PLMD::multicolvar::ActionVolume Member List

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

accumulateDerivative(const unsigned &ider, const double &df)	PLMD::vesselbase::ActionWithVessel	inlineprotected
Action(const ActionOptions &)	PLMD::Action
ActionAtomistic(const ActionOptions &ao)	PLMD::ActionAtomistic
ActionVolume(const ActionOptions &)	PLMD::multicolvar::ActionVolume
ActionWithInputVessel(const ActionOptions &)	PLMD::vesselbase::ActionWithInputVessel
ActionWithValue(const ActionOptions &ao)	PLMD::ActionWithValue
ActionWithVessel(const ActionOptions &ao)	PLMD::vesselbase::ActionWithVessel
activate()	PLMD::Action	virtual
activateIndexes(const unsigned &, const unsigned &, const std::vector< unsigned > &)	PLMD::vesselbase::ActionWithVessel	inlinevirtual
activateTheseTasks(std::vector< bool > &addtionalTasks)	PLMD::vesselbase::ActionWithVessel
activeAtoms	PLMD::multicolvar::ActionVolume	private
addBoxDerivatives(const Tensor &vir)	PLMD::multicolvar::ActionVolume	inlineprotected
addBridgeForces(const std::vector< double > &bb)	PLMD::vesselbase::ActionWithInputVessel	inlinevirtual
addBridgingVessel(ActionWithVessel *tome)	PLMD::vesselbase::ActionWithVessel	protected
addComponent(const std::string &name)	PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)	PLMD::ActionWithValue
addDependency(Action *)	PLMD::Action
addElementDerivative(const unsigned &, const double &)	PLMD::vesselbase::ActionWithVessel	inline
addElementValue(const unsigned &, const double &)	PLMD::vesselbase::ActionWithVessel	inline
addForcesOnArguments(const std::vector< double > &forces)	PLMD::vesselbase::ActionWithInputVessel	protected
addReferenceAtomDerivatives(const unsigned &iatom, const Vector &der)	PLMD::multicolvar::ActionVolume	inlineprotected
addTaskToList(const unsigned &taskCode)	PLMD::vesselbase::ActionWithVessel	protected
addValue()	PLMD::ActionWithValue
addValueWithDerivatives()	PLMD::ActionWithValue
addVessel(const std::string &name, const std::string &input, const int numlab=0)	PLMD::vesselbase::ActionWithVessel	protected
addVessel(Vessel *vv)	PLMD::vesselbase::ActionWithVessel	protected
apply()	PLMD::multicolvar::ActionVolume	inlinevirtual
applyBridgeForces(const std::vector< double > &bb)	PLMD::multicolvar::ActionVolume	virtual
applyForces()	PLMD::ActionAtomistic
atoms	PLMD::ActionAtomistic	protected
bead	PLMD::multicolvar::ActionVolume	private
bridgeVariable	PLMD::vesselbase::ActionWithVessel	protected
buildDataStashes()	PLMD::vesselbase::ActionWithVessel	virtual
calculate()	PLMD::multicolvar::ActionVolume	inlinevirtual
calculateAllVessels()	PLMD::vesselbase::ActionWithVessel	protected
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)	PLMD::ActionAtomistic
calculateFromPDB(const PDB &)	PLMD::Action
calculateNumberInside(const Vector &cpos, HistogramBead &bead, Vector &derivatives)=0	PLMD::multicolvar::ActionVolume	pure virtual
calculateNumericalDerivatives(ActionWithValue *a=NULL)	PLMD::multicolvar::ActionVolume	virtual
chainRuleForElementDerivatives(const unsigned &, const unsigned &, const double &, Vessel *)	PLMD::vesselbase::ActionWithVessel
chainRuleForElementDerivatives(const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)	PLMD::vesselbase::ActionWithVessel
changeBox(const Tensor &newbox)	PLMD::ActionAtomistic
checkFieldsAllowed()	PLMD::ActionWithValue	inlinevirtual
checkNeedsGradients() const	PLMD::Action	inlinevirtual
PLMD::checkNumericalDerivatives() const	PLMD::Action	inlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const	PLMD::ActionWithValue	inlinevirtual
checkRead()	PLMD::Action
cite(const std::string &s)	PLMD::Action
clearAfterTask()	PLMD::vesselbase::ActionWithVessel	protected
clearDependencies()	PLMD::Action
clearDerivatives()	PLMD::multicolvar::ActionVolume	inlinevirtual
clearDerivativesAfterTask(const unsigned &ider)	PLMD::multicolvar::ActionVolume	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
