| Action(const ActionOptions &) | PLMD::Action | explicit |
| Action(const Action &a)=delete | PLMD::Action | private |
| ActionAnyorder(const ActionOptions &ao) | PLMD::ActionAnyorder | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| actionHasForces() | PLMD::ActionAtomistic | virtual |
| ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
| activate() | PLMD::Action | virtual |
| active | PLMD::Action | private |
| addDependency(Action *) | PLMD::Action | |
| addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f) | PLMD::ActionAtomistic | inline |
| after | PLMD::Action | private |
| apply() override | PLMD::GenericMolInfo | inlinevirtual |
| atom_value_ind | PLMD::ActionAtomistic | private |
| atom_value_ind_grouped | PLMD::ActionAtomistic | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| boxValue | PLMD::ActionAtomistic | private |
| calculate() override | PLMD::GenericMolInfo | inlinevirtual |
| 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) override | PLMD::ActionAtomistic | virtual |
| PLMD::castToActionAtomistic() noexcept | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::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 | PLMD::Action | inlinevirtual |
| castToActionWithValue() noexcept | PLMD::Action | 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 |
| checkForAtom(AtomNumber a) const | PLMD::GenericMolInfo | |
| checkForDependency(Action *) | PLMD::Action | |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| checkRead() | PLMD::Action | |
| checkUpdate() const | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearDependencies() | PLMD::Action | |
| clearOptions() | PLMD::Action | virtual |
| comm | PLMD::Action | |
| deactivate() | PLMD::Action | inlinevirtual |
| defaults | PLMD::Action | private |
| Dependencies typedef | PLMD::Action | |
| doCheckPoint | PLMD::Action | private |
| donotforce | PLMD::ActionAtomistic | private |
| doNotForce() | PLMD::ActionAtomistic | inline |
| donotretrieve | PLMD::ActionAtomistic | private |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| enablePythonInterpreter | PLMD::GenericMolInfo | private |
| energy | PLMD::ActionAtomistic | private |
| error(const std::string &msg) const | PLMD::Action | |
| exit(int c=0) | PLMD::Action | |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forceOnEnergy | PLMD::ActionAtomistic | private |
| forceOnExtraCV | PLMD::ActionAtomistic | private |
| forces | PLMD::ActionAtomistic | private |
| GenericMolInfo(const ActionOptions &ao) | PLMD::GenericMolInfo | explicit |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getAtomName(AtomNumber a) const | PLMD::GenericMolInfo | |
| 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 |
| getBackbone(std::vector< std::string > &resstrings, const std::string &fortype, std::vector< std::vector< AtomNumber > > &backbone) | PLMD::GenericMolInfo | |
| getBox() const | PLMD::ActionAtomistic | inline |
| getChainID(AtomNumber a) const | PLMD::GenericMolInfo | |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| 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 |
| 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 | |
| getKBoltzmann() const | PLMD::Action | protected |
| getkBT() | PLMD::Action | |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPDBsize() const | PLMD::GenericMolInfo | |
| getPosition(AtomNumber a) const | PLMD::GenericMolInfo | |
| PLMD::ActionAtomistic::getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getResidueName(AtomNumber a) const | PLMD::GenericMolInfo | |
| getResidueNumber(AtomNumber a) const | PLMD::GenericMolInfo | |
| getRestart() const | PLMD::Action | inline |
| getSpecialKeywords() | PLMD::GenericMolInfo | static |
| getStep() const | PLMD::Action | |
| getStride() const | PLMD::ActionPilot | |
| 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 | |
| indexes | PLMD::ActionAtomistic | private |
| 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 |
| interpretSymbol(const std::string &symbol, std::vector< AtomNumber > &atoms) | PLMD::GenericMolInfo | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isWhole() const | PLMD::GenericMolInfo | |
| iswhole_ | PLMD::GenericMolInfo | private |
| keywords | PLMD::Action | |
| label | PLMD::Action | private |
| line | PLMD::Action | private |
| lockRequestAtoms | PLMD::ActionAtomistic | private |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| 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 | |
| mytype | PLMD::GenericMolInfo | private |
| name | PLMD::Action | private |
| never_activate | PLMD::Action | private |
| onStep() const | PLMD::ActionPilot | virtual |
| operator=(const Action &a)=delete | PLMD::Action | private |
| options | PLMD::Action | private |
| 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 | |
| pbc | PLMD::ActionAtomistic | private |
| 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 |
| pdb | PLMD::GenericMolInfo | private |
| pdb_fwd | PLMD::GenericMolInfo | private |
| plumed | PLMD::Action | |
| positions | PLMD::ActionAtomistic | private |
| prepare() override | PLMD::GenericMolInfo | virtual |
| pythonCmd | PLMD::GenericMolInfo | private |
| read_backbone | PLMD::GenericMolInfo | private |
| PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| reference | PLMD::GenericMolInfo | private |
| registerKeywords(Keywords &keys) | PLMD::GenericMolInfo | static |
| replica_index | PLMD::Action | private |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| resetStoredTimestep() | PLMD::Action | |
| restart | PLMD::Action | private |
| retrieveAtoms(const bool &force=false) | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| selector | PLMD::GenericMolInfo | private |
| selector_running | PLMD::GenericMolInfo | private |
| 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 |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setStride(const int &n) | PLMD::ActionPilot | |
| setupConstantValues(const bool &have_atoms) | PLMD::Action | |
| stride | PLMD::ActionPilot | private |
| timestep | PLMD::Action | private |
| unique | PLMD::ActionAtomistic | private |
| unique_local | PLMD::ActionAtomistic | private |
| unique_local_needs_update | PLMD::ActionAtomistic | private |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| update_from | PLMD::Action | private |
| update_until | PLMD::Action | private |
| updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l) | PLMD::ActionAtomistic | private |
| usingNaturalUnits() const | PLMD::Action | protected |
| value_depends | PLMD::ActionAtomistic | 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 | |
| ~GenericMolInfo() | PLMD::GenericMolInfo | |
1.8.17