| Action(const ActionOptions &) | PLMD::Action | |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | |
| ActionSetup(const ActionOptions &ao) | PLMD::ActionSetup | |
| activate() | PLMD::Action | virtual |
| addDependency(Action *) | PLMD::Action | |
| apply() | PLMD::ActionSetup | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| calculate() | PLMD::ActionSetup | 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) | PLMD::ActionAtomistic | virtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| checkRead() | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearDependencies() | PLMD::Action | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| comm | PLMD::Action | |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| 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 | |
| files_iterator typedef | PLMD::Action | |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inline |
| getAtomName(AtomNumber a) const | PLMD::SetupMolInfo | |
| getBackbone(std::vector< std::string > &resstrings, const std::string &fortype, std::vector< std::vector< AtomNumber > > &backbone) | PLMD::SetupMolInfo | |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | 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 |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getResidueName(AtomNumber a) const | PLMD::SetupMolInfo | |
| getResidueNumber(AtomNumber a) const | PLMD::SetupMolInfo | |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| interpretSymbol(const std::string &symbol, std::vector< AtomNumber > &atoms) const | PLMD::SetupMolInfo | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| keywords | PLMD::Action | |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| 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 | |
| mytype | PLMD::SetupMolInfo | 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 | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| pdb | PLMD::SetupMolInfo | private |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| read_backbone | PLMD::SetupMolInfo | private |
| PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::SetupMolInfo | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| SetupMolInfo(const ActionOptions &ao) | PLMD::SetupMolInfo | |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionAtomistic::unlockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| warning(const std::string &msg) | PLMD::Action | |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~SetupMolInfo() | PLMD::SetupMolInfo | |
1.8.7