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 Direction::calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& args,
ReferenceValuePack& myder, const bool& squared ) const {
plumed_assert( squared );
for(unsigned i=0;i<getNumberOfReferenceArguments();++i) myder.addArgumentDerivatives( i, -2.*getReferenceArgument(i) );
for(unsigned i=0;i<getNumberOfAtoms();++i) myder.getAtomsDisplacementVector()[i]=getReferencePosition(i);
return 0.0;
}
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;
}
double SimpleRMSD::projectAtomicDisplacementOnVector( const std::vector<Vector>& vecs, const std::vector<Vector>& pos, ReferenceValuePack& mypack ) const {
plumed_dbg_assert( mypack.calcUsingPCAOption() ); Vector comder; comder.zero();
for(unsigned j=0;j<pos.size();++j){
for(unsigned k=0;k<3;++k) comder[k] += getAlign()[j]*vecs[j][k];
}
double proj=0; mypack.clear();
for(unsigned j=0;j<pos.size();++j){
for(unsigned k=0;k<3;++k){
proj += vecs[j][k]*mypack.getAtomsDisplacementVector()[j][k];
}
mypack.setAtomDerivatives( j, vecs[j] - comder );
}
if( !mypack.updateComplete() ) mypack.updateDynamicLists();
return proj;
}