| ablocks | PLMD::multicolvar::MultiColvarBase | protected |
| accumulateDerivative(const unsigned &ider, const double &df) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| accumulateWeightedAverageAndDerivatives(const unsigned &iatom, const double &weight) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| Action(const ActionOptions &) | PLMD::Action | |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | |
| activate() | PLMD::Action | virtual |
| activateIndexes(const unsigned &istart, const unsigned &number, const std::vector< unsigned > &indexes) | PLMD::multicolvar::MultiColvarBase | virtual |
| activateTheseTasks(std::vector< bool > &addtionalTasks) | PLMD::vesselbase::ActionWithVessel | |
| addAtomsDerivatives(const unsigned &, const unsigned &, const Vector &) | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| addBoxDerivatives(const unsigned &, const Tensor &) | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| addBoxDerivatives(const Tensor &) | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| addBoxDerivativesOfWeight(const Tensor &vir) | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
| addCentralAtomDerivatives(const unsigned &iatom, const Tensor &der) | PLMD::multicolvar::MultiColvarBase | protected |
| addCentralAtomDerivativeToFunction(const unsigned &iatom, const unsigned &jout, const unsigned &base_cv_no, const Vector &der, MultiColvarFunction *func) | PLMD::multicolvar::MultiColvarBase | |
| addCentralAtomsDerivatives(const unsigned &, const unsigned &, const Vector &) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addDerivativeOfCentralAtomPos(const unsigned &iatom, const Tensor &der) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| addDerivativesOnMatrixElement(const unsigned &ielem, const unsigned &jrow, const double &df, Matrix< double > &der) | PLMD::multicolvar::AdjacencyMatrixAction | protected |
| addElementDerivative(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| addElementValue(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| addOrientationDerivatives(const unsigned &iatom, const std::vector< double > &der) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| addOrientationDerivativesToBase(const unsigned &iatom, const unsigned &jstore, const unsigned &base_cv_no, const std::vector< double > &weight, MultiColvarFunction *func) | PLMD::multicolvar::MultiColvarBase | virtual |
| addStoredDerivative(const unsigned &, const unsigned &, const unsigned &, const double &) | PLMD::multicolvar::MultiColvarFunction | |
| addTaskToList(const unsigned &taskCode) | PLMD::multicolvar::MultiColvarBase | 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 |
| addWeightedValueDerivatives(const unsigned &iatom, const unsigned &base_cv_no, const double &weight, MultiColvarFunction *func) | PLMD::multicolvar::MultiColvarBase | virtual |
| AdjacencyMatrixAction(const ActionOptions &) | PLMD::multicolvar::AdjacencyMatrixAction | |
| apply() | PLMD::multicolvar::Sprint | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atomHasDerivative(const unsigned &iatom) | PLMD::multicolvar::MultiColvarFunction | inline |
| atoms | PLMD::ActionAtomistic | protected |
| atoms_with_derivatives | PLMD::multicolvar::MultiColvarBase | protected |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| buildAtomListWithPairs(const bool &allow_intra_group) | PLMD::multicolvar::MultiColvarFunction | protected |
| buildDataStashes() | PLMD::multicolvar::MultiColvarBase | virtual |
| buildSymmetryFunctionLists() | PLMD::multicolvar::MultiColvarFunction | protected |
| calculate() | PLMD::multicolvar::MultiColvarFunction | virtual |
| calculateAllVessels() | PLMD::vesselbase::ActionWithVessel | protected |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateCentralAtomPosition() | PLMD::multicolvar::MultiColvarFunction | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::multicolvar::MultiColvarFunction | virtual |
| calculateWeight() | PLMD::multicolvar::AdjacencyMatrixAction | 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 &ider) | PLMD::multicolvar::MultiColvarBase | virtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| comm | PLMD::Action | |
| completeCalculation() | PLMD::multicolvar::Sprint | virtual |
| 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 |
| compute() | PLMD::multicolvar::AdjacencyMatrixAction | virtual |
| contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | protected |
| convertToLocalIndex(const unsigned &index, const unsigned &mcv_code) const | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| copyActiveAtomsToFunction(MultiColvarBase *myfunction, const unsigned &start) | PLMD::multicolvar::MultiColvarBase | |
| copyAtomListToFunction(MultiColvarBase *myfunction) | PLMD::multicolvar::MultiColvarBase | |
| copyElementsToBridgedColvar(const double &weight, ActionVolume *) | PLMD::multicolvar::MultiColvarBase | virtual |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| current_atoms | PLMD::multicolvar::MultiColvarBase | protected |
| 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 |
| decoder | PLMD::multicolvar::MultiColvarBase | protected |
| Dependencies typedef | PLMD::Action | |
| derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
| doCalculation() | PLMD::multicolvar::MultiColvarBase | virtual |
| doJobsRequiredBeforeTaskList() | PLMD::multicolvar::AdjacencyMatrixAction | virtual |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inline |
| doNotCalculateDirector() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| eigenvecs | PLMD::multicolvar::Sprint | private |
| eigvals | PLMD::multicolvar::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() | PLMD::vesselbase::ActionWithVessel | virtual |
| finishTaskListUpdate() | PLMD::multicolvar::MultiColvarFunction | virtual |
| finishWeightedAverageCalculation(MultiColvarFunction *func) | PLMD::multicolvar::MultiColvarBase | virtual |
| 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 |
