PLMD::generic::WholeMolecules Member List

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

Action(const ActionOptions &)	PLMD::Action
ActionAtomistic(const ActionOptions &ao)	PLMD::ActionAtomistic
ActionPilot(const ActionOptions &)	PLMD::ActionPilot
activate()	PLMD::Action	virtual
addDependency(Action *)	PLMD::Action
apply()	PLMD::generic::WholeMolecules	inlinevirtual
applyForces()	PLMD::ActionAtomistic
atoms	PLMD::ActionAtomistic	protected
calculate()	PLMD::generic::WholeMolecules	virtual
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
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
getStep() const	PLMD::Action
getStride() const	PLMD::ActionPilot	protected
getTime() const	PLMD::Action
getTimeStep() const	PLMD::Action
getTotAtoms() const	PLMD::ActionAtomistic	inline
getUnique() const	PLMD::ActionAtomistic	inline
groups	PLMD::generic::WholeMolecules	private
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
onStep() const	PLMD::ActionPilot
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
PLMD::readAtomsFromPDB(const PDB &)	PLMD::Action	inlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb)	PLMD::ActionAtomistic	virtual
registerKeywords(Keywords &keys)	PLMD::generic::WholeMolecules	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
PLMD::unlockRequests()	PLMD::Action	inlinevirtual
PLMD::ActionAtomistic::unlockRequests()	PLMD::ActionAtomistic	inlinevirtual
update()	PLMD::Action	inlinevirtual
warning(const std::string &msg)	PLMD::Action
WholeMolecules(const ActionOptions &ao)	PLMD::generic::WholeMolecules
~Action()	PLMD::Action	virtual
~ActionAtomistic()	PLMD::ActionAtomistic