PLMD::crystallization::Q3 Member List

This is the complete list of members for PLMD::crystallization::Q3, including all inherited members.

ablocks	PLMD::multicolvar::MultiColvarBase	protected
Action(const ActionOptions &)	PLMD::Action	explicit
ActionAtomistic(const ActionOptions &ao)	PLMD::ActionAtomistic	explicit
ActionWithValue(const ActionOptions &ao)	PLMD::ActionWithValue	explicit
ActionWithVessel(const ActionOptions &ao)	PLMD::vesselbase::ActionWithVessel	explicit
activate()	PLMD::Action	virtual
activateTheseTasks(std::vector< unsigned > &addtionalTasks)	PLMD::vesselbase::ActionWithVessel
addBridgingVessel(ActionWithVessel *tome)	PLMD::vesselbase::ActionWithVessel	protected
addColvar(const std::vector< unsigned > &newatoms)	PLMD::multicolvar::MultiColvar	protected
addComponent(const std::string &name)	PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)	PLMD::ActionWithValue
addDependency(Action *)	PLMD::Action
addForcesOnAtoms(const std::vector< double > &inforces)	PLMD::crystallization::VectorMultiColvar	protected
addTaskToList(const unsigned &taskCode)	PLMD::multicolvar::MultiColvarBase	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
allowToAccessGlobalForces()	PLMD::ActionAtomistic	inline
apply()	PLMD::multicolvar::MultiColvarBase	virtual
applyBridgeForces(const std::vector< double > &bb)	PLMD::vesselbase::ActionWithVessel	inlinevirtual
applyForces()	PLMD::ActionAtomistic
applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) const	PLMD::multicolvar::MultiColvarBase
atoms	PLMD::ActionAtomistic	protected
bridgeVariable	PLMD::vesselbase::ActionWithVessel	protected
buildDataStashes(const bool &allow_wcutoff, const double &wtol)	PLMD::vesselbase::ActionWithVessel
calculate()	PLMD::multicolvar::MultiColvar	virtual
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)	PLMD::vesselbase::ActionWithVessel	protected
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)	PLMD::ActionAtomistic
calculateFromPDB(const PDB &)	PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)	PLMD::ActionAtomistic	virtual
calculateVector(multicolvar::AtomValuePack &myatoms) const	PLMD::crystallization::Steinhardt	virtual
calculateWeight(AtomValuePack &myatoms) const	PLMD::multicolvar::MultiColvarBase	virtual
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
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
coeff_poly	PLMD::crystallization::Steinhardt	protected
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
compute(const unsigned &tindex, multicolvar::AtomValuePack &myatoms) const	PLMD::crystallization::VectorMultiColvar	inlinevirtual
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(const unsigned &task_index)	PLMD::vesselbase::ActionWithVessel	virtual
deactivateAllTasks()	PLMD::vesselbase::ActionWithVessel	protected
deactivateTasksInRange(const unsigned &lower, const unsigned &upper)	PLMD::vesselbase::ActionWithVessel	protected
decodeIndexToAtoms(const unsigned &taskCode, std::vector< unsigned > &atoms) const	PLMD::multicolvar::MultiColvarBase	protected
decoder	PLMD::multicolvar::MultiColvarBase	protected
Dependencies typedef	PLMD::Action
deriv_poly(const unsigned &, const double &, double &) const	PLMD::crystallization::Steinhardt
derivativesAreRequired() const	PLMD::vesselbase::ActionWithVessel	inline
doCalculation(const unsigned &taskIndex, multicolvar::AtomValuePack &myatoms) const	PLMD::crystallization::VectorMultiColvar	virtual
doJobsRequiredBeforeTaskList()	PLMD::vesselbase::ActionWithVessel	virtual
doNotCalculateDerivatives() const	PLMD::ActionWithValue	inline
doNotCalculateDirector()	PLMD::crystallization::VectorMultiColvar	virtual
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(const std::vector< double > &buffer)	PLMD::vesselbase::ActionWithVessel	virtual
