| ActionAtomistic class | PLMD::Atoms | friend |
| actions | PLMD::Atoms | private |
| ActionWithVirtualAtom class | PLMD::Atoms | friend |
| add(ActionAtomistic *) | PLMD::Atoms | |
| addVirtualAtom(ActionWithVirtualAtom *) | PLMD::Atoms | |
| asyncSent | PLMD::Atoms | private |
| Atoms(PlumedMain &plumed) | PLMD::Atoms | explicit |
| atomsNeeded | PLMD::Atoms | private |
| box | PLMD::Atoms | private |
| boxHasBeenSet | PLMD::Atoms | private |
| boxWasSet() const | PLMD::Atoms | inline |
| charges | PLMD::Atoms | private |
| chargesHaveBeenSet | PLMD::Atoms | private |
| chargesWereSet() const | PLMD::Atoms | inline |
| clearFullList() | PLMD::Atoms | |
| collectEnergy | PLMD::Atoms | private |
| createFullList(const TypesafePtr &) | PLMD::Atoms | |
| dataCanBeSet | PLMD::Atoms | private |
| dd | PLMD::Atoms | private |
| ddStep | PLMD::Atoms | private |
| double2MD(const double &d, const TypesafePtr &m) const | PLMD::Atoms | |
| energy | PLMD::Atoms | private |
| energyHasBeenSet | PLMD::Atoms | private |
| forceOnEnergy | PLMD::Atoms | private |
| forces | PLMD::Atoms | private |
| forcesHaveBeenSet | PLMD::Atoms | private |
| fullList | PLMD::Atoms | private |
| g2l | PLMD::Atoms | private |
| gatindex | PLMD::Atoms | private |
| getDdStep() const | PLMD::Atoms | inline |
| getEnergy() const | PLMD::Atoms | inline |
| getExtraCV(const std::string &name) | PLMD::Atoms | |
| getFullList(const TypesafePtr &) | PLMD::Atoms | |
| getGatindex() const | PLMD::Atoms | inline |
| getKBoltzmann() const | PLMD::Atoms | |
| getKbT() const | PLMD::Atoms | |
| getLocalForces(std::vector< Vector > &) | PLMD::Atoms | |
| getLocalMasses(std::vector< double > &) | PLMD::Atoms | |
| getLocalMDForces(std::vector< Vector > &) | PLMD::Atoms | |
| getLocalPositions(std::vector< Vector > &) | PLMD::Atoms | |
| getMDKBoltzmann() const | PLMD::Atoms | |
| getMDUnits() | PLMD::Atoms | inline |
| getNatoms() const | PLMD::Atoms | inline |
| getNVirtualAtoms() const | PLMD::Atoms | inline |
| getPbc() const | PLMD::Atoms | inline |
| getRealPrecision() const | PLMD::Atoms | |
| getTimeStep() const | PLMD::Atoms | |
| getUnits() | PLMD::Atoms | inline |
| getVirial() const | PLMD::Atoms | inline |
| getVirtualAtomsAction(AtomNumber) const | PLMD::Atoms | inline |
| groups | PLMD::Atoms | private |
| init() | PLMD::Atoms | |
| insertGroup(const std::string &name, const std::vector< AtomNumber > &a) | PLMD::Atoms | |
| isEnergyNeeded() const | PLMD::Atoms | inline |
| isExtraCVNeeded(const std::string &name) const | PLMD::Atoms | |
| isVirtualAtom(AtomNumber) const | PLMD::Atoms | inline |
| kbT | PLMD::Atoms | private |
| massAndChargeOK | PLMD::Atoms | private |
| masses | PLMD::Atoms | private |
| massesHaveBeenSet | PLMD::Atoms | private |
| MD2double(const TypesafePtr &m, double &d) const | PLMD::Atoms | |
| md_energy | PLMD::Atoms | private |
| mdatoms | PLMD::Atoms | private |
| MDnaturalUnits | PLMD::Atoms | private |
| MDUnits | PLMD::Atoms | private |
