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lammps/lib/atc/AtomToMoleculeTransfer.cpp
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AtomToMoleculeTransfer.cpp
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// ATC headers
#include "AtomToMoleculeTransfer.h"
#include "ATC_Method.h"
namespace ATC {
//--------------------------------------------------------
//--------------------------------------------------------
// Class SmallMoleculeCentroid
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
SmallMoleculeCentroid::SmallMoleculeCentroid(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions) : AtomToSmallMoleculeTransfer<double>(atc, source, smallMoleculeSet), atomPositions_(atomPositions)
{
atomPositions_->register_dependence(this);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
SmallMoleculeCentroid::~SmallMoleculeCentroid()
{
atomPositions_->remove_dependence(this);
}
//--------------------------------------------------------
// Quantity
//--------------------------------------------------------
void SmallMoleculeCentroid::reset_quantity() const
{
const LammpsInterface * lammps(atc_->lammps_interface());
const DENS_MAT & sourceMatrix(source_->quantity()); // source is always a scalar quantity here \sum m_i \x_i
double xi[3], xj[3], xjImage[3];
const DENS_MAT & atomPosMatrix(atomPositions_->quantity());
int nLocalMol = smallMoleculeSet_->local_molecule_count();
quantity_.reset(nLocalMol,atc_->nsd());
for (int i = 0; i < nLocalMol; i++) {
const set<int> & atomsLocalMolArray = smallMoleculeSet_->atoms_by_local_molecule(i);
set<int>::const_iterator atomsLocalMolID;
double totalSourceMol = 0.0; // for total source
for (atomsLocalMolID = atomsLocalMolArray.begin(); atomsLocalMolID != atomsLocalMolArray.end(); atomsLocalMolID++) {
totalSourceMol += sourceMatrix(*atomsLocalMolID,0);
} // compute total source
atomsLocalMolID = atomsLocalMolArray.begin();
for (int j = 0; j < atc_->nsd(); j++) {
xi[j] = atomPosMatrix(*atomsLocalMolID,j);
}
for (atomsLocalMolID = atomsLocalMolArray.begin(); atomsLocalMolID != atomsLocalMolArray.end(); atomsLocalMolID++) {
for (int j = 0; j < atc_->nsd(); j++){
xj[j] = atomPosMatrix(*atomsLocalMolID,j);
}
lammps->closest_image(xi,xj,xjImage);
for (int j = 0; j < atc_->nsd() ; j++) {
quantity_(i,j) += sourceMatrix(*atomsLocalMolID,0) * xjImage[j]/totalSourceMol;
}
}
}
}
//--------------------------------------------------------
//--------------------------------------------------------
// Class SmallMoleculeDipoleMoment
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
SmallMoleculeDipoleMoment::SmallMoleculeDipoleMoment(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions, SmallMoleculeCentroid * centroid) : SmallMoleculeCentroid(atc, source, smallMoleculeSet, atomPositions), centroid_(centroid) //check here
{
centroid_->register_dependence(this);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
SmallMoleculeDipoleMoment::~SmallMoleculeDipoleMoment()
{
centroid_->remove_dependence(this);
}
//--------------------------------------------------------
// Quantity
//--------------------------------------------------------
void SmallMoleculeDipoleMoment::reset_quantity() const
{
const LammpsInterface * lammps(atc_->lammps_interface());
const DENS_MAT & sourceMatrix(source_->quantity()); // source is always a scalar quantity here \sum m_i
const DENS_MAT & atomPosMatrix(atomPositions_->quantity());
int nLocalMol = smallMoleculeSet_->local_molecule_count();
int nsd = atc_->nsd();
quantity_.reset(nLocalMol,nsd);
double dx[3];
//call the SmallMoleculeCentroid here to find Centroid ....
