| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| ActionWithInputMatrix(const ActionOptions &) | PLMD::adjmat::ActionWithInputMatrix | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
| activate() | PLMD::Action | virtual |
| activateTheseTasks(std::vector< unsigned > &addtionalTasks) | PLMD::vesselbase::ActionWithVessel | |
| active_elements | PLMD::adjmat::Sprint | private |
| 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 | |
| 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::adjmat::Sprint | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| buildDataStashes(const bool &allow_wcutoff, const double &wtol, ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
| calculate() | PLMD::adjmat::Sprint | 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 | |
| PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
| PLMD::ActionAtomistic::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionAtomistic | virtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| checkNumericalDerivatives() const | 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 | |
| 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(const unsigned &task_index) | 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 |
| dertime | PLMD::vesselbase::ActionWithVessel | protected |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| eigenvecs | PLMD::adjmat::Sprint | private |
| eigvals | PLMD::adjmat::Sprint | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| files_iterator typedef | PLMD::Action | |
| finishComputations(const std::vector< double > &buffer) | 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 |
| getAbsoluteIndexOfCentralAtom(const unsigned &i) const | PLMD::adjmat::ActionWithInputMatrix | |
| getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getAdjacencyVessel() const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getBaseMultiColvar(const unsigned &igrp) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| 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 |
| 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 |
| getNumberOfAtomsInGroup(const unsigned &igrp) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::adjmat::ActionWithInputMatrix | virtual |
| getNumberOfNodes() const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getNumberOfNodeTypes() const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getNumberOfQuantities() | PLMD::adjmat::ActionWithInputMatrix | virtual |
| 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(const unsigned &iatom) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| PLMD::ActionAtomistic::getPosition(int) const | PLMD::ActionAtomistic | inline |
| PLMD::ActionAtomistic::getPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getRestart() const | PLMD::Action | inline |
| getSeparation(const Vector &vec1, const Vector &vec2) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| 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 |
| getVectorDerivatives(const unsigned &ind, const bool &normed, MultiValue &myder0) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getVectorForTask(const unsigned &ind, const bool &normed, std::vector< double > &orient0) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| isActive() const | PLMD::Action | inline |
| isCurrentlyActive(const unsigned &ind) const | PLMD::adjmat::ActionWithInputMatrix | protected |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::adjmat::ActionWithInputMatrix | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| maxeig | PLMD::adjmat::Sprint | private |
| 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 | |
| mydata | PLMD::vesselbase::ActionWithVessel | protected |
| mymatrix | PLMD::adjmat::Sprint | private |
| needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| 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 | |
| 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 | PLMD::adjmat::Sprint | inlinevirtual |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::adjmat::Sprint | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| 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 |
| 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 | |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| Sprint(const ActionOptions &) | PLMD::adjmat::Sprint | explicit |
| sqrtn | PLMD::adjmat::Sprint | private |
| taskIsCurrentlyActive(const unsigned &index) const | PLMD::vesselbase::ActionWithVessel | protected |
| threadSafe() const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
| turnOnDerivatives() | PLMD::adjmat::ActionWithInputMatrix | virtual |
| unlockContributors() | PLMD::vesselbase::ActionWithVessel | |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::unlockRequests() | PLMD::ActionAtomistic | 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 |
| weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
1.8.7