finishTaskListUpdate()	PLMD::vesselbase::ActionWithVessel	inlinevirtual
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::ActionAtomistic	inline
getCentralAtomPack(const unsigned &basn, const unsigned &curr)	PLMD::multicolvar::MultiColvarBase	virtual
getCentralAtomPos(const unsigned &curr)	PLMD::multicolvar::MultiColvarBase	virtual
getCharge(int i) const	PLMD::ActionAtomistic	inline
getComponentsList() const	PLMD::ActionWithValue
getComponentsVector() const	PLMD::ActionWithValue
getCurrentNumberOfActiveTasks() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getDependencies() const	PLMD::Action	inline
getDocumentation() const	PLMD::Action	virtual
getEnergy() const	PLMD::ActionAtomistic	inline
getExchangeStep() const	PLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)	PLMD::vesselbase::ActionWithVessel	protected
getFullNumberOfTasks() const	PLMD::vesselbase::ActionWithVessel	inline
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
getNumberOfComponentsInVector() const	PLMD::crystallization::VectorMultiColvar	inline
getNumberOfDerivatives()	PLMD::multicolvar::MultiColvarBase	inlinevirtual
getNumberOfQuantities()	PLMD::crystallization::VectorMultiColvar	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::ActionAtomistic	inline
getPntrToComponent(int i)	PLMD::ActionWithValue	protected
getPntrToComponent(const std::string &name)	PLMD::ActionWithValue	protected
getPntrToValue()	PLMD::ActionWithValue	protected
getPntrToVessel(const unsigned &i)	PLMD::vesselbase::ActionWithVessel	inlineprotected
getPosition(unsigned) const	PLMD::multicolvar::MultiColvar
PLMD::multicolvar::MultiColvarBase::getPosition(int) const	PLMD::ActionAtomistic	inline
PLMD::multicolvar::MultiColvarBase::getPosition(AtomNumber) const	PLMD::ActionAtomistic	inline
getPositionInFullTaskList(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inline
getPositionOfAtomForLinkCells(const unsigned &iatom) const	PLMD::multicolvar::MultiColvar	inlinevirtual
getPositions() const	PLMD::ActionAtomistic	inline
getRestart() const	PLMD::Action	inline
getSeparation(const Vector &vec1, const Vector &vec2) const	PLMD::multicolvar::MultiColvarBase	protected
getSizeOfBuffer(unsigned &bufsize)	PLMD::vesselbase::ActionWithVessel	protected
getStep() const	PLMD::Action
getTaskCode(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inline
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
hasDifferentiableOrientation() const	PLMD::crystallization::VectorMultiColvar	inlinevirtual
isActive() const	PLMD::Action	inline
isCurrentlyActive(const unsigned &bno, const unsigned &code)	PLMD::multicolvar::MultiColvar	inlinevirtual
isDensity() const	PLMD::multicolvar::MultiColvarBase	inlinevirtual
isOptionOn(const std::string &s) const	PLMD::Action	inline
isPeriodic()	PLMD::crystallization::VectorMultiColvar	inlinevirtual
keywords	PLMD::Action
lockContributors()	PLMD::vesselbase::ActionWithVessel
lockRequests()	PLMD::ActionAtomistic	inlinevirtual
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
MultiColvar(const ActionOptions &)	PLMD::multicolvar::MultiColvar	explicit
MultiColvarBase(const ActionOptions &)	PLMD::multicolvar::MultiColvarBase	explicit
nblock	PLMD::multicolvar::MultiColvarBase	protected
needsDerivatives()	PLMD::vesselbase::ActionWithVessel	protected
noAnalyticalDerivatives(Keywords &keys)	PLMD::ActionWithValue	static
normaliz	PLMD::crystallization::Steinhardt	protected
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
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const	PLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) const	PLMD::ActionAtomistic
performTask(const unsigned &, const unsigned &, MultiValue &) const	PLMD::multicolvar::MultiColvarBase	virtual
