void Mapping::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned cur = getCurrentTask(), frameno=ider*getNumberOfReferencePoints() + cur;
for(unsigned i=0;i<getNumberOfArguments();++i){
accumulateDerivative( i, df*dfframes[frameno]*mymap->getArgumentDerivative(cur,i) );
}
if( getNumberOfAtoms()>0 ){
Vector ader; Tensor tmpvir; tmpvir.zero();
unsigned n=getNumberOfArguments();
for(unsigned i=0;i<getNumberOfAtoms();++i){
ader=mymap->getAtomDerivatives( cur, i );
accumulateDerivative( n, df*dfframes[frameno]*ader[0] ); n++;
accumulateDerivative( n, df*dfframes[frameno]*ader[1] ); n++;
accumulateDerivative( n, df*dfframes[frameno]*ader[2] ); n++;
tmpvir += -1.0*Tensor( getPosition(i), ader );
}
Tensor vir;
if( !mymap->getVirial( cur, vir ) ) vir=tmpvir;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,2) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,2) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,2) );
}
}
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();
}
}
PathBase::PathBase(const ActionOptions& ao):
Action(ao),
Mapping(ao)
{
bool noz; parseFlag("NOZPATH",noz);
parse("LAMBDA",lambda);
// Create the list of tasks
for(unsigned i=0;i<getNumberOfReferencePoints();++i) addTaskToList( i );
std::string empty="LABEL=zpath";
if(!noz) addVessel("ZPATH",empty,0);
}
void Mapping::prepare(){
if( mymap->mappingNeedsSetup() ){
// Get the arguments and atoms that are required
std::vector<AtomNumber> atoms; std::vector<std::string> args;
mymap->getAtomAndArgumentRequirements( atoms, args );
requestAtoms( atoms ); std::vector<Value*> req_args;
interpretArgumentList( args, req_args ); requestArguments( req_args );
// Duplicate all frames (duplicates are used by sketch-map)
mymap->duplicateFrameList();
// Get the number of frames in the path
unsigned nfram=getNumberOfReferencePoints();
fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
plumed_assert( !mymap->mappingNeedsSetup() );
// Resize all derivative arrays
mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
// Resize forces array
forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
}
}
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<ReferenceConfiguration*>& myconfs=getAllReferenceConfigurations();
for(unsigned i=0; i<myconfs.size(); ++i) myconfs[i]->print( pathfile, ofmt, atoms.getUnits().getLength()/0.1 );
pathfile.flush();
}
}