| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| actionHasForces() | PLMD::ActionAtomistic | virtual |
| actionMoldat | PLMD::ActionAtomistic | private |
| actionPbc | PLMD::ActionAtomistic | private |
| actionPositions | PLMD::ActionAtomistic | private |
| PLMD::ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| ActionWithVector(const ActionOptions &) | PLMD::ActionWithVector | explicit |
| activate() | PLMD::Action | virtual |
| active_cells | PLMD::contour::FindContour | private |
| active_tasks | PLMD::ActionWithVector | private |
| addComponent(const std::string &valname, const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &valname, const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | virtual |
| addDependency(Action *) | PLMD::Action | |
| addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f) | PLMD::ActionAtomistic | inline |
| addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind) | PLMD::ActionWithArguments | |
| addValue(const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | |
| addValueWithDerivatives(const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | virtual |
| apply() override | PLMD::ActionWithVector | virtual |
| applyNonZeroRankForces(std::vector< double > &outforces) | PLMD::ActionWithVector | inlinevirtual |
| arguments | PLMD::ActionWithArguments | private |
| atom_value_ind | PLMD::ActionAtomistic | private |
| atom_value_ind_grouped | PLMD::ActionAtomistic | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| boxValue | PLMD::ActionAtomistic | private |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calculate() override | PLMD::contour::FindContour | virtual |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateConstantValues(const bool &have_atoms) | PLMD::ActionWithArguments | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *av) override | PLMD::ActionWithVector | virtual |
| calculateOnUpdate() | PLMD::ActionWithValue | virtual |
| castToActionAtomistic() noexcept final | PLMD::ActionAtomistic | inlinevirtual |
| castToActionForInterface() noexcept | PLMD::Action | inlinevirtual |
| castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
| castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
| castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
| castToActionWithArguments() noexcept final | PLMD::ActionWithArguments | inlinevirtual |
| castToActionWithValue() noexcept final | PLMD::ActionWithValue | inlinevirtual |
| castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
| castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
| castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| charges | PLMD::ActionAtomistic | private |
| chargesWereSet | PLMD::ActionAtomistic | protected |
| chargev | PLMD::ActionAtomistic | private |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkForDependency(Action *) | PLMD::Action | |
| checkForForces() | PLMD::ActionWithVector | protected |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
| checkRead() | PLMD::Action | |
| checkTaskIsActive(const unsigned &taskno) const override | PLMD::contour::FindContour | virtual |
| checkUpdate() const | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearDependencies() | PLMD::Action | |
| clearDerivatives(const bool &force=false) | PLMD::ActionWithValue | virtual |
| clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
| clearOptions() | PLMD::Action | virtual |
| comm | PLMD::Action | |
| componentIsNotPeriodic(const std::string &valname) | PLMD::ActionWithValue | |
| componentIsPeriodic(const std::string &valname, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| copyOutput(const std::string &valname) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| donotforce | PLMD::ActionAtomistic | private |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| donotretrieve | PLMD::ActionAtomistic | private |
| DumpContour class | PLMD::contour::FindContour | friend |
| energy | PLMD::ActionAtomistic | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &valname) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| FindContour(const ActionOptions &ao) | PLMD::contour::FindContour | explicit |
| firststep | PLMD::contour::FindContour | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forceOnEnergy | PLMD::ActionAtomistic | private |
| forceOnExtraCV | PLMD::ActionAtomistic | private |
| forces | PLMD::ActionAtomistic | private |
| forcesForApply | PLMD::ActionWithValue | private |
| gbuffer | PLMD::contour::FindContour | private |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getAtomValuesFromPlumedObject(const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev) | PLMD::ActionAtomistic | static |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getCharges(const bool allowempty=false) const | PLMD::ActionAtomistic | inline |
| getComponent(const std::string &valname) const | PLMD::ActionWithValue | private |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getConstPntrToComponent(unsigned i) const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getDefaultString() const | PLMD::Action | inline |
| getDependencies() const | PLMD::Action | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForce(const std::pair< std::size_t, std::size_t > &a) const | PLMD::ActionAtomistic | inline |
| getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
| getGlobalPosition(const std::pair< std::size_t, std::size_t > &) const | PLMD::ActionAtomistic | inline |
| getGradient(const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const | PLMD::ActionAtomistic | |
| getInputData(std::vector< double > &inputdata) const override | PLMD::contour::FindContour | virtual |
| getInputGridObject() const | PLMD::contour::FindContour | inline |
| getKBoltzmann() const | PLMD::Action | protected |
