double MultiColvarBase::getCentralAtomDerivative( const unsigned& iatom, const unsigned& jcomp, const Vector& df ){
plumed_dbg_assert( atomsWithCatomDer.isActive(iatom) && jcomp<3 );
unsigned nder = 3*getNumberOfAtoms() + 9;
return df[0]*getElementDerivative( (getCentralAtomElementIndex()+0)*nder + 3*iatom + jcomp ) +
df[1]*getElementDerivative( (getCentralAtomElementIndex()+1)*nder + 3*iatom + jcomp ) +
df[2]*getElementDerivative( (getCentralAtomElementIndex()+2)*nder + 3*iatom + jcomp );
}
void MultiColvarBase::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned vstart=getNumberOfDerivatives()*ider;
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=3*atoms_with_derivatives[i];
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) );
}
unsigned nvir=3*getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
}
void MultiColvarBase::copyElementsToBridgedColvar( BridgedMultiColvarFunction* func ){
func->setElementValue( 0, getElementValue(0) );
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned n=atoms_with_derivatives[i], nx=3*n;
func->atoms_with_derivatives.activate(n);
func->addElementDerivative( nx+0, getElementDerivative(nx+0) );
func->addElementDerivative( nx+1, getElementDerivative(nx+1) );
func->addElementDerivative( nx+2, getElementDerivative(nx+2) );
}
unsigned nvir=3*getNumberOfAtoms();
for(unsigned i=0;i<9;++i){
func->addElementDerivative( nvir, getElementDerivative(nvir) ); nvir++;
}
}
double OrientationSphere::compute(){
// Make sure derivatives for central atom are only calculated once
VectorMultiColvar* vv = dynamic_cast<VectorMultiColvar*>( getBaseMultiColvar(0) );
vv->firstcall=true;
weightHasDerivatives=true; // The weight has no derivatives really
double sw, value=0, denom=0, dot, f_dot, dot_df, dfunc; Vector distance;
getVectorForBaseTask(0, catom_orient );
for(unsigned i=1;i<getNAtoms();++i){
distance=getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(i) );
sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
if( sw>=getTolerance() ){
getVectorForBaseTask( i, this_orient );
// Calculate the dot product wrt to this position
dot=0; for(unsigned k=0;k<catom_orient.size();++k) dot+=catom_orient[k]*this_orient[k];
f_dot = transformDotProduct( dot, dot_df );
// N.B. We are assuming here that the imaginary part of the dot product is zero
for(unsigned k=0;k<catom_orient.size();++k){
this_orient[k]*=sw*dot_df; catom_der[k]=sw*dot_df*catom_orient[k];
}
// Set the derivatives wrt of the numerator
addOrientationDerivatives( 0, this_orient );
addOrientationDerivatives( i, catom_der );
addCentralAtomsDerivatives( 0, 0, f_dot*(-dfunc)*distance );
addCentralAtomsDerivatives( i, 0, f_dot*(dfunc)*distance );
addBoxDerivatives( f_dot*(-dfunc)*Tensor(distance,distance) );
value += sw*f_dot;
// Set the derivatives wrt to the numerator
addCentralAtomsDerivatives( 0, 1, (-dfunc)*distance );
addCentralAtomsDerivatives( i, 1, (dfunc)*distance );
addBoxDerivativesOfWeight( (-dfunc)*Tensor(distance,distance) );
denom += sw;
}
}
// Now divide everything
unsigned nder = getNumberOfDerivatives();
for(unsigned i=0;i<nder;++i){
setElementDerivative( i, getElementDerivative(i)/denom - (value*getElementDerivative(nder+i))/(denom*denom) );
setElementDerivative( nder + i, 0.0 );
}
weightHasDerivatives=false; // Weight has no derivatives we just use the holder for weight to store some stuff
return value / denom;
}
void MultiColvarBase::quotientRule( const unsigned& uder, const unsigned& vder, const unsigned& iout ){
unsigned ustart=uder*getNumberOfDerivatives();
unsigned vstart=vder*getNumberOfDerivatives();
unsigned istart=iout*getNumberOfDerivatives();
double weight = getElementValue( vder ), pref = getElementValue( uder ) / (weight*weight);
if( !doNotCalculateDerivatives() ){
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned n=3*atoms_with_derivatives[i], nx=n, ny=n+1, nz=n+2;
setElementDerivative( istart + nx, getElementDerivative(ustart+nx) / weight - pref*getElementDerivative(vstart+nx) );
setElementDerivative( istart + ny, getElementDerivative(ustart+ny) / weight - pref*getElementDerivative(vstart+ny) );
setElementDerivative( istart + nz, getElementDerivative(ustart+nz) / weight - pref*getElementDerivative(vstart+nz) );
}
unsigned vbase=3*getNumberOfAtoms();
for(unsigned i=0;i<9;++i){
setElementDerivative( istart + vbase + i, getElementDerivative(ustart+vbase+i) / weight - pref*getElementDerivative(vstart+vbase+i) );
}
}
thisval_wasset[iout]=false; setElementValue( iout, getElementValue(uder) / weight );
}
void BridgedMultiColvarFunction::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned vstart=getNumberOfDerivatives()*ider;
// Merge atom derivatives
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=3*atoms_with_derivatives[i];
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) );
}
// Merge virial derivatives
unsigned nvir=3*mycolv->getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
// Merge local atom derivatives
for(unsigned j=0;j<getNumberOfAtoms();++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
plumed_dbg_assert( nvir==getNumberOfDerivatives() );
}