr<const Mesh> mesh,
std::size_t dim, const MeshDomains& domains)
: Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _mesh(mesh), _dim(0), _size(0)
{
dolfin_assert(_mesh);
// Initialise MeshFunction
init(dim);
// Initialise mesh
mesh->init(dim);
// Set MeshFunction with default value
set_all(std::numeric_limits<T>::max());
// Get mesh dimension
const std::size_t D = _mesh->topology().dim();
dolfin_assert(dim <= D);
// Get domain data
const std::map<std::size_t, std::size_t>& data = domains.markers(dim);
// Iterate over all values and copy into MeshFunctions
std::map<std::size_t, std::size_t>::const_iterator it;
for (it = data.begin(); it != data.end(); ++it)
{
// Get value collection entry data
const std::size_t entity_index = it->first;
const T value = it->second;
dolfin_assert(entity_index < _size);
_values[entity_index] = value;
}
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>::MeshFunction(const MeshFunction<T>& f) :
Variable("f", "unnamed MeshFunction"),
Hierarchical<MeshFunction<T> >(*this), _dim(0), _size(0)
{
*this = f;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>& MeshFunction<T>::operator= (const MeshFunction<T>& f)
{
if (_size != f._size)
_values.reset(new T[f._size]);
_mesh = f._mesh;
_dim = f._dim;
_size = f._size;
std::copy(f._values.get(), f._values.get() + _size, _values.get());
Hierarchical<MeshFunction<T> >::operator=(f);
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
MeshFunction<T>& MeshFunction<T>::operator=(const MeshValueCollection<T>& mesh_value_collection)
{
_dim = mesh_value_collection.dim();
init(_dim);
dolfin_assert(_mesh);
// Get mesh connectivity D --> d
const std::size_t d = _dim;
const std::size_t D = _mesh->topology().dim();
dolfin_assert(d <= D);
// Generate connectivity if it does not excist
_mesh->init(D, d);
const MeshConnectivity& connectivity = _mesh->topology()(D, d);
dolfin_assert(!connectivity.empty());
// Set MeshFunction with default value
set_all(std::numeric_limits<T>::max());
// Iterate over all values
boost::unordered_set<std::size_t> entities_values_set;
typename std::map<std::pair<std::size_t, std::size_t>, T>::const_iterator it;
const std::map<std::pair<std::size_t, std::size_t>, T>& values
= mesh_value_collection.values();
for (it = values.begin(); it != values.end(); ++it)
{
// Get value collection entry data
const std::size_t cell_index = it->first.first;
const std::size_t local_entity = it->first.second;
const T value = it->second;
std::size_t entity_index = 0;
if (d != D)
{
// Get global (local to to process) entity index
dolfin_assert(cell_index < _mesh->num_cells());
entity_index = connectivity(cell_index)[local_entity];
}
else
{
entity_index = cell_index;
dolfin_assert(local_entity == 0);
}
// Set value for entity
dolfin_assert(entity_index < _size);
_values[entity_index] = value;
// Add entity index to set (used to check that all values are set)
entities_values_set.insert(entity_index);
}
// Check that all values have been set, if not issue a debug message
if (entities_values_set.size() != _size)
dolfin_debug("Mesh value collection does not contain all values for all entities");
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
boost::shared_ptr<const Mesh> MeshFunction<T>::mesh() const
{
dolfin_assert(_mesh);
return _mesh;
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshFunction<T>::dim() const
{
return _dim;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshFunction<T>::empty() const
{
return _size == 0;
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshFunction<T>::size() const
{
return _size;
}
//---------------------------------------------------------------------------
template <typename T>
const T* MeshFunction<T>::values() const
{
return _values.get();
}
//---------------------------------------------------------------------------
template <typename T>
T* MeshFunction<T>::values()
{
return _values.get();
}
//---------------------------------------------------------------------------
template <typename T>
T& MeshFunction<T>::operator[] (const MeshEntity& entity)
{
dolfin_assert(_values);
dolfin_assert(&entity.mesh() == _mesh.get());
dolfin_assert(entity.dim() == _dim);
