PLMD::vesselbase::ActionWithAveraging Member List

This is the complete list of members for PLMD::vesselbase::ActionWithAveraging, including all inherited members.

accumulateAverage(MultiValue &myvals) constPLMD::vesselbase::ActionWithAveraginginlinevirtual
Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithAveraging(const ActionOptions &)PLMD::vesselbase::ActionWithAveragingexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
activatedPLMD::vesselbase::ActionWithAveragingprivate
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()=0PLMD::Actionpure virtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
applyForces()PLMD::ActionAtomistic
atomsPLMD::ActionAtomisticprotected
AveragingVessel classPLMD::vesselbase::ActionWithAveragingfriend
beforeUpdate()PLMD::Actioninlinevirtual
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
buildDataStashes(ActionWithVessel *actionThatUses)PLMD::vesselbase::ActionWithVessel
calculate()=0PLMD::Actionpure virtual
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
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(PLMD::ActionWithValue *)PLMD::vesselbase::ActionWithAveragingvirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() constPLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearAverage()PLMD::vesselbase::ActionWithAveragingvirtual
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
clearstridePLMD::vesselbase::ActionWithAveragingprotected
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
cweightPLMD::vesselbase::ActionWithAveragingprotected
deactivate()PLMD::Actioninlinevirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
Dependencies typedefPLMD::Action
derivativesAreRequired() constPLMD::vesselbase::ActionWithVesselinline
dertimePLMD::vesselbase::ActionWithVesselprotected
difference(int, double, double) constPLMD::ActionWithArgumentsinline
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
f enum valuePLMD::vesselbase::ActionWithAveragingprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
finishAveraging()PLMD::vesselbase::ActionWithAveraginginlinevirtual
finishComputations(const std::vector< double > &buffer)PLMD::vesselbase::ActionWithVesselvirtual
fopen(const char *path, const char *mode)PLMD::Action
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments()PLMD::vesselbase::ActionWithAveraginginline
getArguments() constPLMD::vesselbase::ActionWithAveraginginline
PLMD::ActionWithArguments::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
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNLTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfArguments() constPLMD::vesselbase::ActionWithAveraginginlinevirtual
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::vesselbase::ActionWithAveraginginlinevirtual
getNumberOfQuantities() constPLMD::vesselbase::ActionWithAveragingvirtual
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
getRestart() constPLMD::Actioninline
getSizeOfBuffer(unsigned &bufsize)PLMD::vesselbase::ActionWithVesselprotected
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
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
ignoreNormalization() constPLMD::vesselbase::ActionWithAveraging
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()=0PLMD::vesselbase::ActionWithVesselpure virtual
keywordsPLMD::Action
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests()PLMD::vesselbase::ActionWithAveragingvirtual
logPLMD::Action
lweightPLMD::vesselbase::ActionWithAveragingprotected
makeWhole()PLMD::ActionAtomistic
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
my_analysis_objectPLMD::vesselbase::ActionWithAveragingprivate
myaveragePLMD::vesselbase::ActionWithAveragingprivate
mydataPLMD::vesselbase::ActionWithVesselprotected
ndata enum valuePLMD::vesselbase::ActionWithAveragingprivate
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noNormalization() constPLMD::vesselbase::ActionWithAveraginginlineprotected
normalizationPLMD::vesselbase::ActionWithAveragingprivate
normalizeVector(std::vector< double > &vals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
onStep() constPLMD::ActionPilotvirtual
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
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
performOperations(const bool &from_update)PLMD::vesselbase::ActionWithAveragingvirtual
performTask(const unsigned &task_index, const unsigned &current, MultiValue &myvals) constPLMD::vesselbase::ActionWithAveragingvirtual
plumedPLMD::Action
prepare()PLMD::Actionvirtual
prepareForAveraging()PLMD::vesselbase::ActionWithAveraginginlinevirtual
PLMD::readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb)PLMD::ActionAtomisticvirtual
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::vesselbase::ActionWithAveragingstatic
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::vesselbase::ActionWithAveragingvirtual
runTask(const unsigned &current, MultiValue &myvals) constPLMD::vesselbase::ActionWithAveraginginlinevirtual
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setAveragingAction(std::unique_ptr< AveragingVessel > av_vessel, const bool &usetasks)PLMD::vesselbase::ActionWithAveragingprotected
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
setStride(const int &n)PLMD::ActionPilot
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
storeThenAverage() constPLMD::vesselbase::ActionWithAveraginginlineprotected
t enum valuePLMD::vesselbase::ActionWithAveragingprivate
taskFlagsPLMD::vesselbase::ActionWithVesselprotected
taskIsCurrentlyActive(const unsigned &index) constPLMD::vesselbase::ActionWithVessel
threadSafe() constPLMD::vesselbase::ActionWithVesselinlinevirtual
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::vesselbase::ActionWithVesselvirtual
turnOnDerivatives()PLMD::ActionWithValuevirtual
unlockRequests()PLMD::vesselbase::ActionWithAveragingvirtual
update()PLMD::vesselbase::ActionWithAveragingvirtual
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
useRunAllTasksPLMD::vesselbase::ActionWithAveragingprotected
usingLowMem() constPLMD::vesselbase::ActionWithVesselinlineprotected
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightsPLMD::vesselbase::ActionWithAveragingprivate
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
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