/usr/include/dolfin/mesh/MeshValueCollection.h is in libdolfin-dev 2016.2.0-2.
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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 Chris Richardson, 2013.
//
// First added: 2006-08-30
// Last changed: 2013-05-22
#ifndef __MESH_VALUE_COLLECTION_H
#define __MESH_VALUE_COLLECTION_H
#include <map>
#include <utility>
#include <memory>
#include <dolfin/common/NoDeleter.h>
#include <dolfin/common/Variable.h>
#include <dolfin/log/log.h>
#include "Cell.h"
#include "Mesh.h"
#include "MeshEntity.h"
#include "MeshFunction.h"
namespace dolfin
{
/// The MeshValueCollection class can be used to store data
/// associated with a subset of the entities of a mesh of a given
/// topological dimension. It differs from the MeshFunction class in
/// two ways. First, data does not need to be associated with all
/// entities (only a subset). Second, data is associated with
/// entities through the corresponding cell index and local entity
/// number (relative to the cell), not by global entity index, which
/// means that data may be stored robustly to file.
template <typename T>
class MeshValueCollection : public Variable
{
public:
/// Create empty mesh value collection
///
MeshValueCollection();
/// Create an empty mesh value collection on a given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh.
explicit MeshValueCollection(std::shared_ptr<const Mesh> mesh);
/// Create a mesh value collection from a MeshFunction
///
/// *Arguments*
/// mesh_function (_MeshFunction_ <T>)
/// The mesh function for creating a MeshValueCollection.
explicit MeshValueCollection(const MeshFunction<T>& mesh_function);
/// Create a mesh value collection of entities of given dimension
/// on a given mesh
///
/// *Arguments*
/// mesh (_Mesh_)
/// The mesh associated with the collection.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
MeshValueCollection(std::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Create a mesh value collection from a file.
///
/// *Arguments*
/// mesh (Mesh)
/// A mesh associated with the collection. The mesh is used to
/// map collection values to the appropriate process.
/// filename (std::string)
/// The XML file name.
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
MeshValueCollection(std::shared_ptr<const Mesh> mesh, const std::string filename);
/// Destructor
~MeshValueCollection() {}
/// Assignment operator
///
/// *Arguments*
/// mesh_function (_MeshFunction_)
/// A _MeshFunction_ object used to construct a
/// MeshValueCollection.
MeshValueCollection<T>& operator=(const MeshFunction<T>& mesh_function);
/// Assignment operator
///
/// *Arguments*
/// mesh_value_collection (_MeshValueCollection_)
/// A _MeshValueCollection_ object used to construct a
/// MeshValueCollection.
MeshValueCollection<T>&
operator=(const MeshValueCollection<T>& mesh_value_collection);
/// Initialise MeshValueCollection with mesh and dimension
///
/// *Arguments*
/// mesh (_mesh))
/// The mesh on which the value collection is defined
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
void init(std::shared_ptr<const Mesh> mesh, std::size_t dim);
/// Set dimension. This function should not generally be used. It is
/// for reading MeshValueCollections as the dimension is not
/// generally known at construction.
///
/// *Arguments*
/// dim (std::size_t)
/// The mesh entity dimension for the mesh value collection.
void init(std::size_t dim);
/// Return topological dimension
///
/// *Returns*
/// std::size_t
/// The dimension.
std::size_t dim() const;
/// Return associated mesh
///
/// *Returns*
/// _Mesh_
/// The mesh.
std::shared_ptr<const Mesh> mesh() const;
/// Return true if the subset is empty
///
/// *Returns*
/// bool
/// True if the subset is empty.
bool empty() const;
/// Return size (number of entities in subset)
///
/// *Returns*
/// std::size_t
/// The size.
std::size_t size() const;
/// Set marker value for given entity defined by a cell index and
/// a local entity index
///
/// *Arguments*
/// cell_index (std::size_t)
/// The index of the cell.
/// local_entity (std::size_t)
/// The local index of the entity relative to the cell.
/// marker_value (T)
/// The value of the marker.
///
/// *Returns*
/// bool
/// True is a new value is inserted, false if overwriting
/// an existing value.
bool set_value(std::size_t cell_index, std::size_t local_entity,
const T& value);
/// Set value for given entity index
///
/// *Arguments*
/// entity_index (std::size_t)
/// Index of the entity.
/// value (T).
/// The value of the marker.
/// mesh (_Mesh_)
/// The mesh.
