PLMD::mapping::Mapping Member List

This is the complete list of members for PLMD::mapping::Mapping, 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
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
addForcesOnArguments(const std::vector< double > &forces)	PLMD::ActionWithArguments
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
allowToAccessGlobalForces()	PLMD::ActionAtomistic	inline
apply()	PLMD::mapping::Mapping	virtual
applyBridgeForces(const std::vector< double > &bb)	PLMD::vesselbase::ActionWithVessel	inlinevirtual
applyForces()	PLMD::ActionAtomistic
atoms	PLMD::ActionAtomistic	protected
bridgeVariable	PLMD::vesselbase::ActionWithVessel	protected
bringBackInPbc(int i, double d1) const	PLMD::ActionWithArguments	inline
buildDataStashes(const bool &allow_wcutoff, const double &wtol)	PLMD::vesselbase::ActionWithVessel
calculate()=0	PLMD::Action	pure 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
calculateDistanceFunction(const unsigned &ifunc, ReferenceValuePack &myder, const bool &squared) const	PLMD::mapping::Mapping	protected
calculateFromPDB(const PDB &)	PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)	PLMD::mapping::Mapping	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
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(const unsigned &task_index)	PLMD::vesselbase::ActionWithVessel	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
dfframes	PLMD::mapping::Mapping	private
difference(int, double, double) const	PLMD::ActionWithArguments	inline
doJobsRequiredBeforeTaskList()	PLMD::vesselbase::ActionWithVessel	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
expandArgKeywordInPDB(PDB &pdb)	PLMD::ActionWithArguments	protected
fclose(FILE *fp)	PLMD::Action
fflush()	PLMD::Action
fframes	PLMD::mapping::Mapping	protected
files	PLMD::Action
files_iterator typedef	PLMD::Action
finishComputations(const std::vector< double > &buffer)	PLMD::vesselbase::ActionWithVessel	virtual
finishPackSetup(const unsigned &ifunc, ReferenceValuePack &mypack) const	PLMD::mapping::Mapping	protected
finishTaskListUpdate()	PLMD::vesselbase::ActionWithVessel	inlinevirtual
fopen(const char *path, const char *mode)	PLMD::Action
forcesToApply	PLMD::mapping::Mapping	private
getAbsoluteIndex(int i) const	PLMD::ActionAtomistic	inline
getAbsoluteIndexes() const	PLMD::ActionAtomistic	inline
getActiveTask(const unsigned &ii) const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getArgument(const unsigned n) const	PLMD::ActionWithArguments	inline
getArgumentName(unsigned &iarg)	PLMD::mapping::Mapping
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
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
getLambda()	PLMD::mapping::Mapping	virtual
getMass(int i) const	PLMD::ActionAtomistic	inline
getName() const	PLMD::Action	inline
getNLTolerance() const	PLMD::vesselbase::ActionWithVessel	inlineprotected
getNumberOfArguments() const	PLMD::ActionWithArguments	inline
getNumberOfAtoms() const	PLMD::ActionAtomistic	inline
getNumberOfComponents() const	PLMD::ActionWithValue	inline
getNumberOfDerivatives()	PLMD::mapping::Mapping	inlinevirtual
getNumberOfProperties() const	PLMD::mapping::Mapping	inline
getNumberOfQuantities()	PLMD::vesselbase::ActionWithVessel	inlinevirtual
getNumberOfReferencePoints() const	PLMD::mapping::Mapping	inlineprotected
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
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
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
getPositions() const	PLMD::ActionAtomistic	inline
getProjection(unsigned i, unsigned j) const	PLMD::ActionWithArguments
getPropertyIndex(const std::string &name) const	PLMD::mapping::Mapping
getPropertyName(const unsigned &iprop) const	PLMD::mapping::Mapping	inline
getPropertyValue(const unsigned &current, const unsigned &iprop) const	PLMD::mapping::Mapping	inline
getReferenceConfiguration(const unsigned &ifunc)	PLMD::mapping::Mapping	protected
getRestart() const	PLMD::Action	inline
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
getWeight(const unsigned &weight) const	PLMD::mapping::Mapping	inlineprotected
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
isPeriodic()	PLMD::mapping::Mapping	inlinevirtual
keywords	PLMD::Action
lockContributors()	PLMD::vesselbase::ActionWithVessel
lockRequests()	PLMD::mapping::Mapping	inlinevirtual
log	PLMD::Action
makeWhole()	PLMD::ActionAtomistic
Mapping(const ActionOptions &)	PLMD::mapping::Mapping	explicit
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
mymap	PLMD::mapping::Mapping	private
needsDerivatives()	PLMD::vesselbase::ActionWithVessel	protected
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
performTask(const unsigned &, const unsigned &, MultiValue &) const =0	PLMD::vesselbase::ActionWithVessel	pure virtual
plumed	PLMD::Action
prepare()	PLMD::mapping::Mapping	virtual
readAtomsFromPDB(const PDB &pdb)	PLMD::ActionAtomistic	virtual
readVesselKeywords()	PLMD::vesselbase::ActionWithVessel	protected
registerKeywords(Keywords &keys)	PLMD::mapping::Mapping	static
requestArguments(const std::vector< Value * > &arg)	PLMD::ActionWithArguments
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
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)	PLMD::ActionAtomistic
setGradientsIfNeeded()	PLMD::ActionWithValue
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
setValue(const double &d)	PLMD::ActionWithValue	inlineprotected
setValue(Value *, double)	PLMD::ActionWithValue
storeDistanceFunction(const unsigned &ifunc)	PLMD::mapping::Mapping	inlineprotected
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) const	PLMD::vesselbase::ActionWithVessel	virtual
transformHD(const double &dist, double &df) const =0	PLMD::mapping::Mapping	pure virtual
turnOnDerivatives()	PLMD::mapping::Mapping	virtual
unlockContributors()	PLMD::vesselbase::ActionWithVessel
unlockRequests()	PLMD::mapping::Mapping	inlinevirtual
update()	PLMD::Action	inlinevirtual
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
weightWithDerivatives() const	PLMD::vesselbase::ActionWithVessel	inline
~Action()	PLMD::Action	virtual
~ActionAtomistic()	PLMD::ActionAtomistic
~ActionWithArguments()	PLMD::ActionWithArguments	inlinevirtual
~ActionWithValue()	PLMD::ActionWithValue
~ActionWithVessel()	PLMD::vesselbase::ActionWithVessel
~Mapping()	PLMD::mapping::Mapping