PLMD::multicolvar::Sprint Member List

This is the complete list of members for PLMD::multicolvar::Sprint, 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
addComponent(const std::string &name)	PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)	PLMD::ActionWithValue
addDependency(Action *)	PLMD::Action
addDerivativesOnMatrixElement(const unsigned &ielem, const unsigned &jrow, const double &df, Matrix< double > &der)	PLMD::multicolvar::AdjacencyMatrixAction	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
AdjacencyMatrixAction(const ActionOptions &)	PLMD::multicolvar::AdjacencyMatrixAction	explicit
allowToAccessGlobalForces()	PLMD::ActionAtomistic	inline
apply()	PLMD::multicolvar::Sprint	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
buildAtomListWithPairs(const bool &allow_intra_group)	PLMD::multicolvar::MultiColvarFunction	protected
buildDataStashes(const bool &allow_wcutoff, const double &wtol)	PLMD::vesselbase::ActionWithVessel
buildSets()	PLMD::multicolvar::MultiColvarFunction	protected
buildSymmetryFunctionLists()	PLMD::multicolvar::MultiColvarFunction	protected
calculate()	PLMD::multicolvar::MultiColvarFunction	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::multicolvar::MultiColvarFunction	virtual
calculateWeight(AtomValuePack &myatoms) const	PLMD::multicolvar::AdjacencyMatrixAction	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
comm	PLMD::Action
completeCalculation()	PLMD::multicolvar::Sprint	virtual
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, AtomValuePack &myatoms) const	PLMD::multicolvar::AdjacencyMatrixAction	virtual
contributorsAreUnlocked	PLMD::vesselbase::ActionWithVessel	protected
convertToLocalIndex(const unsigned &index, const unsigned &mcv_code) const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
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
derivativesAreRequired() const	PLMD::vesselbase::ActionWithVessel	inline
doCalculation(const unsigned &tindex, AtomValuePack &myatoms) const	PLMD::multicolvar::MultiColvarBase	virtual
doJobsRequiredBeforeTaskList()	PLMD::multicolvar::AdjacencyMatrixAction	virtual
doNotCalculateDerivatives() const	PLMD::ActionWithValue	inline
doNotCalculateDirector()	PLMD::multicolvar::MultiColvarBase	inlinevirtual
doNotForce()	PLMD::ActionAtomistic	inline
doNotRetrieve()	PLMD::ActionAtomistic	inline
eigenvecs	PLMD::multicolvar::Sprint	private
eigvals	PLMD::multicolvar::Sprint	private
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
getActiveMatrixElement(const unsigned &ival) const	PLMD::multicolvar::AdjacencyMatrixAction	inlineprotected
getActiveTask(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getAdjacencyVessel()	PLMD::multicolvar::AdjacencyMatrixAction	inlineprotected
getBaseColvarNumber(const unsigned &iatom) const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
getBaseMultiColvar(const unsigned &icolv) const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
getBox() const	PLMD::ActionAtomistic	inline
getCentralAtom()	PLMD::multicolvar::AdjacencyMatrixAction	inline
getCentralAtomPack(const unsigned &basn, const unsigned &curr)	PLMD::multicolvar::MultiColvarBase	virtual
getCentralAtomPackFromInput(const unsigned &ind) const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
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
getFullNumberOfBaseTasks() const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
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
getNumberOfActiveMatrixElements()	PLMD::multicolvar::AdjacencyMatrixAction	inlineprotected
getNumberOfAtoms() const	PLMD::ActionAtomistic	inline
getNumberOfBaseMultiColvars() const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
getNumberOfComponents() const	PLMD::ActionWithValue	inline
getNumberOfDerivatives()	PLMD::multicolvar::MultiColvarBase	inlinevirtual
getNumberOfQuantities()	PLMD::vesselbase::ActionWithVessel	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(int) const	PLMD::ActionAtomistic	inline
getPosition(AtomNumber) const	PLMD::ActionAtomistic	inline
getPositionInFullTaskList(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inline
getPositionOfAtomForLinkCells(const unsigned &iatom) const	PLMD::multicolvar::MultiColvarFunction	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
getVectorDerivatives(const unsigned &ind, const bool &normed, MultiValue &myder0) const	PLMD::multicolvar::MultiColvarFunction	protected
getVectorForTask(const unsigned &ind, const bool &normed, std::vector< double > &orient0) const	PLMD::multicolvar::MultiColvarFunction	inlineprotected
getVesselWithName(const std::string &mynam)	PLMD::vesselbase::ActionWithVessel
hasDifferentiableOrientation() const	PLMD::multicolvar::MultiColvarBase	inlinevirtual
isActive() const	PLMD::Action	inline
isCurrentlyActive(const unsigned &bno, const unsigned &code)	PLMD::multicolvar::MultiColvarFunction	inlinevirtual
isDensity() const	PLMD::multicolvar::MultiColvarBase	inlinevirtual
isOptionOn(const std::string &s) const	PLMD::Action	inline
isPeriodic()	PLMD::multicolvar::AdjacencyMatrixAction	inlinevirtual
keywords	PLMD::Action
lockContributors()	PLMD::vesselbase::ActionWithVessel
lockRequests()	PLMD::ActionAtomistic	inlinevirtual
log	PLMD::Action
makeWhole()	PLMD::ActionAtomistic
maxeig	PLMD::multicolvar::Sprint	private
mergeVectorDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const	PLMD::multicolvar::MultiColvarFunction	protected
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(const ActionOptions &)	PLMD::multicolvar::MultiColvarBase	explicit
MultiColvarFunction(const ActionOptions &)	PLMD::multicolvar::MultiColvarFunction	explicit
mymatrix	PLMD::multicolvar::Sprint	private
nblock	PLMD::multicolvar::MultiColvarBase	protected
needsDerivatives()	PLMD::vesselbase::ActionWithVessel	protected
noAnalyticalDerivatives(Keywords &keys)	PLMD::ActionWithValue	static
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
readAtomsFromPDB(const PDB &pdb)	PLMD::ActionAtomistic	virtual
readVesselKeywords()	PLMD::vesselbase::ActionWithVessel	protected
registerKeywords(Keywords &keys)	PLMD::multicolvar::Sprint	static
requestAtoms(const std::vector< AtomNumber > &a)	PLMD::ActionAtomistic
resizeFunctions()	PLMD::vesselbase::ActionWithVessel	protected
retrieveAdjacencyLists(std::vector< unsigned > &nneigh, Matrix< unsigned > &adj_list)	PLMD::multicolvar::AdjacencyMatrixAction	protected
retrieveAtoms()	PLMD::ActionAtomistic
retrieveDomain(std::string &min, std::string &max)	PLMD::vesselbase::ActionWithVessel	virtual
retrieveMatrix(Matrix< double > &mymatrix)	PLMD::multicolvar::AdjacencyMatrixAction	protected
runAllTasks()	PLMD::vesselbase::ActionWithVessel	protected
runFinalJobs()	PLMD::Action	inlinevirtual
serialCalculation() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
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
setMatrixIndexesForTask(const unsigned &ii)	PLMD::multicolvar::AdjacencyMatrixAction	protected
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
Sprint(const ActionOptions &)	PLMD::multicolvar::Sprint	explicit
sqrtn	PLMD::multicolvar::Sprint	private
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::MultiColvarFunction	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
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
~MultiColvarBase()	PLMD::multicolvar::MultiColvarBase	inline