| ablocks | PLMD::multicolvar::MultiColvarBase | protected |
| accumulateSymmetryFunction(const int &ival, const unsigned &iatom, const double &val, const Vector &der, const Tensor &vir, multicolvar::AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
| activate() | PLMD::Action | virtual |
| addAtomDerivatives(const int &, const unsigned &, const Vector &, multicolvar::AtomValuePack &) const | PLMD::multicolvar::MultiColvarBase | |
| 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 | |
| addDerivativesOnMatrixElement(const unsigned &ielem, const unsigned &jrow, const double &df, Matrix< double > &der) | PLMD::adjmat::AdjacencyMatrixBase | protected |
| 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(std::unique_ptr< Vessel > vv) | PLMD::vesselbase::ActionWithVessel | protected |
| AdjacencyMatrixBase(const ActionOptions &) | PLMD::adjmat::AdjacencyMatrixBase | explicit |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| apply() override | PLMD::multicolvar::MultiColvarBase | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::multicolvar::MultiColvarBase | |
| atom_lab | PLMD::multicolvar::MultiColvarBase | protected |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bookeeping | PLMD::multicolvar::MultiColvarBase | protected |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| buildDataStashes(ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
| buildSets() | PLMD::multicolvar::MultiColvarBase | protected |
| calculate() override | PLMD::multicolvar::MultiColvarBase | 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::multicolvar::MultiColvarBase | virtual |
| calculateWeight(const unsigned &taskCode, const double &weight, multicolvar::AtomValuePack &myatoms) const override | PLMD::adjmat::ContactMatrix | virtual |
| 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 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 | |
| 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 |
| compute(const unsigned &tindex, multicolvar::AtomValuePack &myatoms) const override | PLMD::adjmat::ContactMatrix | virtual |
| ContactMatrix(const ActionOptions &) | PLMD::adjmat::ContactMatrix | explicit |
| 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 |
| decodeIndexToAtoms(const unsigned &taskCode, std::vector< unsigned > &atoms) const | PLMD::multicolvar::MultiColvarBase | protected |
| decoder | PLMD::multicolvar::MultiColvarBase | protected |
| Dependencies typedef | PLMD::Action | |
| derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
| dertime | PLMD::vesselbase::ActionWithVessel | protected |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| doNotCalculateDerivatives() const override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| doNotCalculateDirector() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| 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 | |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| filtersUsedAsInput() | PLMD::multicolvar::MultiColvarBase | protected |
| finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getAbsoluteIndexOfCentralAtom(const unsigned &i) const | PLMD::adjmat::AdjacencyMatrixBase | inlinevirtual |
| getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
| getAdjacencyVessel() | PLMD::adjmat::AdjacencyMatrixBase | inlineprotected |
| getBaseColvarNumber(const unsigned &) const | PLMD::adjmat::AdjacencyMatrixBase | inlineprotected |
| getBaseMultiColvar(const unsigned &icolv) const | PLMD::multicolvar::MultiColvarBase | inline |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCentralAtom() | PLMD::adjmat::AdjacencyMatrixBase | inline |
| getCentralAtomPack(const unsigned &basn, const unsigned &curr, CatomPack &mypack) | PLMD::multicolvar::MultiColvarBase | virtual |
| getCentralAtomPos(const unsigned &curr) | PLMD::multicolvar::MultiColvarBase | virtual |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| 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 |
| getInputData(const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient) const | PLMD::multicolvar::MultiColvarBase | virtual |
| getInputDerivatives(const unsigned &iatom, const bool &normed, const multicolvar::AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | virtual |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getLinkCellCutoff() const | PLMD::multicolvar::MultiColvarBase | protected |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfBaseMultiColvars() const | PLMD::multicolvar::MultiColvarBase | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| getNumberOfNodeTypes() const | PLMD::adjmat::AdjacencyMatrixBase | protected |
| getNumberOfQuantities() const | PLMD::vesselbase::ActionWithVessel | 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 |
| getPositionOfAtomForLinkCells(const unsigned &iatom) const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getRestart() const | PLMD::Action | inline |
| getSeparation(const Vector &vec1, const Vector &vec2) const | PLMD::multicolvar::MultiColvarBase | |
| getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
| getSizeOfInputVectors() const | PLMD::adjmat::AdjacencyMatrixBase | 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 | |
| hasDifferentiableOrientation() const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| isActive() const | PLMD::Action | inline |
| isCurrentlyActive(const unsigned &code) | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| isDensity() const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::adjmat::AdjacencyMatrixBase | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | |
| lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| matsums | PLMD::multicolvar::MultiColvarBase | protected |
| mergeInputDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
| 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 | |
| MultiColvarBase(const ActionOptions &) | PLMD::multicolvar::MultiColvarBase | explicit |
| mybasedata | PLMD::multicolvar::MultiColvarBase | protected |
| mybasemulticolvars | PLMD::multicolvar::MultiColvarBase | protected |
| mydata | PLMD::vesselbase::ActionWithVessel | protected |
| nblock | PLMD::multicolvar::MultiColvarBase | protected |
| ncol_t | PLMD::adjmat::ContactMatrix | private |
| needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| normalizeVector(std::vector< double > &vals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| normalizeVectorDerivatives(MultiValue &myvals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| 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 | |
| parseConnectionDescriptions(const std::string &key, const bool &multiple, const unsigned &nrow_t) | PLMD::adjmat::AdjacencyMatrixBase | protected |
| parseFlag(const std::string &key, bool &t) | PLMD::Action | |
| parseMultiColvarAtomList(const std::string &key, const int &num, std::vector< AtomNumber > &t) | PLMD::multicolvar::MultiColvarBase | protected |
| 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 override | PLMD::multicolvar::MultiColvarBase | virtual |
| plumed | PLMD::Action | |
| prepare() override | PLMD::multicolvar::MultiColvarBase | virtual |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| readAtomsLikeKeyword(const std::string &key, const int &natoms, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
| readGroupKeywords(const std::string &key0, const std::string &key1, const std::string &key2, const std::string &key3, const bool &no_third_dim_accum, const bool &symmetric, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
| readMaxThreeSpeciesMatrix(const std::string &key0, const std::string &key1, const std::string &key2, const std::string &keym, const bool &symmetric) | PLMD::adjmat::AdjacencyMatrixBase | protected |
| readMaxTwoSpeciesMatrix(const std::string &key0, const std::string &key1, const std::string &key2, const bool &symmetric) | PLMD::adjmat::AdjacencyMatrixBase | protected |
| readThreeGroups(const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2, const bool &no_third_dim_accum, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
| readTwoGroups(const std::string &key0, const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::adjmat::ContactMatrix | static |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| resizeBookeepingArray(const unsigned &num1, const unsigned &num2) | PLMD::multicolvar::MultiColvarBase | protected |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() override | PLMD::multicolvar::MultiColvarBase | virtual |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| retrieveTypeDimensions(unsigned &nrows, unsigned &ncols, unsigned &ntype) const | PLMD::adjmat::AdjacencyMatrixBase | protected |
| runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setAtomsForCentralAtom(const std::vector< bool > &catom_ind) | PLMD::multicolvar::MultiColvarBase | protected |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setLinkCellCutoff(const double &lcut, double tcut=-1.0) | PLMD::multicolvar::MultiColvarBase | protected |
| setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setMatrixIndexesForTask(const unsigned &ii) | PLMD::adjmat::AdjacencyMatrixBase | protected |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setupActiveTaskSet(std::vector< unsigned > &active_tasks, const std::string &input_label) | PLMD::multicolvar::MultiColvarBase | protected |
| setupConnector(const unsigned &id, const unsigned &i, const unsigned &j, const std::vector< std::string > &desc) override | PLMD::adjmat::ContactMatrix | virtual |
| setupCurrentAtomList(const unsigned &taskCode, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
| setupLinkCells() | PLMD::multicolvar::MultiColvarBase | protected |
| setupMultiColvarBase(const std::vector< AtomNumber > &atoms) | PLMD::multicolvar::MultiColvarBase | protected |
| setupNonUseSpeciesLinkCells(const unsigned &) | PLMD::multicolvar::MultiColvarBase | protected |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| splitInputDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
| storedValueIsActive(const unsigned &iatom) | PLMD::multicolvar::MultiColvarBase | |
| switchingFunction | PLMD::adjmat::ContactMatrix | private |
| taskFlags | PLMD::vesselbase::ActionWithVessel | protected |
| taskIsCurrentlyActive(const unsigned &index) const | PLMD::vesselbase::ActionWithVessel | |
| threadSafe() const override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
| transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
| turnOnDerivatives() override | PLMD::multicolvar::MultiColvarBase | virtual |
| unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| updateActiveAtoms(AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | virtual |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usesPbc() const | PLMD::multicolvar::MultiColvarBase | inline |
| usespecies | PLMD::multicolvar::MultiColvarBase | protected |
| 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 | |
| ~MultiColvarBase() | PLMD::multicolvar::MultiColvarBase | inline |
1.8.14