const DENS_MAT & centroidMolMatrix(centroid_->quantity());
for (int i = 0; i < nLocalMol; i++) {
const set<int> & atomsLocalMolArray = smallMoleculeSet_->atoms_by_local_molecule(i);
set<int>::const_iterator atomsLocalMolID;;
for (atomsLocalMolID = atomsLocalMolArray.begin(); atomsLocalMolID != atomsLocalMolArray.end();atomsLocalMolID++) {
for (int j = 0; j < nsd; j++) {
dx[j] = atomPosMatrix(*atomsLocalMolID,j) - centroidMolMatrix(i,j);
}
lammps->minimum_image(dx[0], dx[1], dx[2]);
for(int j = 0; j < nsd; j++) {
quantity_(i,j) += sourceMatrix(*atomsLocalMolID,0) * dx[j];
}
}
}
}
//--------------------------------------------------------
// Class SmallMoleculeQuadrupoleMoment
//--------------------------------------------------------
//--------------------------------------------------------
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
SmallMoleculeQuadrupoleMoment::SmallMoleculeQuadrupoleMoment(ATC_Method * atc, PerAtomQuantity<double> * source, SmallMoleculeSet * smallMoleculeSet, PerAtomQuantity<double> * atomPositions, SmallMoleculeCentroid * centroid) : SmallMoleculeCentroid(atc, source, smallMoleculeSet, atomPositions), centroid_(centroid)
{
centroid_->register_dependence(this);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
SmallMoleculeQuadrupoleMoment::~SmallMoleculeQuadrupoleMoment()
{
centroid_->remove_dependence(this);
}
//--------------------------------------------------------
// Quantity
//--------------------------------------------------------
void SmallMoleculeQuadrupoleMoment::reset_quantity() const
{
const LammpsInterface * lammps(atc_->lammps_interface());
const DENS_MAT & sourceMatrix(source_->quantity()); // source is always a scalar quantity here \sum m_i
const DENS_MAT & atomPosMatrix(atomPositions_->quantity());
int nLocalMol = smallMoleculeSet_->local_molecule_count();
int nsd = atc_->nsd();
quantity_.reset(nLocalMol,nsd);
double dx[3];
//call the SmallMoleculeCentroid here to find Centroid ....
const DENS_MAT & centroidMolMatrix(centroid_->quantity());
for (int i = 0; i < nLocalMol; i++) {
const set<int> & atomsLocalMolArray = smallMoleculeSet_->atoms_by_local_molecule(i);
set<int>::const_iterator atomsLocalMolID;;
for (atomsLocalMolID = atomsLocalMolArray.begin(); atomsLocalMolID != atomsLocalMolArray.end();atomsLocalMolID++) {
for (int j = 0; j < nsd; j++) {
dx[j] = atomPosMatrix(*atomsLocalMolID,j) - centroidMolMatrix(i,j);
}
lammps->minimum_image(dx[0], dx[1], dx[2]);
for(int j = 0; j < nsd; j++) {
quantity_(i,j) += 0.5*sourceMatrix(*atomsLocalMolID,0) * dx[j] * dx[2];
/* quantity_(i,3*j) += 0.5*sourceMatrix(*atomsLocalMolID,0) * dx[j]*dx[0];
quantity_(i,3*j+1) += 0.5*sourceMatrix(*atomsLocalMolID,0) * dx[j]*dx[1];
quantity_(i,3*j+2) += 0.5*sourceMatrix(*atomsLocalMolID,0) * dx[j]*dx[2]; */
}
}
}
}
//--------------------------------------------------------
// Constructor
//--------------------------------------------------------
MotfShapeFunctionRestriction::MotfShapeFunctionRestriction(PerMoleculeQuantity<double> * source,
SPAR_MAN * shapeFunction) :
MatToMatTransfer<double>(source),
shapeFunction_(shapeFunction)
{
shapeFunction_->register_dependence(this);
}
//--------------------------------------------------------
// Destructor
//--------------------------------------------------------
MotfShapeFunctionRestriction::~MotfShapeFunctionRestriction()
{
shapeFunction_->remove_dependence(this);
}
//--------------------------------------------------------
// reset_quantity
//--------------------------------------------------------
void MotfShapeFunctionRestriction::reset_quantity() const
{
// computes nodeData = N*atomData where N are the shape functions
const DENS_MAT & sourceMatrix(source_->quantity());
// reallocate memory only if sizing has changed
const SPAR_MAT & shapeFunctionMatrix(shapeFunction_->quantity());
quantity_.resize(shapeFunctionMatrix.nCols(),sourceMatrix.nCols());
local_restriction(sourceMatrix,shapeFunctionMatrix);
// communicate for total restriction
int count = quantity_.nRows()*quantity_.nCols();
lammpsInterface_->allsum(_workspace_.ptr(),quantity_.ptr(),count);
}
//--------------------------------------------------------
// local_restriction
//--------------------------------------------------------
void MotfShapeFunctionRestriction::local_restriction(const DENS_MAT & sourceMatrix,
const SPAR_MAT & shapeFunctionMatrix) const
{
if (sourceMatrix.nRows() > 0)
_workspace_ = shapeFunctionMatrix.transMat(sourceMatrix);
else
_workspace_.reset(quantity_.nRows(),quantity_.nCols());
}
} // end namespace
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