PLMD::vatom::Center Member List

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

Action(const ActionOptions &)	PLMD::Action	explicit
Action(const Action &a)=delete	PLMD::Action	private
ActionAtomistic(const ActionOptions &ao)	PLMD::ActionAtomistic	explicit
ActionWithVirtualAtom(const ActionOptions &ao)	PLMD::ActionWithVirtualAtom	explicit
activate()	PLMD::Action	virtual
active	PLMD::Action	private
addDependency(Action *)	PLMD::Action
after	PLMD::Action	private
allowToAccessGlobalForces()	PLMD::ActionAtomistic	inline
apply() override	PLMD::ActionWithVirtualAtom	privatevirtual
applyForces()	PLMD::ActionAtomistic
atoms	PLMD::ActionAtomistic	protected
beforeUpdate()	PLMD::Action	inlinevirtual
boxDerivatives	PLMD::ActionWithVirtualAtom	private
calculate() override	PLMD::vatom::Center	virtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)	PLMD::ActionAtomistic
calculateFromPDB(const PDB &)	PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) override	PLMD::ActionAtomistic	virtual
Center(const ActionOptions &ao)	PLMD::vatom::Center	explicit
changeBox(const Tensor &newbox)	PLMD::ActionAtomistic
charge_	PLMD::vatom::Center	private
charges	PLMD::ActionAtomistic	private
chargesWereSet	PLMD::ActionAtomistic	private
checkNeedsGradients() const	PLMD::Action	inlinevirtual
checkNumericalDerivatives() const	PLMD::Action	inlinevirtual
checkRead()	PLMD::Action
checkUpdate() const	PLMD::Action
cite(const std::string &s)	PLMD::Action
clearDependencies()	PLMD::Action
clearOptions()	PLMD::Action	virtual
clearOutputForces()	PLMD::ActionAtomistic
comm	PLMD::Action
dcenter_cos	PLMD::vatom::Center	private
dcenter_sin	PLMD::vatom::Center	private
deactivate()	PLMD::Action	inlinevirtual
defaults	PLMD::Action	private
Dependencies typedef	PLMD::Action
derivatives	PLMD::ActionWithVirtualAtom	private
doCheckPoint	PLMD::Action	private
doNotForce()	PLMD::ActionAtomistic	inline
donotforce	PLMD::ActionAtomistic	private
doNotRetrieve()	PLMD::ActionAtomistic	inline
donotretrieve	PLMD::ActionAtomistic	private
energy	PLMD::ActionAtomistic	private
error(const std::string &msg) const	PLMD::Action
exit(int c=0)	PLMD::Action
extraCV	PLMD::ActionAtomistic	private
fclose(FILE *fp)	PLMD::Action
fflush()	PLMD::Action
files	PLMD::Action
first	PLMD::vatom::Center	private
fopen(const char *path, const char *mode)	PLMD::Action
forceOnEnergy	PLMD::ActionAtomistic	private
forceOnExtraCV	PLMD::ActionAtomistic	private
forces	PLMD::ActionAtomistic	private
getAbsoluteIndex(int i) const	PLMD::ActionAtomistic	inline
getAbsoluteIndexes() const	PLMD::ActionAtomistic	inlinevirtual
getBox() const	PLMD::ActionAtomistic	inline
getCharge(int i) const	PLMD::ActionAtomistic	inline
getCPT() const	PLMD::Action
getDefaultString() const	PLMD::Action	inline
getDependencies() const	PLMD::Action	inline
getEnergy() const	PLMD::ActionAtomistic	inline
getExchangeStep() const	PLMD::Action
getGlobalPosition(AtomNumber) const	PLMD::ActionAtomistic	inline
getGradients() const	PLMD::ActionWithVirtualAtom	inline
getIndex() const	PLMD::ActionWithVirtualAtom	inline
getKeyword(const std::string &key)	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
getPositions() const	PLMD::ActionAtomistic	inline