| getBaseColvarNumber(const unsigned &iatom) const | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getBaseMultiColvar(const unsigned &icolv) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getBaseQuantityIndex(const unsigned &code) | PLMD::multicolvar::MultiColvarFunction | inlinevirtual |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCentralAtom() | PLMD::multicolvar::AdjacencyMatrixAction | inlinevirtual |
| getCentralAtomDerivative(const unsigned &iatom, const unsigned &jcomp, const Vector &df) | PLMD::multicolvar::MultiColvarBase | protected |
| getCentralAtomIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) const | PLMD::multicolvar::MultiColvarBase | protected |
| getCentralAtomPosition(const unsigned &iatom) const | PLMD::multicolvar::MultiColvarBase | |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getColvarIndex(const unsigned &) const | PLMD::multicolvar::MultiColvarFunction | protected |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| 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 |
| getFullNumberOfBaseTasks() const | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
| getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) | PLMD::multicolvar::MultiColvarBase | virtual |
| getInternalIndex(const AtomNumber &iatom) const | PLMD::multicolvar::MultiColvarBase | |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getMatrixElement(const unsigned &ielem) const | PLMD::multicolvar::AdjacencyMatrixAction | inlineprotected |
| getName() const | PLMD::Action | inline |
| getNAtoms() const | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNumberOfActiveMatrixElements() | PLMD::multicolvar::AdjacencyMatrixAction | inlineprotected |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfBaseMultiColvars() const | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| getNumberOfQuantities() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| 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 |
| 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 |
| getPositionOfAtomForLinkCells(const unsigned &iatom) | PLMD::multicolvar::MultiColvarFunction | inlinevirtual |
| getPositionOfCentralAtom(const unsigned &) const | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getSeparation(const Vector &vec1, const Vector &vec2) const | PLMD::multicolvar::MultiColvarBase | protected |
| 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 |
| getValueForBaseTask(const unsigned &iatom, std::vector< double > &vals) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getValueForTask(const unsigned &iatom, std::vector< double > &vals) | PLMD::multicolvar::MultiColvarBase | virtual |
| getVectorForBaseTask(const unsigned &iatom, std::vector< double > &vecs) | PLMD::multicolvar::MultiColvarFunction | inlineprotected |
| getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
| hasDifferentiableOrientation() const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| isActive() const | PLMD::Action | inline |
| isCurrentlyActive(const unsigned &code) | PLMD::multicolvar::MultiColvarFunction | inlinevirtual |
| isDensity() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::multicolvar::AdjacencyMatrixAction | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::multicolvar::MultiColvarFunction | |
| lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| maxeig | PLMD::multicolvar::Sprint | private |
| mergeDerivatives(const unsigned &ider, const double &df) | PLMD::multicolvar::MultiColvarBase | 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 | |
| MultiColvarBase(const ActionOptions &) | PLMD::multicolvar::MultiColvarBase | |
| MultiColvarFunction(const ActionOptions &) | PLMD::multicolvar::MultiColvarFunction | |
| mymatrix | PLMD::multicolvar::Sprint | private |
| natomsper | PLMD::multicolvar::MultiColvarBase | protected |
| nblock | PLMD::multicolvar::MultiColvarBase | protected |
| 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 | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| performTask() | PLMD::multicolvar::MultiColvarBase | virtual |
| plumed | PLMD::Action | |
| prepare() | PLMD::multicolvar::MultiColvarBase | virtual |
| quotientRule(const unsigned &uder, const unsigned &vder, const unsigned &iout) | PLMD::multicolvar::MultiColvarBase | |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::multicolvar::Sprint | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| resizeDynamicArrays() | PLMD::multicolvar::MultiColvarFunction | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| retrieveCentralAtomPos() | PLMD::multicolvar::MultiColvarBase | |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| retrieveMatrix(Matrix< double > &mymatrix) | PLMD::multicolvar::AdjacencyMatrixAction | protected |
| 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 | |
| setLinkCellCutoff(const double &lcut) | PLMD::multicolvar::MultiColvarBase | protected |
| setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setMatrixIndexesForTask(const unsigned &ii) | PLMD::multicolvar::AdjacencyMatrixAction | protected |
| 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 | |
| setupCurrentAtomList(const unsigned &taskCode) | PLMD::multicolvar::MultiColvarBase | protected |
| setupLinkCells() | PLMD::multicolvar::MultiColvarBase | protected |
| setupMultiColvarBase() | PLMD::multicolvar::MultiColvarBase | protected |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| setWeight(const double &weight) | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| Sprint(const ActionOptions &) | PLMD::multicolvar::Sprint | |
| sqrtn | PLMD::multicolvar::Sprint | private |
| thisval_wasset | PLMD::vesselbase::ActionWithVessel | protected |
| turnOnDerivatives() | PLMD::multicolvar::MultiColvarBase | virtual |
| unlockContributors() | PLMD::multicolvar::MultiColvarFunction | |
| unlockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| updateActiveAtoms() | PLMD::multicolvar::MultiColvarFunction | virtual |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usesPbc() const | PLMD::multicolvar::MultiColvarBase | inlineprotected |
| usespecies | PLMD::multicolvar::MultiColvarBase | protected |
| 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 | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
| ~MultiColvarBase() | PLMD::multicolvar::MultiColvarBase | inline |
1.8.7