PLMD::vesselbase::ActionWithVessel Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
actionIsBridgedPLMD::vesselbase::ActionWithVesselprivate
ActionWithInputVessel classPLMD::vesselbase::ActionWithVesselfriend
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addDependency(Action *)PLMD::Action
addTaskToList(const unsigned &taskCode)PLMD::vesselbase::ActionWithVesselprotected
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
afterPLMD::Actionprivate
apply()=0PLMD::Actionpure virtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
beforeUpdate()PLMD::Actioninlinevirtual
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
BridgeVessel classPLMD::vesselbase::ActionWithVesselfriend
bufferPLMD::vesselbase::ActionWithVesselprivate
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
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
checkNumericalDerivatives() constPLMD::Actioninlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearOptions()PLMD::Actionvirtual
commPLMD::Action
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
deactivate()PLMD::Actioninlinevirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
Dependencies typedefPLMD::Action
der_listPLMD::vesselbase::ActionWithVesselprivate
derivativesAreRequired() constPLMD::vesselbase::ActionWithVesselinline
dertimePLMD::vesselbase::ActionWithVesselprotected
dertime_can_be_offPLMD::vesselbase::ActionWithVesselprivate
doCheckPointPLMD::Actionprivate
doJobsRequiredBeforeTaskList()PLMD::vesselbase::ActionWithVesselvirtual
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
finishComputations(const std::vector< double > &buffer)PLMD::vesselbase::ActionWithVesselvirtual
fopen(const char *path, const char *mode)PLMD::Action
fullTaskListPLMD::vesselbase::ActionWithVesselprivate
functionsPLMD::vesselbase::ActionWithVesselprivate
FunctionVessel classPLMD::vesselbase::ActionWithVesselfriend
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getCPT() constPLMD::Action
getCurrentNumberOfActiveTasks() constPLMD::vesselbase::ActionWithVesselinline
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getExchangeStep() constPLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)PLMD::vesselbase::ActionWithVesselprotected
getFullNumberOfTasks() constPLMD::vesselbase::ActionWithVesselinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getName() constPLMD::Actioninline
getNLTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfDerivatives()=0PLMD::vesselbase::ActionWithVesselpure virtual
getNumberOfQuantities() constPLMD::vesselbase::ActionWithVesselinlinevirtual
getNumberOfVessels() constPLMD::vesselbase::ActionWithVesselinline
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinline
getPositionInCurrentTaskList(const unsigned &myind) constPLMD::vesselbase::ActionWithVesselinline
getPositionInFullTaskList(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
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
getVesselWithName(const std::string &mynam)PLMD::vesselbase::ActionWithVessel
indexOfTaskInFullListPLMD::vesselbase::ActionWithVesselprivate
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
isPeriodic()=0PLMD::vesselbase::ActionWithVesselpure virtual
keywordsPLMD::Action
labelPLMD::Actionprivate
linePLMD::Actionprivate
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests()PLMD::Actioninlinevirtual
logPLMD::Action
lowmemPLMD::vesselbase::ActionWithVesselprivate
maxderivativesPLMD::vesselbase::ActionWithVesselprivate
multi_sim_commPLMD::Action
mydataPLMD::vesselbase::ActionWithVesselprotected
nactive_tasksPLMD::vesselbase::ActionWithVesselprivate
namePLMD::Actionprivate
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
nl_tolerancePLMD::vesselbase::ActionWithVesselprivate
noderivPLMD::vesselbase::ActionWithVesselprivate
normalizeVector(std::vector< double > &vals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
OrderingVessel classPLMD::vesselbase::ActionWithVesselfriend
parse(const std::string &key, T &t)PLMD::Action
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
partialTaskListPLMD::vesselbase::ActionWithVesselprivate
performTask(const unsigned &, const unsigned &, MultiValue &) const =0PLMD::vesselbase::ActionWithVesselpure virtual
plumedPLMD::Action
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::vesselbase::ActionWithVesselstatic
replica_indexPLMD::Actionprivate
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
restartPLMD::Actionprivate
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
serialPLMD::vesselbase::ActionWithVesselprivate
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setLowMemOption(const bool &)PLMD::vesselbase::ActionWithVesselinlineprotected
setOption(const std::string &s)PLMD::Actionvirtual
ShortcutVessel classPLMD::vesselbase::ActionWithVesselfriend
stopwatchPLMD::vesselbase::ActionWithVesselprivate
stopwatch_fwdPLMD::vesselbase::ActionWithVesselprivate
StoreDataVessel classPLMD::vesselbase::ActionWithVesselfriend
taskFlagsPLMD::vesselbase::ActionWithVesselprotected
taskIsCurrentlyActive(const unsigned &index) constPLMD::vesselbase::ActionWithVessel
threadSafe() constPLMD::vesselbase::ActionWithVesselinlinevirtual
timersPLMD::vesselbase::ActionWithVesselprivate
tmpforcesPLMD::vesselbase::ActionWithVesselprivate
tolerancePLMD::vesselbase::ActionWithVesselprivate
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::vesselbase::ActionWithVesselvirtual
unlockRequests()PLMD::Actioninlinevirtual
update()PLMD::Actioninlinevirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
usingLowMem() constPLMD::vesselbase::ActionWithVesselinlineprotected
Vessel classPLMD::vesselbase::ActionWithVesselfriend
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
~Action()PLMD::Actionvirtual
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
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