getRestart() const	PLMD::Action	inline
getStep() const	PLMD::Action
getTime() const	PLMD::Action
getTimeStep() const	PLMD::Action
getTotAtoms() const	PLMD::ActionAtomistic	inline
getUnique() const	PLMD::ActionAtomistic	inline
getUniqueLocal() const	PLMD::ActionAtomistic	inline
gradients	PLMD::ActionWithVirtualAtom	private
index	PLMD::ActionWithVirtualAtom	private
indexes	PLMD::ActionAtomistic	private
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)	PLMD::ActionAtomistic
isActive() const	PLMD::Action	inline
isChargeSet_	PLMD::vatom::Center	private
isMassSet_	PLMD::vatom::Center	private
isOptionOn(const std::string &s) const	PLMD::Action	inline
keywords	PLMD::Action
label	PLMD::Action	private
line	PLMD::Action	private
lockRequestAtoms	PLMD::ActionAtomistic	private
lockRequests() override	PLMD::ActionAtomistic	inlinevirtual
log	PLMD::Action
makeWhole()	PLMD::ActionAtomistic
mass_	PLMD::vatom::Center	private
masses	PLMD::ActionAtomistic	private
modifyForceOnEnergy()	PLMD::ActionAtomistic	inline
modifyForceOnExtraCV()	PLMD::ActionAtomistic	inline
modifyForces()	PLMD::ActionAtomistic	inline
modifyGlobalForce(AtomNumber)	PLMD::ActionAtomistic	inline
modifyGlobalPbc()	PLMD::ActionAtomistic	inline
modifyGlobalPosition(AtomNumber)	PLMD::ActionAtomistic	inline
modifyGlobalVirial()	PLMD::ActionAtomistic	inline
modifyVirial()	PLMD::ActionAtomistic	inline
multi_sim_comm	PLMD::Action
name	PLMD::Action	private
nopbc	PLMD::vatom::Center	private
operator=(const Action &a)=delete	PLMD::Action	private
options	PLMD::Action	private
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
pbc	PLMD::ActionAtomistic	private
pbc_fwd	PLMD::ActionAtomistic	private
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const	PLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) const	PLMD::ActionAtomistic
phases	PLMD::vatom::Center	private
plumed	PLMD::Action
positions	PLMD::ActionAtomistic	private
prepare()	PLMD::Action	virtual
readAtomsFromPDB(const PDB &pdb) override	PLMD::ActionAtomistic	virtual
registerKeywords(Keywords &keys)	PLMD::vatom::Center	static
replica_index	PLMD::Action	private
requestAtoms(const std::vector< AtomNumber > &a)	PLMD::ActionWithVirtualAtom	protected
PLMD::ActionAtomistic::requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)	PLMD::ActionAtomistic
restart	PLMD::Action	private
retrieveAtoms()	PLMD::ActionAtomistic	virtual
runFinalJobs()	PLMD::Action	inlinevirtual
setAtomsDerivatives(const std::vector< Tensor > &d)	PLMD::ActionWithVirtualAtom	inlineprotected
setBoxDerivatives(const std::array< Tensor, 3 > &d)	PLMD::ActionWithVirtualAtom	protected
setBoxDerivativesNoPbc()	PLMD::ActionWithVirtualAtom	protected
setCharge(double)	PLMD::ActionWithVirtualAtom	inlineprotected
setExtraCV(const std::string &name)	PLMD::ActionAtomistic	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
unique	PLMD::ActionAtomistic	private
unique_local	PLMD::ActionAtomistic	private
unlockRequests() override	PLMD::ActionAtomistic	inlinevirtual
update()	PLMD::Action	inlinevirtual
update_from	PLMD::Action	private
update_until	PLMD::Action	private
updateUniqueLocal()	PLMD::ActionAtomistic
virial	PLMD::ActionAtomistic	private
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