| natoms | PLMD::Atoms | private |
| naturalUnits | PLMD::Atoms | private |
| pbc | PLMD::Atoms | private |
| pbc_fwd | PLMD::Atoms | private |
| plumed | PLMD::Atoms | private |
| positions | PLMD::Atoms | private |
| positionsHaveBeenSet | PLMD::Atoms | private |
| readBinary(std::istream &) | PLMD::Atoms | |
| remove(ActionAtomistic *) | PLMD::Atoms | |
| removeGroup(const std::string &name) | PLMD::Atoms | |
| removeVirtualAtom(ActionWithVirtualAtom *) | PLMD::Atoms | |
| resetExtraCVNeeded() | PLMD::Atoms | |
| resizeVectors(unsigned) | PLMD::Atoms | private |
| setAtomsContiguous(int) | PLMD::Atoms | |
| setAtomsGatindex(const TypesafePtr &, bool) | PLMD::Atoms | |
| setAtomsNlocal(int) | PLMD::Atoms | |
| setBox(const TypesafePtr &) | PLMD::Atoms | |
| setCharges(const TypesafePtr &) | PLMD::Atoms | |
| setCollectEnergy(bool b) | PLMD::Atoms | inline |
| setDomainDecomposition(Communicator &) | PLMD::Atoms | |
| setEnergy(const TypesafePtr &) | PLMD::Atoms | |
| setExtraCV(const std::string &name, const TypesafePtr &p) | PLMD::Atoms | |
| setExtraCVForce(const std::string &name, const TypesafePtr &p) | PLMD::Atoms | |
| setExtraCVNeeded(const std::string &name, bool needed=true) | PLMD::Atoms | |
| setForces(const TypesafePtr &) | PLMD::Atoms | |
| setForces(const TypesafePtr &, int) | PLMD::Atoms | |
| setKbT(const TypesafePtr &) | PLMD::Atoms | |
| setMasses(const TypesafePtr &) | PLMD::Atoms | |
| setMDChargeUnits(double d) | PLMD::Atoms | inline |
| setMDEnergyUnits(double d) | PLMD::Atoms | inline |
| setMDLengthUnits(double d) | PLMD::Atoms | inline |
| setMDMassUnits(double d) | PLMD::Atoms | inline |
| setMDNaturalUnits(bool n) | PLMD::Atoms | inline |
| setMDTimeUnits(double d) | PLMD::Atoms | inline |
| setNatoms(int) | PLMD::Atoms | |
| setNaturalUnits(bool n) | PLMD::Atoms | inline |
| setPositions(const TypesafePtr &) | PLMD::Atoms | |
| setPositions(const TypesafePtr &, int) | PLMD::Atoms | |
| setRealPrecision(int) | PLMD::Atoms | |
| setTimeStep(const TypesafePtr &) | PLMD::Atoms | |
| setUnits(const Units &u) | PLMD::Atoms | inline |
| setVirial(const TypesafePtr &) | PLMD::Atoms | |
| share(const std::vector< AtomNumber > &) | PLMD::Atoms | private |
| share() | PLMD::Atoms | |
| shareAll() | PLMD::Atoms | |
| shuffledAtoms | PLMD::Atoms | private |
| startStep() | PLMD::Atoms | |
| timestep | PLMD::Atoms | private |
| uniq_index | PLMD::Atoms | private |
| unique | PLMD::Atoms | private |
| unique_serial | PLMD::Atoms | private |
| units | PLMD::Atoms | private |
| updateExtraCVForce(const std::string &name, double f) | PLMD::Atoms | |
| updateForces() | PLMD::Atoms | |
| updateUnits() | PLMD::Atoms | |
| usingNaturalUnits() const | PLMD::Atoms | inline |
| virial | PLMD::Atoms | private |
| virialHasBeenSet | PLMD::Atoms | private |
| virtualAtomsActions | PLMD::Atoms | private |
| wait() | PLMD::Atoms | |
| writeBinary(std::ostream &) const | PLMD::Atoms | |
| zeroallforces | PLMD::Atoms | private |
| ~Atoms() | PLMD::Atoms | |
1.8.17