contributorsAreUnlocked	PLMD::vesselbase::ActionWithVessel	protected
copyOutput(const std::string &name) const	PLMD::ActionWithValue
copyOutput(const unsigned &n) const	PLMD::ActionWithValue
deactivate()	PLMD::Action	inlinevirtual
deactivate_task()	PLMD::multicolvar::ActionVolume	virtual
deactivateAllTasks()	PLMD::vesselbase::ActionWithVessel	protected
deactivateTasksInRange(const unsigned &lower, const unsigned &upper)	PLMD::vesselbase::ActionWithVessel	protected
Dependencies typedef	PLMD::Action
derivativesAreRequired() const	PLMD::vesselbase::ActionWithVessel	inline
doJobsRequiredBeforeTaskList()	PLMD::multicolvar::ActionVolume	virtual
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
fclose(FILE *fp)	PLMD::Action
fflush()	PLMD::Action
files	PLMD::Action
files_iterator typedef	PLMD::Action
finishComputations()	PLMD::vesselbase::ActionWithVessel	virtual
finishTaskListUpdate()	PLMD::multicolvar::ActionVolume	virtual
firsttime	PLMD::multicolvar::ActionVolume	private
fopen(const char *path, const char *mode)	PLMD::Action
getAbsoluteIndex(int i) const	PLMD::ActionAtomistic	inline
getAbsoluteIndexes() const	PLMD::ActionAtomistic	inline
getActiveTask(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getBox() const	PLMD::multicolvar::ActionVolume	inlineprotected
getCharge(int i) const	PLMD::ActionAtomistic	inline
getComponentsList() const	PLMD::ActionWithValue
getComponentsVector() const	PLMD::ActionWithValue
getCurrentNumberOfActiveTasks() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getCurrentPositionInTaskList() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getCurrentTask() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getDependencies() const	PLMD::Action	inline
getDocumentation() const	PLMD::Action	virtual
getElementDerivative(const unsigned &) const	PLMD::vesselbase::ActionWithVessel	inline
getElementValue(const unsigned &ival) const	PLMD::vesselbase::ActionWithVessel	inline
getEnergy() const	PLMD::ActionAtomistic	inline
getExchangeStep() const	PLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)	PLMD::vesselbase::ActionWithVessel	protected
getFullNumberOfTasks() const	PLMD::vesselbase::ActionWithVessel	inline
getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)	PLMD::vesselbase::ActionWithVessel	virtual
getLabel() const	PLMD::Action	inline
getMass(int i) const	PLMD::ActionAtomistic	inline
getName() const	PLMD::Action	inline
getNLTolerance() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getNumberOfAtoms() const	PLMD::ActionAtomistic	inline
getNumberOfComponents() const	PLMD::ActionWithValue	inline
getNumberOfDerivatives()	PLMD::multicolvar::ActionVolume	inlinevirtual
getNumberOfQuantities()	PLMD::multicolvar::ActionVolume	inlinevirtual
getNumberOfVessels() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getOutputQuantity(const unsigned j) const	PLMD::ActionWithValue	inline
getOutputQuantity(const std::string &name) const	PLMD::ActionWithValue	inline
getPbc() const	PLMD::multicolvar::ActionVolume	inlineprotected
getPntrToArgument()	PLMD::vesselbase::ActionWithInputVessel	inlineprotected
getPntrToComponent(int i)	PLMD::ActionWithValue	protected
getPntrToComponent(const std::string &name)	PLMD::ActionWithValue	protected
getPntrToMultiColvar()	PLMD::multicolvar::ActionVolume	inlineprotected
getPntrToValue()	PLMD::ActionWithValue	protected
getPntrToVessel(const unsigned &i)	PLMD::vesselbase::ActionWithVessel	inlineprotected
getPosition(int iatom)	PLMD::multicolvar::ActionVolume	inlineprotected
PLMD::ActionAtomistic::getPosition(int) const	PLMD::ActionAtomistic	inline
PLMD::ActionAtomistic::getPosition(AtomNumber) const	PLMD::ActionAtomistic	inline
getPositionInFullTaskList(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getPositions() const	PLMD::ActionAtomistic	inline
getSigma() const	PLMD::multicolvar::ActionVolume	inlineprotected
getStep() const	PLMD::Action
getTime() const	PLMD::Action
