| activateIndices(ActionWithVessel *) | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
| AdjacencyMatrixVessel(const vesselbase::VesselOptions &) | PLMD::multicolvar::AdjacencyMatrixVessel | explicit |
| applyForce(std::vector< double > &) | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
| bufstart | PLMD::vesselbase::Vessel | protected |
| calculate(const unsigned ¤t, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const | PLMD::multicolvar::AdjacencyMatrixVessel | virtual |
| checkRead() | PLMD::vesselbase::Vessel | |
| comm | PLMD::vesselbase::Vessel | protected |
| completeSetup(const unsigned &, const unsigned &) | PLMD::vesselbase::StoreDataVessel | protected |
| description() | PLMD::vesselbase::StoreDataVessel | inlinevirtual |
| error(const std::string &errmsg) | PLMD::vesselbase::Vessel | protected |
| finish(const std::vector< double > &buffer) | PLMD::multicolvar::AdjacencyMatrixVessel | virtual |
| finished | PLMD::multicolvar::AdjacencyMatrixVessel | private |
| function | PLMD::multicolvar::AdjacencyMatrixVessel | private |
| getAction() const | PLMD::vesselbase::Vessel | inlineprotected |
| getAllInput() | PLMD::vesselbase::Vessel | protected |
| getLabel() const | PLMD::vesselbase::Vessel | |
| getLocalDerivative(const unsigned &ibuf) | PLMD::vesselbase::StoreDataVessel | protected |
| getName() const | PLMD::vesselbase::Vessel | |
| getNLTolerance() const | PLMD::vesselbase::Vessel | inlineprotected |
| getNumberOfComponents() const | PLMD::vesselbase::StoreDataVessel | inline |
| getNumberOfDerivatives(const unsigned &) | PLMD::vesselbase::StoreDataVessel | |
| getNumberOfDerivativeSpacesPerComponent() const | PLMD::vesselbase::StoreDataVessel | inlineprotected |
| getNumberOfStoredValues() const | PLMD::vesselbase::StoreDataVessel | inline |
| getNumericalLabel() const | PLMD::vesselbase::Vessel | inlineprotected |
| getSizeOfDerivativeList() const | PLMD::vesselbase::StoreDataVessel | inline |
| getTolerance() const | PLMD::vesselbase::Vessel | inlineprotected |
| hard_cut | PLMD::vesselbase::StoreDataVessel | protected |
| log | PLMD::vesselbase::Vessel | |
| parse(const std::string &key, T &t) | PLMD::vesselbase::Vessel | protected |
| parseFlag(const std::string &key, bool &t) | PLMD::vesselbase::Vessel | protected |
| parseVector(const std::string &key, std::vector< T > &t) | PLMD::vesselbase::Vessel | protected |
| prepare() | PLMD::multicolvar::AdjacencyMatrixVessel | virtual |
| registerKeywords(Keywords &keys) | PLMD::multicolvar::AdjacencyMatrixVessel | static |
| resize() | PLMD::vesselbase::StoreDataVessel | virtual |
| resizeBuffer(const unsigned &n) | PLMD::vesselbase::Vessel | inlineprotected |
| retrieveDerivatives(const unsigned &myelem, const bool &normed, MultiValue &myvals) | PLMD::vesselbase::StoreDataVessel | |
| retrieveValue(const unsigned &myelem, const bool &normed, std::vector< double > &values) const | PLMD::vesselbase::StoreDataVessel | |
| setActiveValsAndDerivatives(const std::vector< unsigned > &der_index) | PLMD::vesselbase::StoreDataVessel | |
| setBufferStart(unsigned &start) | PLMD::multicolvar::AdjacencyMatrixVessel | inlinevirtual |
| setFinishedTrue() | PLMD::multicolvar::AdjacencyMatrixVessel | |
| setHardCutoffOnWeight(const double &mytol) | PLMD::vesselbase::StoreDataVessel | |
| setLocalDerivative(const unsigned &ibuf, const double &val) | PLMD::vesselbase::StoreDataVessel | protected |
| StoreDataVessel(const VesselOptions &) | PLMD::vesselbase::StoreDataVessel | explicit |
| storeDerivatives(const unsigned &, MultiValue &myvals, std::vector< double > &, std::vector< unsigned > &) const | PLMD::vesselbase::StoreDataVessel | protected |
| storedValueIsActive(const unsigned &iatom) | PLMD::vesselbase::StoreDataVessel | inline |
| storeValues(const unsigned &, MultiValue &, std::vector< double > &) const | PLMD::vesselbase::StoreDataVessel | protected |
| transformDerivatives(const unsigned ¤t, MultiValue &myvals, MultiValue &bvals) | PLMD::vesselbase::Vessel | inlinevirtual |
| transformName(const std::string &name) | PLMD::vesselbase::Vessel | static |
| usingLowMem() | PLMD::vesselbase::StoreDataVessel | inlineprotected |
| VectorMultiColvar class | PLMD::multicolvar::AdjacencyMatrixVessel | friend |
| Vessel(const VesselOptions &da) | PLMD::vesselbase::Vessel | explicit |
| weightCutoffIsOn() const | PLMD::vesselbase::StoreDataVessel | |
| weightHasDerivatives() | PLMD::vesselbase::StoreDataVessel | inlineprotected |
| wtol | PLMD::vesselbase::StoreDataVessel | protected |
| ~Vessel() | PLMD::vesselbase::Vessel | inlinevirtual |
1.8.10