dolfin_assert(entity.index() < _size);
return _values[entity.index()];
}
//---------------------------------------------------------------------------
template <typename T>
const T& MeshFunction<T>::operator[] (const MeshEntity& entity) const
{
dolfin_assert(_values);
dolfin_assert(&entity.mesh() == _mesh.get());
dolfin_assert(entity.dim() == _dim);
dolfin_assert(entity.index() < _size);
return _values[entity.index()];
}
//---------------------------------------------------------------------------
template <typename T>
T& MeshFunction<T>::operator[] (std::size_t index)
{
dolfin_assert(_values);
dolfin_assert(index < _size);
return _values[index];
}
//---------------------------------------------------------------------------
template <typename T>
const T& MeshFunction<T>::operator[] (std::size_t index) const
{
dolfin_assert(_values);
dolfin_assert(index < _size);
return _values[index];
}
//---------------------------------------------------------------------------
template <typename T>
const MeshFunction<T>& MeshFunction<T>::operator= (const T& value)
{
set_all(value);
//Hierarchical<MeshFunction<T> >::operator=(value);
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(std::size_t dim)
{
if (!_mesh)
{
dolfin_error("MeshFunction.h",
"initialize mesh function",
"Mesh has not been specified for mesh function");
}
_mesh->init(dim);
init(_mesh, dim, _mesh->size(dim));
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(std::size_t dim, std::size_t size)
{
if (!_mesh)
{
dolfin_error("MeshFunction.h",
"initialize mesh function",
"Mesh has not been specified for mesh function");
}
_mesh->init(dim);
init(_mesh, dim, size);
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(const Mesh& mesh, std::size_t dim)
{
mesh.init(dim);
init(mesh, dim, mesh.size(dim));
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(boost::shared_ptr<const Mesh> mesh,
std::size_t dim)
{
dolfin_assert(mesh);
mesh->init(dim);
init(mesh, dim, mesh->size(dim));
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(const Mesh& mesh, std::size_t dim,
std::size_t size)
{
// Initialize mesh for entities of given dimension
mesh.init(dim);
dolfin_assert(mesh.size(dim) == size);
// Initialize data
if (_size != size)
_values.reset(new T[size]);
_mesh = reference_to_no_delete_pointer(mesh);
_dim = dim;
_size = size;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::init(boost::shared_ptr<const Mesh> mesh,
std::size_t dim, std::size_t size)
{
dolfin_assert(mesh);
// Initialize mesh for entities of given dimension
mesh->init(dim);
dolfin_assert(mesh->size(dim) == size);
// Initialize data
if (_size != size)
_values.reset(new T[size]);
_mesh = mesh;
_dim = dim;
_size = size;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::set_value(std::size_t index, const T& value)
{
dolfin_assert(_values);
dolfin_assert(index < _size);
_values[index] = value;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::set_values(const std::vector<T>& values)
{
dolfin_assert(_values);
dolfin_assert(_size == values.size());
std::copy(values.begin(), values.end(), _values.get());
}
//---------------------------------------------------------------------------
template <typename T>
void MeshFunction<T>::set_all(const T& value)
{
dolfin_assert(_values);
std::fill(_values.get(), _values.get() + _size, value);
}
//---------------------------------------------------------------------------
template <typename T>
std::string MeshFunction<T>::str(bool verbose) const
{
std::stringstream s;
if (verbose)
{
s << str(false) << std::endl << std::endl;
warning("Verbose output of MeshFunctions must be implemented manually.");
// This has been disabled as it severely restricts the ease with which
// templated MeshFunctions can be used, e.g. it is not possible to
// template over std::vector.
//for (std::size_t i = 0; i < _size; i++)
// s << " (" << _dim << ", " << i << "): " << _values[i] << std::endl;
}
else
{
s << "<MeshFunction of topological dimension " << dim()
<< " containing " << size() << " values>";
}
return s.str();
}
//---------------------------------------------------------------------------
}
#endif
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