int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceLincsAlgorithm::apply";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
// ---------------------------------------------------------------------------------------
if (_numberOfConstraints == 0)
return SimTKOpenMMCommon::DefaultReturn;
if( !_hasInitialized )
initialize(numberOfAtoms, inverseMasses);
// Calculate the direction of each constraint, along with the initial RHS and solution vectors.
for (int i = 0; i < _numberOfConstraints; i++) {
int atom1 = _atomIndices[i][0];
int atom2 = _atomIndices[i][1];
_constraintDir[i] = RealVec(atomCoordinatesP[atom1][0]-atomCoordinatesP[atom2][0],
atomCoordinatesP[atom1][1]-atomCoordinatesP[atom2][1],
atomCoordinatesP[atom1][2]-atomCoordinatesP[atom2][2]);
RealOpenMM invLength = (RealOpenMM)(1/SQRT((RealOpenMM)_constraintDir[i].dot(_constraintDir[i])));
_constraintDir[i][0] *= invLength;
_constraintDir[i][1] *= invLength;
_constraintDir[i][2] *= invLength;
_rhs1[i] = _solution[i] = _sMatrix[i]*(one/invLength-_distance[i]);
}
// Build the coupling matrix.
for (int c1 = 0; c1 < (int)_couplingMatrix.size(); c1++) {
RealVec& dir1 = _constraintDir[c1];
for (int j = 0; j < (int)_couplingMatrix[c1].size(); j++) {
int c2 = _linkedConstraints[c1][j];
RealVec& dir2 = _constraintDir[c2];
if (_atomIndices[c1][0] == _atomIndices[c2][0] || _atomIndices[c1][1] == _atomIndices[c2][1])
_couplingMatrix[c1][j] = (RealOpenMM)(-inverseMasses[_atomIndices[c1][0]]*_sMatrix[c1]*dir1.dot(dir2)*_sMatrix[c2]);
else
_couplingMatrix[c1][j] = (RealOpenMM)(inverseMasses[_atomIndices[c1][1]]*_sMatrix[c1]*dir1.dot(dir2)*_sMatrix[c2]);
}
}
// Solve the matrix equation and update the positions.
solveMatrix();
updateAtomPositions(numberOfAtoms, atomCoordinatesP, inverseMasses);
// Correct for rotational lengthening.
for (int i = 0; i < _numberOfConstraints; i++) {
int atom1 = _atomIndices[i][0];
int atom2 = _atomIndices[i][1];
RealVec delta(atomCoordinatesP[atom1][0]-atomCoordinatesP[atom2][0],
atomCoordinatesP[atom1][1]-atomCoordinatesP[atom2][1],
atomCoordinatesP[atom1][2]-atomCoordinatesP[atom2][2]);
RealOpenMM p2 = (RealOpenMM)(two*_distance[i]*_distance[i]-delta.dot(delta));
if (p2 < zero)
p2 = zero;
_rhs1[i] = _solution[i] = _sMatrix[i]*(_distance[i]-SQRT(p2));
}
solveMatrix();
updateAtomPositions(numberOfAtoms, atomCoordinatesP, inverseMasses);
return SimTKOpenMMCommon::DefaultReturn;
}
MBPolReferenceDispersionForce::MBPolReferenceDispersionForce( ) : _nonbondedMethod(NoCutoff), _cutoff(1.0e+10) {
_periodicBoxDimensions = RealVec( 0.0, 0.0, 0.0 );
}