| getkBT() | PLMD::Action | |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getListOfActiveTasks(ActionWithVector *action) | PLMD::ActionWithVector | virtual |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getMasses() const | PLMD::ActionAtomistic | inline |
| getMatrixColumnTitles(std::vector< std::string > &argnames) const | PLMD::ActionWithValue | virtual |
| getName() const | PLMD::Action | inline |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::contour::FindContour | virtual |
| getNumberOfForceDerivatives() const | PLMD::ActionWithVector | |
| getNumberOfMasks() const | PLMD::ActionWithVector | inline |
| getNumberOfTasks(unsigned &ntasks) override | PLMD::contour::FindContour | virtual |
| getOutputComponentDescription(const std::string &cname, const Keywords &keys) const override | PLMD::contour::FindContour | virtual |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &valname) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getPntrToComponent(unsigned i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &valname) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| getRestart() const | PLMD::Action | inline |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTotAtoms() const | PLMD::ActionAtomistic | |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getUniqueLocal() const | PLMD::ActionAtomistic | inline |
| getUnits() const | PLMD::Action | protected |
| getValueIndices(const AtomNumber &i) const | PLMD::ActionAtomistic | protected |
| getVirial() const | PLMD::ActionAtomistic | |
| ignoreMaskArguments() | PLMD::ActionWithVector | inlineprotected |
| indexes | PLMD::ActionAtomistic | private |
| input_type typedef | PLMD::contour::FindContour | |
| interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg) | PLMD::ActionWithArguments | static |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| interpretAtomList(std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | static |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| keywords | PLMD::Action | |
| lockRequestArguments | PLMD::ActionWithArguments | private |
| lockRequestAtoms | PLMD::ActionAtomistic | private |
| lockRequests() override | PLMD::ActionWithVector | virtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| masses | PLMD::ActionAtomistic | private |
| massesWereSet | PLMD::ActionAtomistic | protected |
| masv | PLMD::ActionAtomistic | private |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| nmask | PLMD::ActionWithVector | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| NoMasksUsed | PLMD::ActionWithVector | privatestatic |
| numericalDerivatives | PLMD::ActionWithValue | private |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseArgumentList(const std::string &key, std::vector< Value * > &args) | PLMD::ActionWithArguments | |
| parseArgumentList(const std::string &key, int i, 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 | |
| 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 | inline |
| performTask(std::size_t task_index, const ContourFindingObject< gridtools::EvaluateGridFunction > &actiondata, ParallelActionsInput &input, ParallelActionsOutput &output) | PLMD::contour::FindContour | static |
| plumed | PLMD::Action | |
| prepare() override | PLMD::ActionWithVector | virtual |
| PTM typedef | PLMD::contour::FindContour | |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::contour::FindContour | static |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
| resetStoredTimestep() | PLMD::Action | |
| retrieveAtoms(const bool &force=false) | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | protected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned &ind) | PLMD::ActionAtomistic | |
| setForcesOnCell(const std::vector< double > &forcesToApply, unsigned &ind) | PLMD::ActionAtomistic | |
| setForcesOnCell(const double *forcesToApply, std::size_t size, unsigned &ind) | PLMD::ActionAtomistic | |
| setGlobalPosition(const std::pair< std::size_t, std::size_t > &, const Vector &pos) | PLMD::ActionAtomistic | inline |
| setGradients(Value *myval, unsigned &start) const | PLMD::ActionWithArguments | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | virtual |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setupConstantValues(const bool &have_atoms) | PLMD::Action | |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| taskmanager | PLMD::contour::FindContour | private |
| transferForcesToStash(const std::vector< unsigned > &partialTaskList, std::vector< double > &stash) const | PLMD::ActionWithVector | virtual |
| transferStashToValues(const std::vector< unsigned > &partialTaskList, const std::vector< double > &stash) | PLMD::ActionWithVector | virtual |
| tree | PLMD::ActionAtomistic | private |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| unique | PLMD::ActionAtomistic | private |
| unique_local | PLMD::ActionAtomistic | private |
| unique_local_needs_update | PLMD::ActionAtomistic | private |
| unlockRequests() override | PLMD::ActionWithVector | virtual |
| update() | PLMD::Action | inlinevirtual |
| updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l) | PLMD::ActionAtomistic | private |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usingNaturalUnits() const | PLMD::Action | protected |
| valsToForce | PLMD::ActionWithValue | private |
| value_depends | PLMD::ActionAtomistic | private |
| values | PLMD::ActionWithValue | private |
| warning(const std::string &msg) | PLMD::Action | |
| writeInGraph() const | PLMD::Action | virtual |
| xpos | PLMD::ActionAtomistic | private |
| ypos | PLMD::ActionAtomistic | private |
| zpos | PLMD::ActionAtomistic | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVector() | PLMD::ActionWithVector | inlinevirtual |
1.13.2