CatomPack MultiColvarBase::getCentralAtomPack( const unsigned& basn, const unsigned& taskIndex ){
unsigned curr=getTaskCode( taskIndex );
CatomPack mypack;
if(usespecies){
mypack.resize(1);
mypack.setIndex( 0, basn + curr );
mypack.setDerivative( 0, Tensor::identity() );
} else if( ablocks.size()<4 ){
mypack.resize(ablocks.size());
unsigned k=0;
std::vector<unsigned> atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ){
mypack.setIndex( k, basn + atoms[i] );
mypack.setDerivative( k, numberForCentralAtom*Tensor::identity() );
k++;
}
}
} else {
unsigned k=0;
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ){
mypack.setIndex( k, basn + ablocks[i][curr] );
mypack.setDerivative( k, numberForCentralAtom*Tensor::identity() );
k++;
}
}
}
return mypack;
}
void AtomValuePack::addComDerivatives( const int& ind, const Vector& der, CatomPack& catom_der ){
if( ind<0 ){
for(unsigned ider=0;ider<catom_der.getNumberOfAtomsWithDerivatives();++ider){
unsigned jder=3*catom_der.getIndex(ider);
myvals.addTemporyDerivative( jder+0, catom_der.getDerivative(ider,0,der) );
myvals.addTemporyDerivative( jder+1, catom_der.getDerivative(ider,1,der) );
myvals.addTemporyDerivative( jder+2, catom_der.getDerivative(ider,2,der) );
}
} else {
for(unsigned ider=0;ider<catom_der.getNumberOfAtomsWithDerivatives();++ider){
unsigned jder=3*catom_der.getIndex(ider);
myvals.addDerivative( ind, jder+0, catom_der.getDerivative(ider,0,der) );
myvals.addDerivative( ind, jder+1, catom_der.getDerivative(ider,1,der) );
myvals.addDerivative( ind, jder+2, catom_der.getDerivative(ider,2,der) );
}
}
}
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] );
}
}
}
}
