void MultiColvarFilter::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
invals.copyValues( outvals );
if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
// Retrive the value of the multicolvar and apply filter
double val=invals.get(1), df, weight=applyFilter( val, df );
// Now propegate derivatives
if( !getPntrToMultiColvar()->weightHasDerivatives ){
outvals.setValue( 0, weight );
if( derivativesAreRequired() ){
for(unsigned i=0;i<invals.getNumberActive();++i){
unsigned jder=invals.getActiveIndex(i);
outvals.addDerivative( 0, jder, df*invals.getDerivative(1, jder ) );
}
}
} else {
double ww=outvals.get(0); outvals.setValue( 0, ww*weight );
if( derivativesAreRequired() ){
for(unsigned i=0;i<outvals.getNumberActive();++i){
unsigned ider=outvals.getActiveIndex(i);
outvals.setDerivative( 0, ider, weight*outvals.getDerivative(1,ider) + ww*df*outvals.getDerivative(0,ider) );
}
}
}
}
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 VolumeGradientBase::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
if( getPntrToMultiColvar()->isDensity() ) {
outvals.setValue(0, 1.0); outvals.setValue(1, 1.0);
} else {
// Copy derivatives of the colvar and the value of the colvar
invals.copyValues( outvals );
if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
}
calculateAllVolumes( curr, outvals );
}
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++;
}
}
}
void VolumeGradientBase::setNumberInVolume( const unsigned& ivol, const unsigned& curr, const double& weight,
const Vector& wdf, const Tensor& virial, const std::vector<Vector>& refders,
MultiValue& outvals ) const {
MultiColvarBase* mcolv=getPntrToMultiColvar();
if( !mcolv->weightHasDerivatives ) {
outvals.setValue(ivol, weight );
if( derivativesAreRequired() ) {
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, refders[i][0] );
outvals.addDerivative( ivol, iatom+1, refders[i][1] );
outvals.addDerivative( ivol, iatom+2, refders[i][2] );
}
}
} else if(ivol==0) {
double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
if( derivativesAreRequired() ) {
plumed_merror("This needs testing");
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, weight*outvals.getDerivative(ivol,jatom+0) + ww*catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, weight*outvals.getDerivative(ivol,jatom+1) + ww*catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, weight*outvals.getDerivative(ivol,jatom+2) + ww*catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
}
}
} else {
double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
if( derivativesAreRequired() ) {
plumed_merror("This needs testing");
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, ww*catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, ww*catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, ww*catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
}
}
}
}
