double ReferenceArguments::calculateArgumentDistance( const std::vector<Value*> & vals, const std::vector<double>& arg,
ReferenceValuePack& myder, const bool& squared ) const {
double r=0; std::vector<double> arg_ders( vals.size() );
if( hasmetric ) {
for(unsigned i=0; i<reference_args.size(); ++i) {
unsigned ik=arg_der_index[i]; arg_ders[ ik ]=0;
double dp_i=vals[ik]->difference( reference_args[i], arg[ik] );
for(unsigned j=0; j<reference_args.size(); ++j) {
double dp_j;
unsigned jk=arg_der_index[j];
if(i==j) dp_j=dp_i;
else dp_j=vals[jk]->difference( reference_args[j], arg[jk] );
arg_ders[ ik ]+=2.0*metric(i,j)*dp_j; // Factor of two for off diagonal terms as you have terms from ij and ji
r+=dp_i*dp_j*metric(i,j);
}
}
} else {
for(unsigned i=0; i<reference_args.size(); ++i) {
unsigned ik=arg_der_index[i];
double dp_i=vals[ik]->difference( reference_args[i], arg[ik] );
r+=weights[i]*dp_i*dp_i; arg_ders[ik]=2.0*weights[i]*dp_i;
}
}
if(!squared) {
r=sqrt(r); double ir=1.0/(2.0*r);
for(unsigned i=0; i<arg_ders.size(); ++i) myder.setArgumentDerivatives( i, arg_ders[i]*ir );
} else {
for(unsigned i=0; i<arg_ders.size(); ++i) myder.setArgumentDerivatives( i, arg_ders[i] );
}
return r;
}
double DotProductDistance::calculateArgumentDistance( const std::vector<Value*> & vals, const std::vector<double>& arg,
ReferenceValuePack& myder, const bool& squared ) const {
double dot=0.0;
for (unsigned long i=0; i<vals.size(); ++i) dot+=getReferenceArgument(i)*arg[i];
for (unsigned long i=0; i<vals.size(); ++i) myder.setArgumentDerivatives( i, -getReferenceArgument(i)/dot );
return -log(dot);
}
double ReferenceArguments::projectArgDisplacementOnVector( const std::vector<double>& eigv, const std::vector<Value*>& vals, const std::vector<double>& arg, ReferenceValuePack& mypack ) const {
if( hasmetric ) {
plumed_error();
} else {
double proj=0;
for(unsigned j=0; j<reference_args.size(); ++j) {
unsigned jk=arg_der_index[j];
proj += eigv[j]*sqrtweight[j]*vals[jk]->difference( reference_args[j], arg[jk] );
mypack.setArgumentDerivatives( jk, eigv[j]*sqrtweight[j] );
}
return proj;
}
}