getTimeStep() const	PLMD::Action
getTolerance() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getTotAtoms() const	PLMD::ActionAtomistic	inline
getUnique() const	PLMD::ActionAtomistic	inline
getVesselWithName(const std::string &mynam)	PLMD::vesselbase::ActionWithVessel
isActive() const	PLMD::Action	inline
isOptionOn(const std::string &s) const	PLMD::Action	inline
isPeriodic()	PLMD::multicolvar::ActionVolume	virtual
keywords	PLMD::Action
lockContributors()	PLMD::vesselbase::ActionWithVessel
lockRequests()	PLMD::ActionAtomistic	inlinevirtual
log	PLMD::Action
mergeDerivatives(const unsigned &ider, const double &df)	PLMD::multicolvar::ActionVolume	virtual
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
MultiColvarBase class	PLMD::multicolvar::ActionVolume	friend
myBridgeVessel	PLMD::multicolvar::ActionVolume	private
mycolv	PLMD::multicolvar::ActionVolume	private
needsDerivatives()	PLMD::vesselbase::ActionWithVessel	protected
noAnalyticalDerivatives(Keywords &keys)	PLMD::ActionWithValue	static
not_in	PLMD::multicolvar::ActionVolume	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
pbcDistance(const Vector &v1, const Vector &v2) const	PLMD::multicolvar::ActionVolume	inlineprotected
performTask()	PLMD::multicolvar::ActionVolume	virtual
plumed	PLMD::Action
prepare()	PLMD::multicolvar::ActionVolume	virtual
readArgument(const std::string &type)	PLMD::vesselbase::ActionWithInputVessel	protected
readAtomsFromPDB(const PDB &pdb)	PLMD::ActionAtomistic	virtual
readVesselKeywords()	PLMD::vesselbase::ActionWithVessel	protected
registerKeywords(Keywords &keys)	PLMD::multicolvar::ActionVolume	static
requestAtoms(const std::vector< AtomNumber > &atoms)	PLMD::multicolvar::ActionVolume	protected
resizeFunctions()	PLMD::vesselbase::ActionWithVessel	protected
retrieveAtoms()	PLMD::ActionAtomistic
retrieveDomain(std::string &min, std::string &max)	PLMD::vesselbase::ActionWithVessel	virtual
runAllTasks()	PLMD::vesselbase::ActionWithVessel	protected
runFinalJobs()	PLMD::Action	inlinevirtual
serialCalculation() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
setElementDerivative(const unsigned &, const double &)	PLMD::vesselbase::ActionWithVessel	inline
setElementValue(const unsigned &, const double &)	PLMD::vesselbase::ActionWithVessel	inline
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)	PLMD::ActionAtomistic
setGradientsIfNeeded()	PLMD::ActionWithValue
setLowMemOption(const bool &)	PLMD::vesselbase::ActionWithVessel	inlineprotected
setMaximumNumberOfDerivatives(const unsigned &)	PLMD::vesselbase::ActionWithVessel	protected
setNotPeriodic()	PLMD::ActionWithValue
setOption(const std::string &s)	PLMD::Action	virtual
setPeriodic(const std::string &min, const std::string &max)	PLMD::ActionWithValue
setupRegion()=0	PLMD::multicolvar::ActionVolume	pure virtual
setValue(const double &d)	PLMD::ActionWithValue	inlineprotected
setValue(Value *, double)	PLMD::ActionWithValue
sigma	PLMD::multicolvar::ActionVolume	private
thisval_wasset	PLMD::vesselbase::ActionWithVessel	protected
tmp_p	PLMD::multicolvar::ActionVolume	private
tmpforces	PLMD::multicolvar::ActionVolume	private
turnOnDerivatives()	PLMD::multicolvar::ActionVolume	virtual
unlockContributors()	PLMD::vesselbase::ActionWithVessel
unlockRequests()	PLMD::ActionAtomistic	inlinevirtual
update()	PLMD::Action	inlinevirtual
updateFreq	PLMD::multicolvar::ActionVolume	private
useCustomisableComponents(Keywords &keys)	PLMD::ActionWithValue	static
useNumericalDerivatives()	PLMD::ActionWithValue	inline
usingLowMem() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
warning(const std::string &msg)	PLMD::Action
weightHasDerivatives	PLMD::vesselbase::ActionWithVessel	protected
~Action()	PLMD::Action	virtual
~ActionAtomistic()	PLMD::ActionAtomistic
~ActionWithInputVessel()	PLMD::vesselbase::ActionWithInputVessel	inlinevirtual
~ActionWithValue()	PLMD::ActionWithValue
~ActionWithVessel()	PLMD::vesselbase::ActionWithVessel