double OptimalRMSD::calc( const std::vector<Vector>& pos, const bool& squared ){
if( fast ){
if( getAlign()==getDisplace() ) return myrmsd.optimalAlignment<false,true>(getAlign(),getDisplace(),pos,getReferencePositions(),atom_ders,squared);
return myrmsd.optimalAlignment<false,false>(getAlign(),getDisplace(),pos,getReferencePositions(),atom_ders,squared);
} else {
if( getAlign()==getDisplace() ) return myrmsd.optimalAlignment<true,true>(getAlign(),getDisplace(),pos,getReferencePositions(),atom_ders,squared);
return myrmsd.optimalAlignment<true,false>(getAlign(),getDisplace(),pos,getReferencePositions(),atom_ders,squared);
}
}
double SimpleRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
if( myder.getAtomsDisplacementVector().size()!=pos.size() ) myder.getAtomsDisplacementVector().resize( pos.size() );
double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), myder.getAtomVector(), myder.getAtomsDisplacementVector(), squared );
myder.clear(); for(unsigned i=0;i<pos.size();++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
if( !myder.updateComplete() ) myder.updateDynamicLists();
return d;
}
double OptimalRMSD::projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& vecs, ReferenceValuePack& mypack ) const {
plumed_dbg_assert( mypack.calcUsingPCAOption() );
double proj=0.0; mypack.clear();
for(unsigned i=0; i<vecs.size(); ++i) {
proj += dotProduct( mypack.getAtomsDisplacementVector()[i], vecs[i] );
}
for(unsigned a=0; a<3; a++) {
for(unsigned b=0; b<3; b++) {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
double tmp1=0.;
for(unsigned n=0; n<getNumberOfAtoms(); n++) tmp1+=mypack.centeredpos[n][b]*vecs[n][a];
if( normalized ) mypack.addAtomDerivatives( iat, getDisplace()[iat]*mypack.DRotDPos[a][b][iat]*tmp1 );
else mypack.addAtomDerivatives( iat, mypack.DRotDPos[a][b][iat]*tmp1 );
}
}
}
Tensor trot=mypack.rot[0].transpose();
Vector v1; v1.zero(); double prefactor = 1. / static_cast<double>( getNumberOfAtoms() );
for(unsigned n=0; n<getNumberOfAtoms(); n++) v1+=prefactor*matmul(trot,vecs[n]);
if( normalized ) {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, getDisplace()[iat]*(matmul(trot,vecs[iat]) - v1) );
} else {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, (matmul(trot,vecs[iat]) - v1) );
}
if( !mypack.updateComplete() ) mypack.updateDynamicLists();
return proj;
}
double OptimalRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
double d;
if( myder.calcUsingPCAOption() ) {
std::vector<Vector> centeredreference( getNumberOfAtoms () );
d=myrmsd.calc_PCAelements(pos,myder.getAtomVector(),myder.rot[0],myder.DRotDPos,myder.getAtomsDisplacementVector(),myder.centeredpos,centeredreference,squared);
unsigned nat = pos.size();
for(unsigned i=0; i<nat; ++i) { myder.getAtomsDisplacementVector()[i] -= getReferencePosition(i); myder.getAtomsDisplacementVector()[i] *= getDisplace()[i]; }
} else if( fast ) {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<false,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<false,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
} else {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<true,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<true,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
}
myder.clear(); for(unsigned i=0; i<pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
if( !myder.updateComplete() ) myder.updateDynamicLists();
return d;
}
void SimpleRMSD::extractAtomicDisplacement( const std::vector<Vector>& pos, const bool& anflag, std::vector<Vector>& direction ) const {
std::vector<Vector> tder( getNumberOfAtoms() );
double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), tder, direction, true );
double scale=1.0; if( anflag ) scale = 1.0 / static_cast<double>( pos.size() );
for(unsigned i=0;i<pos.size();++i) direction[i] = scale*direction[i];
}
double SimpleRMSD::calc( const std::vector<Vector>& pos, const bool& squared ){
return myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), atom_ders, displacement, squared );
}
void OptimalRMSD::extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const {
std::vector<Tensor> rot(1); Matrix<std::vector<Vector> > DRotDPos( 3, 3 );
std::vector<Vector> centeredreference( getNumberOfAtoms() ), centeredpos( getNumberOfAtoms() ), avector( getNumberOfAtoms() );
double d=myrmsd.calc_PCAelements(pos,avector,rot[0],DRotDPos,direction,centeredpos,centeredreference,true);
unsigned nat = pos.size(); for(unsigned i=0; i<nat; ++i) direction[i] = getDisplace()[i]*( direction[i] - getReferencePosition(i) );
}