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AtomToMoleculeTransfer.h
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Sat, Apr 5, 08:52

AtomToMoleculeTransfer.h
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// A class for defining transfer operations molecular centers of mass (centroid), dipole moments, quadrupole moments
#ifndef ATOM_TO_MOLECULE_TRANSFER_H
#define ATOM_TO_MOLECULE_TRANSFER_H
#include <set>
// ATC_Method headers
#include "TransferOperator.h"
#include "MoleculeSet.h"
#include "PaqAtcUtility.h"
namespace ATC {
// forward declarations
class ATC_Method;
/**
* @class PerMoleculeQuantity
*
*/
template <typename T>
class PerMoleculeQuantity : public DenseMatrixTransfer<T> {
public:
PerMoleculeQuantity(ATC_Method * atc):DenseMatrixTransfer<T>(), atc_(atc) {};
virtual ~PerMoleculeQuantity() {};
protected:
/** utility object for atc information */
ATC_Method * atc_;
private:
//do not define
PerMoleculeQuantity();
};
/**
* @class AtomtoSmallMoleculeTransfer
* @brief Class for defining objects to transfer total mass or charge of a molecule
*/
template <typename T>
class AtomToSmallMoleculeTransfer : public PerMoleculeQuantity<T> {
public:
//constructor
// had to define all functions in header, not sure why (JAT, 12/14/11)
AtomToSmallMoleculeTransfer(ATC_Method * atc, PerAtomQuantity<T> * source, SmallMoleculeSet * smallMoleculeSet) :
PerMoleculeQuantity<T>(atc),
source_(source),
smallMoleculeSet_(smallMoleculeSet)
{
source_->register_dependence(this);
smallMoleculeSet_->register_dependence(this);
};
//destructor
virtual ~AtomToSmallMoleculeTransfer()
{
source_->remove_dependence(this);
smallMoleculeSet_->remove_dependence(this);
};
// apply transfer operator
void reset_quantity() const
{
const DenseMatrix<T> & sourceMatrix(source_->quantity());
int nLocalMol = smallMoleculeSet_->local_molecule_count();
(this->quantity_).reset(nLocalMol,sourceMatrix.nCols());
for (int i = 0; i < nLocalMol ; i++) {
const std::set<int> & atomsLocalMolArray = smallMoleculeSet_->atoms_by_local_molecule(i);
std::set<int>::const_iterator atomsLocalMolID;
for (atomsLocalMolID = atomsLocalMolArray.begin(); atomsLocalMolID!= atomsLocalMolArray.end();atomsLocalMolID++) {
for (int j = 0; j < sourceMatrix.nCols(); j++){
(this->quantity_)(i,j) += sourceMatrix(*atomsLocalMolID,j);
}
}
}
};
protected:
// pointer to source atomic quantity data
PerAtomQuantity<T> * source_;
// pointer to molecule data
SmallMoleculeSet * smallMoleculeSet_;
private:
// do not define
AtomToSmallMoleculeTransfer();
};
/**
* @class SmallMoleculeCentroid
* @brief Class for defining objects to transfer molecular centroid (center of mass)
*/
class SmallMoleculeCentroid : public AtomToSmallMoleculeTransfer<double> {
public:
//constructor
SmallMoleculeCentroid(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions);
//destructor
virtual ~SmallMoleculeCentroid();
// apply transfer operator
virtual void reset_quantity() const;
protected:
// pointer to source atomic quantity date : positions of atoms in a molecule
PerAtomQuantity<double> * atomPositions_;
private:
//do not define
SmallMoleculeCentroid();
};
/**
* @class SmallMoleculeDipoleMoment
* @brief Class for defining objects to transfer molecular dipole moments
*/
class SmallMoleculeDipoleMoment : public SmallMoleculeCentroid {
public:
//constructor
SmallMoleculeDipoleMoment(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions, SmallMoleculeCentroid * centroid);
//destructor
virtual ~SmallMoleculeDipoleMoment();
// apply transfer operator
virtual void reset_quantity() const;
protected:
//pointer to the centroid data
SmallMoleculeCentroid * centroid_;
private:
//do not define
SmallMoleculeDipoleMoment();
};
/**
* @class AtomToFeTransfer
* @brief Class for defining objects to transfer molecular quadrupole moments
*/
class SmallMoleculeQuadrupoleMoment : public SmallMoleculeCentroid {
public:
//constructor
SmallMoleculeQuadrupoleMoment(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions, SmallMoleculeCentroid * centroid);
//destructor
virtual ~SmallMoleculeQuadrupoleMoment();
//apply transfer operator
virtual void reset_quantity() const;
protected:
//pointer to the centroid data
SmallMoleculeCentroid * centroid_;
private:
//do not define
SmallMoleculeQuadrupoleMoment();
};
/**
* @class MotfShapeFunctionRestriction
* @brief Class for defining objects that transfer atomistic quantities to FE using shape functions
* (implements restrict_volumetric_quantity)
*/
class MotfShapeFunctionRestriction : public MatToMatTransfer<double> {
public:
// constructor
MotfShapeFunctionRestriction(PerMoleculeQuantity<double> * source,
SPAR_MAN * shapeFunction);
// destructor
virtual ~MotfShapeFunctionRestriction();
/** apply transfer operator */
virtual void reset_quantity() const;
protected:
/** reference to shape function matrix */
SPAR_MAN * shapeFunction_;
/** persistant workspace */
mutable DENS_MAT _workspace_;
/** applies restriction operation on this processor */
virtual void local_restriction(const DENS_MAT & sourceMatrix,
const SPAR_MAT & shapeFunctionMatrix) const;
private:
// do not define
MotfShapeFunctionRestriction();
};
}
#endif

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