| accumulateDerivative(const unsigned &ider, const double &df) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| Action(const ActionOptions &) | PLMD::Action | |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | |
| ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | |
| activate() | PLMD::Action | virtual |
| activateIndexes(const unsigned &, const unsigned &, const std::vector< unsigned > &) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| activateTheseTasks(std::vector< bool > &addtionalTasks) | PLMD::vesselbase::ActionWithVessel | |
| addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addElementDerivative(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| addElementValue(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
| 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(Vessel *vv) | PLMD::vesselbase::ActionWithVessel | protected |
| apply() | PLMD::mapping::Mapping | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| buildDataStashes() | PLMD::vesselbase::ActionWithVessel | virtual |
| calculate() | PLMD::mapping::PathBase | virtual |
| calculateAllVessels() | PLMD::vesselbase::ActionWithVessel | protected |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateDistanceFunction(const unsigned &ifunc, const bool &squared) | PLMD::mapping::Mapping | protected |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::mapping::Mapping | virtual |
| chainRuleForElementDerivatives(const unsigned &, const unsigned &, const double &, Vessel *) | PLMD::vesselbase::ActionWithVessel | |
| chainRuleForElementDerivatives(const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *) | PLMD::vesselbase::ActionWithVessel | |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::checkNumericalDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| checkRead() | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearAfterTask() | PLMD::vesselbase::ActionWithVessel | protected |
| clearDependencies() | PLMD::Action | |
| clearDerivatives() | PLMD::ActionWithValue | virtual |
| clearDerivativesAfterTask(const unsigned &) | PLMD::vesselbase::ActionWithVessel | virtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| 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 |
| deactivate_task() | PLMD::vesselbase::ActionWithVessel | virtual |
| deactivateAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| deactivateTasksInRange(const unsigned &lower, const unsigned &upper) | PLMD::vesselbase::ActionWithVessel | protected |
| Dependencies typedef | PLMD::Action | |
| derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inline |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| fframes | PLMD::mapping::Mapping | protected |
| files | PLMD::Action | |
| files_iterator typedef | PLMD::Action | |
| finishComputations() | PLMD::vesselbase::ActionWithVessel | virtual |
| finishTaskListUpdate() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inline |
| getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArgumentName(unsigned &iarg) | PLMD::mapping::Mapping | |
| getArguments() | PLMD::ActionWithArguments | inline |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCurrentHighDimFunctionValue(const unsigned &ider) const | PLMD::mapping::Mapping | inline |
| getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getCurrentPositionInTaskList() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getCurrentTask() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getElementDerivative(const unsigned &) const | PLMD::vesselbase::ActionWithVessel | inline |
| getElementValue(const unsigned &ival) const | PLMD::vesselbase::ActionWithVessel | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
| getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
| getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) | PLMD::vesselbase::ActionWithVessel | virtual |
| getLabel() const | PLMD::Action | inline |
| getLambda() | PLMD::mapping::PathBase | virtual |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inline |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::mapping::Mapping | inlinevirtual |
| getNumberOfProperties() const | PLMD::mapping::Mapping | inline |
| getNumberOfQuantities() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| getNumberOfReferencePoints() const | PLMD::mapping::Mapping | inlineprotected |
| getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | 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 | inlineprotected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| getPropertyIndex(const std::string &name) const | PLMD::mapping::Mapping | |
| getPropertyName(const unsigned &iprop) const | PLMD::mapping::Mapping | inline |
| getPropertyValue(const unsigned &iprop) const | PLMD::mapping::Mapping | inline |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
| getWeight() const | PLMD::mapping::Mapping | inlineprotected |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::mapping::Mapping | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | |
| lockRequests() | PLMD::mapping::Mapping | inlinevirtual |
| log | PLMD::Action | |
| Mapping(const ActionOptions &) | PLMD::mapping::Mapping | |
| mergeDerivatives(const unsigned &, const double &) | PLMD::mapping::Mapping | virtual |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseArgumentList(const std::string &key, std::vector< Value * > &args) | PLMD::ActionWithArguments | |
| 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 | |
| PathBase(const ActionOptions &) | PLMD::mapping::PathBase | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| performTask() | PLMD::mapping::PathBase | virtual |
| plumed | PLMD::Action | |
| prepare() | PLMD::mapping::Mapping | virtual |
| PropertyMap(const ActionOptions &) | PLMD::mapping::PropertyMap | |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::mapping::PropertyMap | static |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setElementDerivative(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| setElementValue(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setMaximumNumberOfDerivatives(const unsigned &) | PLMD::vesselbase::ActionWithVessel | protected |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| storeDistanceFunction(const unsigned &ifunc) | PLMD::mapping::Mapping | inlineprotected |
| thisval_wasset | PLMD::vesselbase::ActionWithVessel | protected |
| transformHD(const double &dist, double &df) | PLMD::mapping::PathBase | virtual |
| turnOnDerivatives() | PLMD::mapping::Mapping | virtual |
| unlockContributors() | PLMD::vesselbase::ActionWithVessel | |
| unlockRequests() | PLMD::mapping::Mapping | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| warning(const std::string &msg) | PLMD::Action | |
| weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
| ~Mapping() | PLMD::mapping::Mapping | |
1.8.7