plumed	PLMD::Action
prepare()	PLMD::Action	virtual
Q3(const ActionOptions &ao)	PLMD::crystallization::Q3	explicit
readAtoms(int &natoms)	PLMD::multicolvar::MultiColvar	protected
readAtomsFromPDB(const PDB &pdb)	PLMD::ActionAtomistic	virtual
readAtomsLikeKeyword(const std::string &key, int &natoms, std::vector< AtomNumber > &all_atoms)	PLMD::multicolvar::MultiColvar	protected
readSpeciesKeyword(const std::string &str1, const std::string &str2, int &natoms, std::vector< AtomNumber > &all_atoms)	PLMD::multicolvar::MultiColvar	protected
readThreeGroups(const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2, std::vector< AtomNumber > &all_atoms)	PLMD::multicolvar::MultiColvar	protected
readTwoGroups(const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms)	PLMD::multicolvar::MultiColvar	protected
readVesselKeywords()	PLMD::vesselbase::ActionWithVessel	protected
registerKeywords(Keywords &keys)	PLMD::crystallization::Q3	static
requestAtoms(const std::vector< AtomNumber > &a)	PLMD::ActionAtomistic
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
setAngularMomentum(const unsigned &ang)	PLMD::crystallization::Steinhardt	protected
setAtomsForCentralAtom(const std::vector< bool > &catom_ind)	PLMD::multicolvar::MultiColvarBase	protected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)	PLMD::ActionAtomistic
setGradientsIfNeeded()	PLMD::ActionWithValue
setLinkCellCutoff(const double &lcut)	PLMD::multicolvar::MultiColvarBase	protected
setLowMemOption(const bool &)	PLMD::vesselbase::ActionWithVessel	inlineprotected
setNotPeriodic()	PLMD::ActionWithValue
setOption(const std::string &s)	PLMD::Action	virtual
setPeriodic(const std::string &min, const std::string &max)	PLMD::ActionWithValue
setupCurrentAtomList(const unsigned &taskCode, AtomValuePack &myatoms) const	PLMD::multicolvar::MultiColvarBase	protected
setupLinkCells()	PLMD::multicolvar::MultiColvarBase	protected
setupMultiColvarBase()	PLMD::multicolvar::MultiColvarBase	protected
setValue(const double &d)	PLMD::ActionWithValue	inlineprotected
setValue(Value *, double)	PLMD::ActionWithValue
setVectorDimensionality(const unsigned &, const int &)	PLMD::crystallization::VectorMultiColvar	protected
Steinhardt(const ActionOptions &ao)	PLMD::crystallization::Steinhardt	explicit
storedValueIsActive(const unsigned &iatom)	PLMD::multicolvar::MultiColvarBase
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) const	PLMD::vesselbase::ActionWithVessel	virtual
turnOnDerivatives()	PLMD::multicolvar::MultiColvarBase	virtual
unlockContributors()	PLMD::vesselbase::ActionWithVessel
unlockRequests()	PLMD::ActionAtomistic	inlinevirtual
update()	PLMD::Action	inlinevirtual
updateActiveAtoms(AtomValuePack &myatoms) const	PLMD::multicolvar::MultiColvar	virtual
useCustomisableComponents(Keywords &keys)	PLMD::ActionWithValue	static
useNumericalDerivatives()	PLMD::ActionWithValue	inline
usesPbc() const	PLMD::multicolvar::MultiColvarBase	inline
usespecies	PLMD::multicolvar::MultiColvarBase	protected
usingLowMem() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
VectorMultiColvar(const ActionOptions &)	PLMD::crystallization::VectorMultiColvar	explicit
warning(const std::string &msg)	PLMD::Action
weightHasDerivatives	PLMD::vesselbase::ActionWithVessel	protected
weightWithDerivatives() const	PLMD::vesselbase::ActionWithVessel	inline
~Action()	PLMD::Action	virtual
~ActionAtomistic()	PLMD::ActionAtomistic
~ActionWithValue()	PLMD::ActionWithValue
~ActionWithVessel()	PLMD::vesselbase::ActionWithVessel
~MultiColvar()	PLMD::multicolvar::MultiColvar	inline
~MultiColvarBase()	PLMD::multicolvar::MultiColvarBase	inline
~VectorMultiColvar()	PLMD::crystallization::VectorMultiColvar	inline