void IntramolecularDRMSD::setup_targets(){
plumed_massert( bounds_were_set, "I am missing a call to DRMSD::setBoundsOnDistances");
for(unsigned i=0;i<nblocks;++i){
for(unsigned iatom=blocks[i]+1;iatom<blocks[i+1];++iatom){
for(unsigned jatom=blocks[i];jatom<iatom;++jatom){
double distance = delta( getReferencePosition(iatom), getReferencePosition(jatom) ).modulo();
if(distance < upper && distance > lower ) targets[std::make_pair(iatom,jatom)] = distance;
}
}
}
}
void DRMSD::setup_targets(){
plumed_massert( bounds_were_set, "I am missing a call to DRMSD::setBoundsOnDistances");
unsigned natoms = getNumberOfReferencePositions();
for(unsigned i=0;i<natoms-1;++i){
for(unsigned j=i+1;j<natoms;++j){
double distance = delta( getReferencePosition(i), getReferencePosition(j) ).modulo();
if(distance < upper && distance > lower ){
targets[std::make_pair(i,j)] = distance;
}
}
}
if( targets.empty() ) error("drmsd will compare no distances - check upper and lower bounds are sensible");
}
double Direction::calc( const std::vector<Vector>& pos, const Pbc& pbc, const std::vector<Value*>& vals, const std::vector<double>& args,
ReferenceValuePack& myder, const bool& squared ) const {
plumed_assert( squared );
for(unsigned i=0;i<getNumberOfReferenceArguments();++i) myder.addArgumentDerivatives( i, -2.*getReferenceArgument(i) );
for(unsigned i=0;i<getNumberOfAtoms();++i) myder.getAtomsDisplacementVector()[i]=getReferencePosition(i);
return 0.0;
}
//
// returns true if the given point lies within the volume of this element
//
bool Tetra4::encloses( const math::Vec3f &globalPosition )
{
// first transform position into reference space
math::Vec3f referencePosition = getReferencePosition(globalPosition);
// now check wether the coordinates are in valid ranges
if( (referencePosition.x >= 0.0f) && (referencePosition.x <= 1.0f)&&
(referencePosition.y >= 0.0f) && (referencePosition.y <= 1.0f)&&
(referencePosition.z >= 0.0f) && (referencePosition.z <= 1.0f - referencePosition.x - referencePosition.y))
return true;
return false;
}
//
// computes the shape function for the given global-space
// coordinate (must be within element boundaries!)
// linear shape function
//
float Tetra4::computeShapeFunction( size_t node, const math::Vec3f &globalPosition )
{
// first transform position into reference space
math::Vec3f referencePosition = getReferencePosition(globalPosition);
// depending on the index of the node (topologic relation) we evaluate
// the form function which is defined from the shape of a tehadron
if( node == 0 )
return 1.0f - referencePosition[0] - referencePosition[1] - referencePosition[2];
if( node == 1 )
return referencePosition[0];
if( node == 2 )
return referencePosition[1];
if( node == 3 )
return referencePosition[2];
return 0.0f;
}
double OptimalRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
double d;
if( myder.calcUsingPCAOption() ) {
std::vector<Vector> centeredreference( getNumberOfAtoms () );
d=myrmsd.calc_PCAelements(pos,myder.getAtomVector(),myder.rot[0],myder.DRotDPos,myder.getAtomsDisplacementVector(),myder.centeredpos,centeredreference,squared);
unsigned nat = pos.size();
for(unsigned i=0; i<nat; ++i) { myder.getAtomsDisplacementVector()[i] -= getReferencePosition(i); myder.getAtomsDisplacementVector()[i] *= getDisplace()[i]; }
} else if( fast ) {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<false,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<false,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
} else {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<true,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<true,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
}
myder.clear(); for(unsigned i=0; i<pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
if( !myder.updateComplete() ) myder.updateDynamicLists();
return d;
}
void Direction::extractAtomicDisplacement( const std::vector<Vector>& pos, const bool& anflag, std::vector<Vector>& dirout ) const {
for(unsigned i=0; i<getNumberOfAtoms(); ++i) dirout[i]=getReferencePosition(i);
}
void OptimalRMSD::extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const {
std::vector<Tensor> rot(1); Matrix<std::vector<Vector> > DRotDPos( 3, 3 );
std::vector<Vector> centeredreference( getNumberOfAtoms() ), centeredpos( getNumberOfAtoms() ), avector( getNumberOfAtoms() );
double d=myrmsd.calc_PCAelements(pos,avector,rot[0],DRotDPos,direction,centeredpos,centeredreference,true);
unsigned nat = pos.size(); for(unsigned i=0; i<nat; ++i) direction[i] = getDisplace()[i]*( direction[i] - getReferencePosition(i) );
}
