51   mymap=dynamic_cast<Mapping*>( getAction() );  in TrigonometricPathVessel()
52   plumed_massert( mymap, "Trigonometric path vessel can only be used with mappings");  in TrigonometricPathVessel()
54 …if( mymap->getNumberOfProperties()!=1 ) error("cannot use trigonometric paths when there are multi…  in TrigonometricPathVessel()
56   for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {  in TrigonometricPathVessel()
57 …if( mymap->getTaskCode(i)!=mymap->getPositionInFullTaskList(i) ) error("mismatched tasks and codes…  in TrigonometricPathVessel()
59   mymap->addComponentWithDerivatives("gspath"); mymap->componentIsNotPeriodic("gspath");  in TrigonometricPathVessel()
60 …sp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); sp->resizeDerivatives( mymap->getNumberO…  in TrigonometricPathVessel()
61   mymap->addComponentWithDerivatives("gzpath"); mymap->componentIsNotPeriodic("gzpath");  in TrigonometricPathVessel()
62 …zp=mymap->copyOutput( mymap->getNumberOfComponents()-1 ); zp->resizeDerivatives( mymap->getNumberO…  in TrigonometricPathVessel()
65   ReferenceConfiguration* ref0=mymap->getReferenceConfiguration(0);  in TrigonometricPathVessel()
66   for(unsigned i=0; i<mymap->getFullNumberOfTasks(); ++i) {  in TrigonometricPathVessel()
67 …if( !(mymap->getReferenceConfiguration(i))->pcaIsEnabledForThisReference() ) error("pca must be im…  in TrigonometricPathVessel()
68 …if( ref0->getName()!=(mymap->getReferenceConfiguration(i))->getName() ) error("cannot use mixed me…  in TrigonometricPathVessel()
69 …if( mymap->getNumberOfAtoms()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferencePosition…  in TrigonometricPathVessel()
70 …if( mymap->getNumberOfArguments()!=(mymap->getReferenceConfiguration(i))->getNumberOfReferenceArgu…  in TrigonometricPathVessel()
73 …cargs.resize( mymap->getNumberOfArguments() ); std::vector<std::string> argument_names( mymap->get…  in TrigonometricPathVessel()
74 …for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) argument_names[i] = (mymap->getPntrToArgum…  in TrigonometricPathVessel()
75 …PDB mypdb; mypdb.setAtomNumbers( mymap->getAbsoluteIndexes() ); mypdb.addBlockEnd( mymap->getAbsol…  in TrigonometricPathVessel()
78 …mypack1.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage(…  in TrigonometricPathVessel()
79 …mypack2.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() ); ref0->setupPCAStorage(…  in TrigonometricPathVessel()
80   mypack3.resize( mymap->getNumberOfArguments(), mymap->getNumberOfAtoms() );  in TrigonometricPathVessel()
81 …for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) { mypack1.setAtomIndex(i,i); mypack2.setAtomIn…  in TrigonometricPathVessel()
82 …mypack1_stashd_atoms.resize( mymap->getNumberOfAtoms() ); mypack1_stashd_args.resize( mymap->getNu…  in TrigonometricPathVessel()
101   for(unsigned i=0; i<cargs.size(); ++i) cargs[i]=mymap->getArgument(i);  in finish()
104   double lambda=mymap->getLambda();  in finish()
135 …double v1v1 = (mymap->getReferenceConfiguration( iclose1 ))->calculate( mymap->getPositions(), mym…  in finish()
136 …double v3v3 = (mymap->getReferenceConfiguration( iclose2 ))->calculate( mymap->getPositions(), mym…  in finish()
137   if( iclose3<0 || iclose3>=mymap->getFullNumberOfTasks() ) {  in finish()
138     ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose1 );  in finish()
139 …v2v2=(mymap->getReferenceConfiguration( iclose2 ))->calc( conf2->getReferencePositions(), mymap->g…  in finish()
141 …(mymap->getReferenceConfiguration( iclose2 ))->extractDisplacementVector( conf2->getReferencePosit…  in finish()
144     ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose3 );  in finish()
145 …v2v2=(mymap->getReferenceConfiguration( iclose1 ))->calc( conf2->getReferencePositions(), mymap->g…  in finish()
147 …(mymap->getReferenceConfiguration( iclose1 ))->extractDisplacementVector( conf2->getReferencePosit…  in finish()
152 …for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) mypack1_stashd_args[i]=mypack1.getArgument…  in finish()
153   if( mymap->getNumberOfAtoms()>0 ) {  in finish()
154 … ReferenceAtoms* at = dynamic_cast<ReferenceAtoms*>( mymap->getReferenceConfiguration( iclose1 ) );  in finish()
156     for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {  in finish()
161 …double v1v2 = (mymap->getReferenceConfiguration(iclose1))->projectDisplacementOnVector( projdir, m…  in finish()
164 …double spacing = mymap->getPropertyValue( iclose1, (mymap->property.begin())->first ) - mymap->get…  in finish()
167 …double path_s = mymap->getPropertyValue(iclose1, (mymap->property.begin())->first ) + spacing * dx…  in finish()
170   for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) {  in finish()
175   unsigned narg=mymap->getNumberOfArguments(); Tensor vir; vir.zero(); fact = 0.5*spacing / v2v2;  in finish()
176   if( mymap->getNumberOfAtoms()>0 ) {  in finish()
177     for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {  in finish()
180       vir-=Tensor( mymap->getPosition(i), ader );  in finish()
183     unsigned nbase=narg+3*mymap->getNumberOfAtoms();  in finish()
187   ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose1 );  in finish()
188 …double v4v4=(mymap->getReferenceConfiguration( iclose2 ))->calc( conf2->getReferencePositions(), m…  in finish()
191 …(mymap->getReferenceConfiguration( iclose2 ))->extractDisplacementVector( conf2->getReferencePosit…  in finish()
194 …double proj = (mymap->getReferenceConfiguration(iclose1))->projectDisplacementOnVector( projdir, m…  in finish()
198 …for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) zp->setDerivative( i, (mypack1_stashd_args…  in finish()
200   if( mymap->getNumberOfAtoms()>0 ) {  in finish()
201     for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {  in finish()
205       vir-=Tensor( mymap->getPosition(i), ader );  in finish()
208     unsigned nbase=narg+3*mymap->getNumberOfAtoms();  in finish()