void AdaptivePath::update() {
double weight2 = -1.*mypathv->dx;
double weight1 = 1.0 + mypathv->dx;
if( weight1>1.0 ) {
weight1=1.0; weight2=0.0;
} else if( weight2>1.0 ) {
weight1=0.0; weight2=1.0;
}
// Add projections to dispalcement accumulators
ReferenceConfiguration* myref = getReferenceConfiguration( mypathv->iclose1 );
myref->extractDisplacementVector( getPositions(), getArguments(), mypathv->cargs, false, displacement );
getReferenceConfiguration( mypathv->iclose2 )->extractDisplacementVector( myref->getReferencePositions(), getArguments(), myref->getReferenceArguments(), false, displacement2 );
displacement.addDirection( -mypathv->dx, displacement2 );
pdisplacements[mypathv->iclose1].addDirection( weight1, displacement );
pdisplacements[mypathv->iclose2].addDirection( weight2, displacement );
// Update weight accumulators
wsum[mypathv->iclose1] *= fadefact;
wsum[mypathv->iclose2] *= fadefact;
wsum[mypathv->iclose1] += weight1;
wsum[mypathv->iclose2] += weight2;
// This does the update of the path if it is time to
if( (getStep()>0) && (getStep()%update_str==0) ) {
wsum[fixedn[0]]=wsum[fixedn[1]]=0.;
for(unsigned inode=0; inode<getNumberOfReferencePoints(); ++inode) {
if( wsum[inode]>0 ) {
// First displace the node by the weighted direction
getReferenceConfiguration( inode )->displaceReferenceConfiguration( 1./wsum[inode], pdisplacements[inode] );
// Reset the displacement
pdisplacements[inode].zeroDirection();
}
}
// Now ensure all the nodes of the path are equally spaced
PathReparameterization myspacings( getPbc(), getArguments(), getAllReferenceConfigurations() );
myspacings.reparameterize( fixedn[0], fixedn[1], tolerance );
}
if( (getStep()>0) && (getStep()%wstride==0) ) {
pathfile.printf("# PATH AT STEP %d TIME %f \n", getStep(), getTime() );
std::vector<std::unique_ptr<ReferenceConfiguration>>& myconfs=getAllReferenceConfigurations();
std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
if( moldat.size()>1 ) error("you should only have one MOLINFO action in your input file");
SetupMolInfo* mymoldat=NULL; if( moldat.size()==1 ) mymoldat=moldat[0];
std::vector<std::string> argument_names( getNumberOfArguments() );
for(unsigned i=0; i<getNumberOfArguments(); ++i) argument_names[i] = getPntrToArgument(i)->getName();
PDB mypdb; mypdb.setArgumentNames( argument_names );
for(unsigned i=0; i<myconfs.size(); ++i) {
pathfile.printf("REMARK TYPE=%s\n", myconfs[i]->getName().c_str() );
mypdb.setAtomPositions( myconfs[i]->getReferencePositions() );
for(unsigned j=0; j<getNumberOfArguments(); ++j) mypdb.setArgumentValue( getPntrToArgument(j)->getName(), myconfs[i]->getReferenceArgument(j) );
mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, pathfile, ofmt );
}
pathfile.flush();
}
}
TrigonometricPathVessel::TrigonometricPathVessel( const vesselbase::VesselOptions& da ):
StoreDataVessel(da),
projdir(ReferenceConfigurationOptions("DIRECTION")),
mydpack1( 1, getAction()->getNumberOfDerivatives() ),
mydpack2( 1, getAction()->getNumberOfDerivatives() ),
mydpack3( 1, getAction()->getNumberOfDerivatives() ),
mypack1( 0, 0, mydpack1 ),
mypack2( 0, 0, mydpack2 ),
mypack3( 0, 0, mydpack3 )
{
mymap=dynamic_cast<Mapping*>( getAction() );
plumed_massert( mymap, "Trigonometric path vessel can only be used with mappings");
// Retrieve the index of the property in the underlying mapping
if( mymap->getNumberOfProperties()!=1 ) error("cannot use trigonometric paths when there are multiple properties");
for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {
if( mymap->getTaskCode(i)!=mymap->getPositionInFullTaskList(i) ) error("mismatched tasks and codes");
}
mymap->addComponentWithDerivatives("gspath"); mymap->componentIsNotPeriodic("gspath");
sp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); sp->resizeDerivatives( mymap->getNumberOfDerivatives() );
mymap->addComponentWithDerivatives("gzpath"); mymap->componentIsNotPeriodic("gzpath");
zp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); zp->resizeDerivatives( mymap->getNumberOfDerivatives() );
// Check we have PCA
ReferenceConfiguration* ref0=mymap->getReferenceConfiguration(0);
for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {
if( !(mymap->getReferenceConfiguration(i))->pcaIsEnabledForThisReference() ) error("pca must be implemented in order to use trigometric path");
if( ref0->getName()!=(mymap->getReferenceConfiguration(i))->getName() ) error("cannot use mixed metrics");
if( mymap->getNumberOfAtoms()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferencePositions() ) error("all frames must use the same set of atoms");
if( mymap->getNumberOfArguments()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferenceArguments() ) error("all frames must use the same set of arguments");
}
cargs.resize( mymap->getNumberOfArguments() ); std::vector<std::string> argument_names( mymap->getNumberOfArguments() );
for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) argument_names[i] = (mymap->getPntrToArgument(i))->getName();
PDB mypdb; mypdb.setAtomNumbers( mymap->getAbsoluteIndexes() ); mypdb.addBlockEnd( mymap->getAbsoluteIndexes().size() );
if( argument_names.size()>0 ) mypdb.setArgumentNames( argument_names );
projdir.read( mypdb );
mypack1.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage( mypack1 );
mypack2.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage( mypack2 );
mypack3.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() );
for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) { mypack1.setAtomIndex(i,i); mypack2.setAtomIndex(i,i); mypack3.setAtomIndex(i,i); }
mypack1_stashd_atoms.resize( mymap->getNumberOfAtoms() ); mypack1_stashd_args.resize( mymap->getNumberOfArguments() );
}