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 MultiDomainRMSD::projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& vecs, ReferenceValuePack& mypack ) const {
double totd=0.; std::vector<Vector> tvecs; mypack.clear();
MultiValue tvals( 1, mypack.getNumberOfDerivatives() ); ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals );
for(unsigned i=0; i<domains.size(); ++i) {
// Must extract appropriate positions here
tvecs.resize( blocks[i+1] - blocks[i] ); domains[i]->setupPCAStorage( tder );
if( tder.centeredpos.size()>0 ) {
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) tder.DRotDPos(p,q).resize( tvecs.size() );
}
// Extract information from storage pack and put in local pack
if( tder.centeredpos.size()>0 ) tder.rot[0]=mypack.rot[i];
unsigned n=0;
for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) {
tder.setAtomIndex(n,j); tvecs[n] = vecs[j]; tder.displacement[n]=mypack.displacement[j] / weights[i];
if( tder.centeredpos.size()>0 ) {
tder.centeredpos[n]=mypack.centeredpos[j];
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) tder.DRotDPos(p,q)[n]=mypack.DRotDPos(p,q)[j];
}
n++;
}
for(unsigned k=n; k<getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*vecs.size()+10);
// Do the calculations
totd += weights[i]*domains[i]->projectAtomicDisplacementOnVector( normalized, tvecs, tder );
// And derivatives
mypack.copyScaledDerivatives( 0, weights[i], tvals );
}
if( !mypack.updateComplete() ) mypack.updateDynamicLists();
return totd;
}
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 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;
}
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 MultiDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
double totd=0.; Tensor tvirial; std::vector<Vector> mypos; MultiValue tvals( 1, 3*pos.size()+9 );
ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals ); myder.clear();
for(unsigned i=0; i<domains.size(); ++i) {
// Must extract appropriate positions here
mypos.resize( blocks[i+1] - blocks[i] );
if( myder.calcUsingPCAOption() ) domains[i]->setupPCAStorage( tder );
unsigned n=0; for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) { tder.setAtomIndex(n,j); mypos[n]=pos[j]; n++; }
for(unsigned k=n; k<getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*pos.size()+10);
// This actually does the calculation
totd += weights[i]*domains[i]->calculate( mypos, pbc, tder, true );
// Now merge the derivative
myder.copyScaledDerivatives( 0, weights[i], tvals );
// If PCA copy PCA stuff
if( myder.calcUsingPCAOption() ) {
unsigned n=0;
if( tder.centeredpos.size()>0 ) myder.rot[i]=tder.rot[0];
for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) {
myder.displacement[j]=weights[i]*tder.displacement[n]; // Multiplication by weights here ensures that normalisation is done correctly
if( tder.centeredpos.size()>0 ) {
myder.centeredpos[j]=tder.centeredpos[n];
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) myder.DRotDPos(p,q)[j]=tder.DRotDPos(p,q)[n];
}
n++;
}
}
// Make sure virial status is set correctly in output derivative pack
// This is only done here so I do this by using class friendship
if( tder.virialWasSet() ) myder.boxWasSet=true;
}
if( !myder.updateComplete() ) myder.updateDynamicLists();
if( !squared ) {
totd=sqrt(totd); double xx=0.5/totd;
myder.scaleAllDerivatives( xx );
}
return totd;
}
double DRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
plumed_dbg_assert(!targets.empty());
Vector distance;
myder.clear();
double drmsd=0.;
for(std::map< std::pair <unsigned,unsigned> , double>::const_iterator it=targets.begin();it!=targets.end();++it){
const unsigned i=getAtomIndex( it->first.first );
const unsigned j=getAtomIndex( it->first.second );
if(nopbc) distance=delta( pos[i] , pos[j] );
else distance=pbc.distance( pos[i] , pos[j] );
const double len = distance.modulo();
const double diff = len - it->second;
const double der = diff / len;
drmsd += diff * diff;
myder.addAtomDerivatives( i, -der * distance );
myder.addAtomDerivatives( j, der * distance );
myder.addBoxDerivatives( - der * Tensor(distance,distance) );
}
const double inpairs = 1./static_cast<double>(targets.size());
double idrmsd;
if(squared){
drmsd = drmsd * inpairs;
idrmsd = 2.0 * inpairs;
} else {
drmsd = sqrt( drmsd * inpairs );
idrmsd = inpairs / drmsd ;
}
myder.scaleAllDerivatives( idrmsd );
return drmsd;
}