///
/// *Returns*
/// bool
/// True is a new value is inserted, false if overwriting
/// an existing value.
bool set_value(std::size_t entity_index, const T& value);
/// Get marker value for given entity defined by a cell index and
/// a local entity index
///
/// *Arguments*
/// cell_index (std::size_t)
/// The index of the cell.
/// local_entity (std::size_t)
/// The local index of the entity relative to the cell.
///
/// *Returns*
/// marker_value (T)
/// The value of the marker.
T get_value(std::size_t cell_index, std::size_t local_entity);
/// Get all values
///
/// *Returns*
/// std::map<std::pair<std::size_t, std::size_t>, T>
/// A map from positions to values.
std::map<std::pair<std::size_t, std::size_t>, T>& values();
/// Get all values (const version)
///
/// *Returns*
/// std::map<std::pair<std::size_t, std::size_t>, T>
/// A map from positions to values.
const std::map<std::pair<std::size_t, std::size_t>, T>& values() const;
/// Clear all values
void clear();
/// 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:
// Associated mesh
std::shared_ptr<const Mesh> _mesh;
// Topological dimension
int _dim;
// The values
std::map<std::pair<std::size_t, std::size_t>, T> _values;
};
//---------------------------------------------------------------------------
// Implementation of MeshValueCollection
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection()
: Variable("m", "unnamed MeshValueCollection"), _dim(-1)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(std::shared_ptr<const Mesh>
mesh) : _mesh(mesh), _dim(-1)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(std::shared_ptr<const Mesh>
mesh, std::size_t dim)
: Variable("m", "unnamed MeshValueCollection"), _mesh(mesh), _dim(dim)
{
// Do nothing
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(const MeshFunction<T>&
mesh_function)
: Variable("m", "unnamed MeshValueCollection"), _mesh(mesh_function.mesh()),
_dim(mesh_function.dim())
{
dolfin_assert(_mesh);
const std::size_t D = _mesh->topology().dim();
// Handle cells as a special case
if ((int) D == _dim)
{
for (std::size_t cell_index = 0; cell_index < mesh_function.size();
++cell_index)
{
const std::pair<std::size_t, std::size_t> key(cell_index, 0);
_values.insert({key, mesh_function[cell_index]});
}
}
else
{
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
dolfin_assert(!connectivity.empty());
for (std::size_t entity_index = 0; entity_index < mesh_function.size();
++entity_index)
{
// Find the cell
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
for (std::size_t i = 0; i < entity.num_entities(D) ; ++i)
{
// Create cell
const Cell cell(*_mesh, connectivity(entity_index)[i]);
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Insert into map
const std::pair<std::size_t, std::size_t> key(cell.index(),
local_entity);
_values.insert({key, mesh_function[entity_index]});
}
}
}
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>::MeshValueCollection(std::shared_ptr<const Mesh> mesh,
const std::string filename)
: Variable("m", "unnamed MeshValueCollection"),
_mesh(mesh), _dim(-1)
{
File file(filename);
file >> *this;
dolfin_assert(_dim > -1);
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>&
MeshValueCollection<T>::operator=(const MeshFunction<T>& mesh_function)
{
_mesh = mesh_function.mesh();
_dim = mesh_function.dim();
dolfin_assert(_mesh);
const std::size_t D = _mesh->topology().dim();
// FIXME: Use iterators
// Handle cells as a special case
if ((int) D == _dim)
{
for (std::size_t cell_index = 0; cell_index < mesh_function.size();
++cell_index)
{
const std::pair<std::size_t, std::size_t> key(cell_index, 0);
_values.insert({key, mesh_function[cell_index]});
}
}
else
{
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
dolfin_assert(!connectivity.empty());
for (std::size_t entity_index = 0; entity_index < mesh_function.size();
++entity_index)
{
// Find the cell
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
for (std::size_t i = 0; i < entity.num_entities(D) ; ++i)
{
// Create cell
const Cell cell(*_mesh, connectivity(entity_index)[i]);
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Insert into map
const std::pair<std::size_t, std::size_t> key(cell.index(),
local_entity);
_values.insert({key, mesh_function[entity_index]});
}
}
}
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
MeshValueCollection<T>&
MeshValueCollection<T>::operator=(const MeshValueCollection<T>&
mesh_value_collection)
{
_mesh = mesh_value_collection._mesh;
_dim = mesh_value_collection.dim();
_values = mesh_value_collection.values();
return *this;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::init(std::shared_ptr<const Mesh> mesh,
