PLMD::mapping::AdaptivePath Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
AdaptivePath(const ActionOptions &)PLMD::mapping::AdaptivePathexplicit
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
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::ActionWithVesselprotected
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
addVessel(const std::string &name, const std::string &input, const int numlab=0)PLMD::vesselbase::ActionWithVesselprotected
addVessel(std::unique_ptr< Vessel > vv)PLMD::vesselbase::ActionWithVesselprotected
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply() overridePLMD::mapping::Mappingvirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
buildDataStashes(ActionWithVessel *actionThatUses)PLMD::vesselbase::ActionWithVessel
calculate() overridePLMD::mapping::AdaptivePathvirtual
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)PLMD::vesselbase::ActionWithVesselprotected
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateDistanceFunction(const unsigned &ifunc, ReferenceValuePack &myder, const bool &squared) constPLMD::mapping::Mappingprotected
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::mapping::Mappingvirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::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::ActionWithValuestatic
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
Dependencies typedefPLMD::Action
derivativesAreRequired() constPLMD::vesselbase::ActionWithVesselinline
dertimePLMD::vesselbase::ActionWithVesselprotected
difference(int, double, double) constPLMD::ActionWithArgumentsinline
displacementPLMD::mapping::AdaptivePathprivate
displacement2PLMD::mapping::AdaptivePathprivate
doJobsRequiredBeforeTaskList()PLMD::vesselbase::ActionWithVesselvirtual
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
doNotForce()PLMD::ActionAtomisticinline
doNotRetrieve()PLMD::ActionAtomisticinline
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(PDB &pdb)PLMD::ActionWithArgumentsprotected
fadefactPLMD::mapping::AdaptivePathprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
fframesPLMD::mapping::Mappingprotected
filesPLMD::Action
finishComputations(const std::vector< double > &buffer)PLMD::vesselbase::ActionWithVesselvirtual
finishPackSetup(const unsigned &ifunc, ReferenceValuePack &mypack) constPLMD::mapping::Mappingprotected
fixednPLMD::mapping::AdaptivePathprivate
fopen(const char *path, const char *mode)PLMD::Action
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getAllReferenceConfigurations()PLMD::mapping::Mappinginlineprotected
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArgumentName(unsigned &iarg)PLMD::mapping::Mapping
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getBox() constPLMD::ActionAtomisticinline
getCharge(int i) constPLMD::ActionAtomisticinline
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getCurrentNumberOfActiveTasks() constPLMD::vesselbase::ActionWithVesselinline
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergy() constPLMD::ActionAtomisticinline
getExchangeStep() constPLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)PLMD::vesselbase::ActionWithVesselprotected
getFullNumberOfTasks() constPLMD::vesselbase::ActionWithVesselinline
getGlobalPosition(AtomNumber) constPLMD::ActionAtomisticinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getLambda() overridePLMD::mapping::AdaptivePathinlinevirtual
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNLTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::mapping::Mappinginlinevirtual
getNumberOfProperties() constPLMD::mapping::Mappinginline
getNumberOfQuantities() constPLMD::vesselbase::ActionWithVesselinlinevirtual
getNumberOfReferencePoints() constPLMD::mapping::Mappinginlineprotected
getNumberOfVessels() constPLMD::vesselbase::ActionWithVesselinline
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToArgument(const unsigned n)PLMD::ActionWithArgumentsinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinline
getPosition(int) constPLMD::ActionAtomisticinline
getPositionInCurrentTaskList(const unsigned &myind) constPLMD::vesselbase::ActionWithVesselinline
getPositionInFullTaskList(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getPositions() constPLMD::ActionAtomisticinline
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
getPropertyValue(const unsigned &current, const std::string &name) constPLMD::mapping::Mappinginline
getReferenceConfiguration(const unsigned &ifunc)PLMD::mapping::Mappingprotected
getRestart() constPLMD::Actioninline
getSizeOfBuffer(unsigned &bufsize)PLMD::vesselbase::ActionWithVesselprotected
getStep() constPLMD::Action
getTaskCode(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
getVesselWithName(const std::string &mynam)PLMD::vesselbase::ActionWithVessel
getWeight(const unsigned &weight) constPLMD::mapping::Mappinginlineprotected
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg)PLMD::ActionWithArguments
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
isPeriodic() overridePLMD::mapping::Mappinginlinevirtual
keywordsPLMD::Action
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests() overridePLMD::mapping::Mappinginlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
Mapping(const ActionOptions &)PLMD::mapping::Mappingexplicit
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForceOnExtraCV()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
mydataPLMD::vesselbase::ActionWithVesselprotected
mypathvPLMD::mapping::AdaptivePathprivate
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
normalizeVector(std::vector< double > &vals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
ofmtPLMD::mapping::AdaptivePathprivate
parse(const std::string &key, T &t)PLMD::Action
parseArgumentList(const std::string &key, std::vector< Value *> &args)PLMD::ActionWithArguments
parseArgumentList(const std::string &key, int i, 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
pathfilePLMD::mapping::AdaptivePathprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
pdisplacementsPLMD::mapping::AdaptivePathprivate
performTask(const unsigned &, const unsigned &, MultiValue &) const overridePLMD::mapping::AdaptivePathvirtual
plumedPLMD::Action
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::mapping::AdaptivePathstatic
requestArguments(const std::vector< Value *> &arg)PLMD::ActionWithArguments
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
retrieveAtoms()PLMD::ActionAtomisticvirtual
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setLowMemOption(const bool &)PLMD::vesselbase::ActionWithVesselinlineprotected
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
taskFlagsPLMD::vesselbase::ActionWithVesselprotected
taskIsCurrentlyActive(const unsigned &index) constPLMD::vesselbase::ActionWithVessel
threadSafe() constPLMD::vesselbase::ActionWithVesselinlinevirtual
tolerancePLMD::mapping::AdaptivePathprivate
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::vesselbase::ActionWithVesselvirtual
transformHD(const double &dist, double &df) const overridePLMD::mapping::AdaptivePathvirtual
turnOnDerivatives() overridePLMD::mapping::Mappingvirtual
unlockRequests() overridePLMD::mapping::Mappinginlinevirtual
update() overridePLMD::mapping::AdaptivePathvirtual
update_strPLMD::mapping::AdaptivePathprivate
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usingLowMem() constPLMD::vesselbase::ActionWithVesselinlineprotected
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
wstridePLMD::mapping::AdaptivePathprivate
wsumPLMD::mapping::AdaptivePathprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
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