| Action(const ActionOptions &) | PLMD::Action | |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | |
| ActionWithVirtualAtom(const ActionOptions &ao) | PLMD::ActionWithVirtualAtom | |
| activate() | PLMD::Action | virtual |
| addDependency(Action *) | PLMD::Action | |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| calculate() | PLMD::vatom::Center | virtual |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionAtomistic | virtual |
| Center(const ActionOptions &ao) | PLMD::vatom::Center | |
| 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 | inline |
| comm | PLMD::Action | |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| 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 |
| 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 | |
| getGradients() const | PLMD::ActionWithVirtualAtom | inline |
| getIndex() const | PLMD::ActionWithVirtualAtom | inline |
| 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 |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getUnique() const | PLMD::ActionAtomistic | inline |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| keywords | PLMD::Action | |
| lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| 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 | |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::vatom::Center | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionWithVirtualAtom | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| setAtomsDerivatives(const std::vector< Tensor > &d) | PLMD::ActionWithVirtualAtom | inlineprotected |
| setCharge(double) | PLMD::ActionWithVirtualAtom | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradients() | PLMD::ActionWithVirtualAtom | |
| setGradientsIfNeeded() | PLMD::ActionWithVirtualAtom | |
| setMass(double) | PLMD::ActionWithVirtualAtom | inlineprotected |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPosition(const Vector &) | PLMD::ActionWithVirtualAtom | inlineprotected |
| unlockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| warning(const std::string &msg) | PLMD::Action | |
| weight_mass | PLMD::vatom::Center | private |
| weights | PLMD::vatom::Center | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithVirtualAtom() | PLMD::ActionWithVirtualAtom | |
1.8.8