std::size_t dim)
{
mesh->init(dim);
_mesh = mesh;
_dim = dim;
_values.clear();
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::init(std::size_t dim)
{
dolfin_assert(_mesh);
dolfin_assert(_dim < 0);
_dim = dim;
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshValueCollection<T>::dim() const
{
dolfin_assert(_dim >= 0);
return _dim;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::empty() const
{
return _values.empty();
}
//---------------------------------------------------------------------------
template <typename T>
std::size_t MeshValueCollection<T>::size() const
{
return _values.size();
}
//---------------------------------------------------------------------------
template <typename T>
std::shared_ptr<const Mesh> MeshValueCollection<T>::mesh() const
{
dolfin_assert(_mesh);
return _mesh;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::set_value(std::size_t cell_index,
std::size_t local_entity,
const T& value)
{
dolfin_assert(_dim >= 0);
if (!_mesh)
{
dolfin_error("MeshValueCollection.h",
"set value",
"A mesh has not been associated with this MeshValueCollection");
}
const std::pair<std::size_t, std::size_t> pos(cell_index, local_entity);
std::pair<typename std::map<std::pair<std::size_t, std::size_t>, T>::iterator, bool>
it = _values.insert({pos, value});
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
//---------------------------------------------------------------------------
template <typename T>
bool MeshValueCollection<T>::set_value(std::size_t entity_index,
const T& value)
{
if (!_mesh)
{
dolfin_error("MeshValueCollection.h",
"set value",
"A mesh has not been associated with this MeshValueCollection");
}
dolfin_assert(_dim >= 0);
// Special case when d = D
const std::size_t D = _mesh->topology().dim();
if (_dim == (int) D)
{
// Set local entity index to zero when we mark a cell
const std::pair<std::size_t, std::size_t> pos(entity_index, 0);
std::pair<typename std::map<std::pair<std::size_t,
std::size_t>, T>::iterator, bool> it;
it = _values.insert({pos, value});
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
// Get mesh connectivity d --> D
_mesh->init(_dim, D);
const MeshConnectivity& connectivity = _mesh->topology()(_dim, D);
// Find the cell
dolfin_assert(!connectivity.empty());
dolfin_assert(connectivity.size(entity_index) > 0);
const MeshEntity entity(*_mesh, _dim, entity_index);
const Cell cell(*_mesh, connectivity(entity_index)[0]); // choose first
// Find the local entity index
const std::size_t local_entity = cell.index(entity);
// Add value
const std::pair<std::size_t, std::size_t> pos(cell.index(), local_entity);
std::pair<typename std::map<std::pair<std::size_t,
std::size_t>, T>::iterator, bool> it;
it = _values.insert({pos, value});
// If an item with same key already exists the value has not been
// set and we need to update it
if (!it.second)
it.first->second = value;
return it.second;
}
//---------------------------------------------------------------------------
template <typename T>
T MeshValueCollection<T>::get_value(std::size_t cell_index,
std::size_t local_entity)
{
dolfin_assert(_dim >= 0);
const std::pair<std::size_t, std::size_t> pos(cell_index, local_entity);
const typename std::map<std::pair<std::size_t,
std::size_t>, T>::const_iterator
it = _values.find(pos);
if (it == _values.end())
{
dolfin_error("MeshValueCollection.h",
"extract value",
"No value stored for cell index: %d and local index: %d",
cell_index, local_entity);
}
return it->second;
}
//---------------------------------------------------------------------------
template <typename T>
std::map<std::pair<std::size_t, std::size_t>, T>&
MeshValueCollection<T>::values()
{
return _values;
}
//---------------------------------------------------------------------------
template <typename T>
const std::map<std::pair<std::size_t, std::size_t>, T>&
MeshValueCollection<T>::values() const
{
return _values;
}
//---------------------------------------------------------------------------
template <typename T>
void MeshValueCollection<T>::clear()
{
_values.clear();
}
//---------------------------------------------------------------------------
template <typename T>
std::string MeshValueCollection<T>::str(bool verbose) const
{
std::stringstream s;
if (verbose)
{
s << str(false) << std::endl << std::endl;
warning("Verbose output of MeshValueCollection must be implemented manually.");
}
else
{
s << "<MeshValueCollection of topological dimension " << dim()
<< " containing " << size() << " values>";
}
return s.str();
}
//---------------------------------------------------------------------------
}
#endif
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