PLMD::Atoms Member List

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

ActionAtomistic classPLMD::Atomsfriend
actionsPLMD::Atomsprivate
ActionWithVirtualAtom classPLMD::Atomsfriend
add(ActionAtomistic *)PLMD::Atoms
addVirtualAtom(ActionWithVirtualAtom *)PLMD::Atoms
asyncSentPLMD::Atomsprivate
Atoms(PlumedMain &plumed)PLMD::Atomsexplicit
atomsNeededPLMD::Atomsprivate
boxPLMD::Atomsprivate
boxHasBeenSetPLMD::Atomsprivate
boxWasSet() constPLMD::Atomsinline
chargesPLMD::Atomsprivate
chargesHaveBeenSetPLMD::Atomsprivate
chargesWereSet() constPLMD::Atomsinline
clearFullList()PLMD::Atoms
collectEnergyPLMD::Atomsprivate
createFullList(int *)PLMD::Atoms
dataCanBeSetPLMD::Atomsprivate
ddPLMD::Atomsprivate
ddStepPLMD::Atomsprivate
double2MD(const double &d, void *m) constPLMD::Atoms
energyPLMD::Atomsprivate
energyHasBeenSetPLMD::Atomsprivate
forceOnEnergyPLMD::Atomsprivate
forcesPLMD::Atomsprivate
forcesHaveBeenSetPLMD::Atomsprivate
fullListPLMD::Atomsprivate
g2lPLMD::Atomsprivate
gatindexPLMD::Atomsprivate
getDdStep() constPLMD::Atomsinline
getEnergy() constPLMD::Atomsinline
getFullList(int **)PLMD::Atoms
getGatindex() constPLMD::Atomsinline
getKBoltzmann() constPLMD::Atoms
getKbT() constPLMD::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() constPLMD::Atoms
getMDUnits()PLMD::Atomsinline
getNatoms() constPLMD::Atomsinline
getPbc() constPLMD::Atomsinline
getRealPrecision() constPLMD::Atoms
getTimeStep() constPLMD::Atoms
getUnits()PLMD::Atomsinline
getVirial() constPLMD::Atomsinline
getVirtualAtomsAction(AtomNumber) constPLMD::Atomsinline
groupsPLMD::Atomsprivate
init()PLMD::Atoms
insertGroup(const std::string &name, const std::vector< AtomNumber > &a)PLMD::Atoms
isEnergyNeeded() constPLMD::Atomsinline
isVirtualAtom(AtomNumber) constPLMD::Atomsinline
kbTPLMD::Atomsprivate
massAndChargeOKPLMD::Atomsprivate
massesPLMD::Atomsprivate
massesHaveBeenSetPLMD::Atomsprivate
MD2double(const void *m, double &d) constPLMD::Atoms
md_energyPLMD::Atomsprivate
mdatomsPLMD::Atomsprivate
MDnaturalUnitsPLMD::Atomsprivate
MDUnitsPLMD::Atomsprivate
natomsPLMD::Atomsprivate
naturalUnitsPLMD::Atomsprivate
pbcPLMD::Atomsprivate
plumedPLMD::Atomsprivate
positionsPLMD::Atomsprivate
positionsHaveBeenSetPLMD::Atomsprivate
readBinary(std::istream &)PLMD::Atoms
remove(ActionAtomistic *)PLMD::Atoms
removeGroup(const std::string &name)PLMD::Atoms
removeVirtualAtom(ActionWithVirtualAtom *)PLMD::Atoms
resizeVectors(unsigned)PLMD::Atomsprivate
setAtomsContiguous(int)PLMD::Atoms
setAtomsGatindex(int *, bool)PLMD::Atoms
setAtomsNlocal(int)PLMD::Atoms
setBox(void *)PLMD::Atoms
setCharges(void *)PLMD::Atoms
setCollectEnergy(bool b)PLMD::Atomsinline
setDomainDecomposition(Communicator &)PLMD::Atoms
setEnergy(void *)PLMD::Atoms
setForces(void *)PLMD::Atoms
setForces(void *, int)PLMD::Atoms
setKbT(void *)PLMD::Atoms
setMasses(void *)PLMD::Atoms
setMDChargeUnits(double d)PLMD::Atomsinline
setMDEnergyUnits(double d)PLMD::Atomsinline
setMDLengthUnits(double d)PLMD::Atomsinline
setMDMassUnits(double d)PLMD::Atomsinline
setMDNaturalUnits(bool n)PLMD::Atomsinline
setMDTimeUnits(double d)PLMD::Atomsinline
setNatoms(int)PLMD::Atoms
setNaturalUnits(bool n)PLMD::Atomsinline
setPositions(void *)PLMD::Atoms
setPositions(void *, int)PLMD::Atoms
setRealPrecision(int)PLMD::Atoms
setTimeStep(void *)PLMD::Atoms
setUnits(const Units &u)PLMD::Atomsinline
setVirial(void *)PLMD::Atoms
share(const std::set< AtomNumber > &)PLMD::Atomsprivate
share()PLMD::Atoms
shareAll()PLMD::Atoms
shuffledAtomsPLMD::Atomsprivate
startStep()PLMD::Atoms
timestepPLMD::Atomsprivate
uniq_indexPLMD::Atomsprivate
uniquePLMD::Atomsprivate
unitsPLMD::Atomsprivate
updateForces()PLMD::Atoms
updateUnits()PLMD::Atoms
usingNaturalUnits() constPLMD::Atomsinline
virialPLMD::Atomsprivate
virialHasBeenSetPLMD::Atomsprivate
virtualAtomsActionsPLMD::Atomsprivate
wait()PLMD::Atoms
writeBinary(std::ostream &) constPLMD::Atoms
zeroallforcesPLMD::Atomsprivate
~Atoms()PLMD::Atoms