| Action(const ActionOptions &) | PLMD::Action | explicit |
| Action(const Action &a)=delete | PLMD::Action | private |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| actionIsBridged | PLMD::vesselbase::ActionWithVessel | private |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
| activate() | PLMD::Action | virtual |
| active | PLMD::Action | private |
| addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
| addColvar(const std::vector< unsigned > &newatoms) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addTaskToList(const unsigned &taskCode) | PLMD::vesselbase::ActionWithVessel | protected |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| addVessel(const std::string &name, const std::string &input, const int numlab=0) | PLMD::vesselbase::ActionWithVessel | protected |
| addVessel(std::unique_ptr< Vessel > vv) | PLMD::vesselbase::ActionWithVessel | protected |
| after | PLMD::Action | private |
| align_atom_1 | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| align_atom_2 | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| align_strands | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| alignType | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| all_atoms | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| apply() override | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| buffer | PLMD::vesselbase::ActionWithVessel | private |
| buildDataStashes(ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
| calculate() override | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) | PLMD::vesselbase::ActionWithVessel | protected |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionAtomistic | virtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| charges | PLMD::ActionAtomistic | private |
| chargesWereSet | PLMD::ActionAtomistic | private |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
| checkRead() | PLMD::Action | |
| checkUpdate() const | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearDependencies() | PLMD::Action | |
| clearDerivatives() | PLMD::ActionWithValue | virtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| colvar_atoms | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| comm | PLMD::Action | |
| componentIsNotPeriodic(const std::string &name) | PLMD::ActionWithValue | |
| componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| componentsAreNotOptional(Keywords &keys) | PLMD::ActionWithValue | static |
| contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | protected |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| deactivate() | PLMD::Action | inlinevirtual |
| deactivateAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| Dependencies typedef | PLMD::Action | |
| der_list | PLMD::vesselbase::ActionWithVessel | private |
| derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
| dertime | PLMD::vesselbase::ActionWithVessel | protected |
| dertime_can_be_off | PLMD::vesselbase::ActionWithVessel | private |
| doCheckPoint | PLMD::Action | private |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| donotforce | PLMD::ActionAtomistic | private |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| donotretrieve | PLMD::ActionAtomistic | private |
| energy | PLMD::ActionAtomistic | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| extraCV | PLMD::ActionAtomistic | private |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forceOnEnergy | PLMD::ActionAtomistic | private |
| forceOnExtraCV | PLMD::ActionAtomistic | private |
| forces | PLMD::ActionAtomistic | private |
| forcesToApply | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| fullTaskList | PLMD::vesselbase::ActionWithVessel | private |
| functions | PLMD::vesselbase::ActionWithVessel | private |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getAtomIndex(const unsigned ¤t, const unsigned &iatom) const | PLMD::secondarystructure::SecondaryStructureRMSD | inlineprivate |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
| getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
| getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| getNumberOfFunctionsInAction() | PLMD::secondarystructure::SecondaryStructureRMSD | inline |
| getNumberOfQuantities() const override | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inline |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | protected |
| getPntrToVessel(const unsigned &i) | PLMD::vesselbase::ActionWithVessel | inline |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositionInCurrentTaskList(const unsigned &myind) const | PLMD::vesselbase::ActionWithVessel | inline |
| getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getRestart() const | PLMD::Action | inline |
| getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
| getStep() const | PLMD::Action | |
| getTaskCode(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getUniqueLocal() const | PLMD::ActionAtomistic | inline |
| getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
| indexes | PLMD::ActionAtomistic | private |
| indexOfTaskInFullList | PLMD::vesselbase::ActionWithVessel | private |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() override | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| keywords | PLMD::Action | |
| label | PLMD::Action | private |
| line | PLMD::Action | private |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | |
| lockRequestAtoms | PLMD::ActionAtomistic | private |
| lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| lowmem | PLMD::vesselbase::ActionWithVessel | private |
| makeWhole() | PLMD::ActionAtomistic | |
| masses | PLMD::ActionAtomistic | private |
| maxderivatives | PLMD::vesselbase::ActionWithVessel | private |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
| modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| mydata | PLMD::vesselbase::ActionWithVessel | protected |
| nactive_tasks | PLMD::vesselbase::ActionWithVessel | private |
| name | PLMD::Action | private |
| needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
| nl_tolerance | PLMD::vesselbase::ActionWithVessel | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| PLMD::noderiv | PLMD::ActionWithValue | private |
| nopbc | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| normalizeVector(std::vector< double > &vals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| normalizeVectorDerivatives(MultiValue &myvals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| numericalDerivatives | PLMD::ActionWithValue | private |
| operator=(const Action &a)=delete | PLMD::Action | private |
| options | PLMD::Action | private |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseAtomList(const std::string &key, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| parseFlag(const std::string &key, bool &t) | PLMD::Action | |
| parseNumbered(const std::string &key, const int no, T &t) | PLMD::Action | |
| parseNumberedVector(const std::string &key, const int no, std::vector< T > &t) | PLMD::Action | |
| parseVector(const std::string &key, std::vector< T > &t) | PLMD::Action | |
| partialTaskList | PLMD::vesselbase::ActionWithVessel | private |
| pbc | PLMD::ActionAtomistic | private |
| pbc_fwd | PLMD::ActionAtomistic | private |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| performTask(const unsigned &, const unsigned &, MultiValue &) const override | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| plumed | PLMD::Action | |
| positions | PLMD::ActionAtomistic | private |
| prepare() | PLMD::Action | virtual |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| readBackboneAtoms(const std::string &backnames, std::vector< unsigned > &chain_lengths) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| references | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| registerKeywords(Keywords &keys) | PLMD::secondarystructure::SecondaryStructureRMSD | static |
| replica_index | PLMD::Action | private |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| restart | PLMD::Action | private |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| s_cutoff2 | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| SecondaryStructureRMSD(const ActionOptions &) | PLMD::secondarystructure::SecondaryStructureRMSD | explicit |
| serial | PLMD::vesselbase::ActionWithVessel | private |
| serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setAtomsFromStrands(const unsigned &atom1, const unsigned &atom2) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setSecondaryStructure(std::vector< Vector > &structure, double bondlength, double units) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| stopwatch | PLMD::vesselbase::ActionWithVessel | private |
| stopwatch_fwd | PLMD::vesselbase::ActionWithVessel | private |
| taskFlags | PLMD::vesselbase::ActionWithVessel | protected |
| taskIsCurrentlyActive(const unsigned &index) const | PLMD::vesselbase::ActionWithVessel | |
| threadSafe() const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| timers | PLMD::vesselbase::ActionWithVessel | private |
| tmpforces | PLMD::vesselbase::ActionWithVessel | private |
| tolerance | PLMD::vesselbase::ActionWithVessel | private |
| transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
| turnOnDerivatives() override | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| unique | PLMD::ActionAtomistic | private |
| unique_local | PLMD::ActionAtomistic | private |
| unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| update_from | PLMD::Action | private |
| update_until | PLMD::Action | private |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| values | PLMD::ActionWithValue | private |
| verbose_output | PLMD::secondarystructure::SecondaryStructureRMSD | private |
| virial | PLMD::ActionAtomistic | private |
| warning(const std::string &msg) | PLMD::Action | |
| weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
| weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
| ~SecondaryStructureRMSD() | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
1.8.17