void ManyRestraintsBase::applyChainRuleForDerivatives( const double& df ){
// Value (this could be optimized more -- GAT)
for(unsigned i=0;i<aves->getNumberOfDerivatives();++i){
setElementDerivative( i, df*aves->getElementDerivative(i) );
}
// And weights
unsigned nder=aves->getNumberOfDerivatives();
for(unsigned i=0;i<aves->getNumberOfDerivatives();++i){
setElementDerivative( nder+i, aves->getElementDerivative(nder+i) );
}
}
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 BridgedMultiColvarFunction::clearDerivativesAfterTask( const unsigned& ider ){
unsigned vstart=getNumberOfDerivatives()*ider;
if( derivativesAreRequired() ){
// Clear atom derivatives
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=vstart+3*atoms_with_derivatives[i];
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 );
}
// Clear virial contribution
unsigned nvir=vstart+3*mycolv->getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
setElementDerivative( nvir, 0.0 ); nvir++;
}
// Clear derivatives of local atoms
for(unsigned j=0;j<getNumberOfAtoms();++j){
setElementDerivative( nvir, 0.0 ); nvir++;
setElementDerivative( nvir, 0.0 ); nvir++;
setElementDerivative( nvir, 0.0 ); nvir++;
}
plumed_dbg_assert( (nvir-vstart)==getNumberOfDerivatives() );
}
// Clear values
thisval_wasset[ider]=false; setElementValue( ider, 0.0 ); thisval_wasset[ider]=false;
}
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 MultiColvarBase::clearDerivativesAfterTask( const unsigned& ider ){
unsigned vstart=getNumberOfDerivatives()*ider;
thisval_wasset[ider]=false; setElementValue( ider, 0.0 );
thisval_wasset[ider]=false;
if( ider>1 && ider<5 && derivativesAreRequired() ){
for(unsigned i=0;i<atomsWithCatomDer.getNumberActive();++i){
unsigned iatom=vstart+3*atomsWithCatomDer[i];
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 );
}
} else if( derivativesAreRequired() ) {
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=vstart+3*atoms_with_derivatives[i];
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 ); iatom++;
setElementDerivative( iatom, 0.0 );
}
unsigned nvir=vstart+3*getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
setElementDerivative( nvir, 0.0 ); nvir++;
}
}
}
