PLMD::Atoms Member List

This is the complete list of members for PLMD::Atoms, including all inherited members.

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
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
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
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::set< 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
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