PLMD::mapping::PCAVars Member List

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

Action(const ActionOptions &)	PLMD::Action	explicit
ActionAtomistic(const ActionOptions &ao)	PLMD::ActionAtomistic	explicit
ActionWithArguments(const ActionOptions &)	PLMD::ActionWithArguments	explicit
ActionWithValue(const ActionOptions &ao)	PLMD::ActionWithValue	explicit
activate()	PLMD::Action	virtual
addComponent(const std::string &name)	PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)	PLMD::ActionWithValue
addDependency(Action *)	PLMD::Action
addForcesOnArguments(const std::vector< double > &forces)	PLMD::ActionWithArguments
addValue()	PLMD::ActionWithValue
addValueWithDerivatives()	PLMD::ActionWithValue
allowToAccessGlobalForces()	PLMD::ActionAtomistic	inline
apply()	PLMD::mapping::PCAVars	virtual
applyForces()	PLMD::ActionAtomistic
arg_eigv	PLMD::mapping::PCAVars	private
atom_eigv	PLMD::mapping::PCAVars	private
atoms	PLMD::ActionAtomistic	protected
bringBackInPbc(int i, double d1) const	PLMD::ActionWithArguments	inline
calculate()	PLMD::mapping::PCAVars	virtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)	PLMD::ActionAtomistic
calculateFromPDB(const PDB &)	PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a)	PLMD::mapping::PCAVars	virtual
changeBox(const Tensor &newbox)	PLMD::ActionAtomistic
checkFieldsAllowed()	PLMD::ActionWithValue	inlinevirtual
checkNeedsGradients() const	PLMD::Action	inlinevirtual
checkNumericalDerivatives() const	PLMD::ActionWithValue	inlinevirtual
checkRead()	PLMD::Action
checkUpdate() const	PLMD::Action
cite(const std::string &s)	PLMD::Action
clearDependencies()	PLMD::Action
clearDerivatives()	PLMD::ActionWithValue	virtual
clearInputForces()	PLMD::ActionWithValue
clearOptions()	PLMD::Action	virtual
clearOutputForces()	PLMD::ActionAtomistic
comm	PLMD::Action
componentIsNotPeriodic(const std::string &name)	PLMD::ActionWithValue
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max)	PLMD::ActionWithValue
componentsAreNotOptional(Keywords &keys)	PLMD::ActionWithValue	static
copyOutput(const std::string &name) const	PLMD::ActionWithValue
copyOutput(const unsigned &n) const	PLMD::ActionWithValue
deactivate()	PLMD::Action	inlinevirtual
Dependencies typedef	PLMD::Action
difference(int, double, double) const	PLMD::ActionWithArguments	inline
doNotCalculateDerivatives() const	PLMD::ActionWithValue	inline
doNotForce()	PLMD::ActionAtomistic	inline
doNotRetrieve()	PLMD::ActionAtomistic	inline
error(const std::string &msg) const	PLMD::Action
exists(const std::string &name) const	PLMD::ActionWithValue
exit(int c=0)	PLMD::Action
expandArgKeywordInPDB(PDB &pdb)	PLMD::ActionWithArguments	protected
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
forces	PLMD::mapping::PCAVars	private
forcesToApply	PLMD::mapping::PCAVars	private
getAbsoluteIndex(int i) const	PLMD::ActionAtomistic	inline
getAbsoluteIndexes() const	PLMD::ActionAtomistic	inline
getArgument(const unsigned n) const	PLMD::ActionWithArguments	inline
getArguments() const	PLMD::ActionWithArguments	inline
getBox() const	PLMD::ActionAtomistic	inline
getCharge(int i) const	PLMD::ActionAtomistic	inline
getComponentsList() const	PLMD::ActionWithValue
getComponentsVector() const	PLMD::ActionWithValue
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
getNumberOfArguments() const	PLMD::ActionWithArguments	inline
getNumberOfAtoms() const	PLMD::ActionAtomistic	inline
getNumberOfComponents() const	PLMD::ActionWithValue	inline
getNumberOfDerivatives()	PLMD::mapping::PCAVars	virtual
getOutputQuantity(const unsigned j) const	PLMD::ActionWithValue	inline
getOutputQuantity(const std::string &name) const	PLMD::ActionWithValue	inline
getPbc() const	PLMD::ActionAtomistic	inline
getPntrToArgument(const unsigned n)	PLMD::ActionWithArguments	inline
getPntrToComponent(int i)	PLMD::ActionWithValue	protected
getPntrToComponent(const std::string &name)	PLMD::ActionWithValue	protected
getPntrToValue()	PLMD::ActionWithValue	protected
getPosition(int) const	PLMD::ActionAtomistic	inline
getPosition(AtomNumber) const	PLMD::ActionAtomistic	inline
getPositions() const	PLMD::ActionAtomistic	inline
getProjection(unsigned i, unsigned j) const	PLMD::ActionWithArguments
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
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)	PLMD::ActionWithArguments
isActive() const	PLMD::Action	inline
isOptionOn(const std::string &s) const	PLMD::Action	inline
keywords	PLMD::Action
lockRequests()	PLMD::mapping::PCAVars	virtual
log	PLMD::Action
makeWhole()	PLMD::ActionAtomistic
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
mypack	PLMD::mapping::PCAVars	private
myref	PLMD::mapping::PCAVars	private
myvals	PLMD::mapping::PCAVars	private
noAnalyticalDerivatives(Keywords &keys)	PLMD::ActionWithValue	static
parse(const std::string &key, T &t)	PLMD::Action
parseArgumentList(const std::string &key, std::vector< Value * > &args)	PLMD::ActionWithArguments
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
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const	PLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) const	PLMD::ActionAtomistic
PCAVars(const ActionOptions &)	PLMD::mapping::PCAVars	explicit
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::mapping::PCAVars	static
requestArguments(const std::vector< Value * > &arg)	PLMD::ActionWithArguments
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
setGradientsIfNeeded()	PLMD::ActionWithValue
setNotPeriodic()	PLMD::ActionWithValue
setOption(const std::string &s)	PLMD::Action	virtual
setPeriodic(const std::string &min, const std::string &max)	PLMD::ActionWithValue
setValue(const double &d)	PLMD::ActionWithValue	inlineprotected
setValue(Value *, double)	PLMD::ActionWithValue
turnOnDerivatives()	PLMD::ActionWithValue	virtual
unlockRequests()	PLMD::mapping::PCAVars	virtual
update()	PLMD::Action	inlinevirtual
useCustomisableComponents(Keywords &keys)	PLMD::ActionWithValue	static
useNumericalDerivatives()	PLMD::ActionWithValue	inline
warning(const std::string &msg)	PLMD::Action
~Action()	PLMD::Action	virtual
~ActionAtomistic()	PLMD::ActionAtomistic
~ActionWithArguments()	PLMD::ActionWithArguments	inlinevirtual
~ActionWithValue()	PLMD::ActionWithValue
~PCAVars()	PLMD::mapping::PCAVars