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PLMD::analysis::Analysis Member List

This is the complete list of members for PLMD::analysis::Analysis, including all inherited members.

accumulate()PLMD::analysis::Analysis
accumulateDerivative(const unsigned &ider, const double &df)PLMD::vesselbase::ActionWithVesselinlineprotected
Action(const ActionOptions &)PLMD::Action
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomistic
ActionPilot(const ActionOptions &)PLMD::ActionPilot
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArguments
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVessel
activate()PLMD::Actionvirtual
activateIndexes(const unsigned &, const unsigned &, const std::vector< unsigned > &)PLMD::vesselbase::ActionWithVesselinlinevirtual
activateTheseTasks(std::vector< bool > &addtionalTasks)PLMD::vesselbase::ActionWithVessel
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addDependency(Action *)PLMD::Action
addElementDerivative(const unsigned &, const double &)PLMD::vesselbase::ActionWithVesselinline
addElementValue(const unsigned &, const double &)PLMD::vesselbase::ActionWithVesselinline
addForcesOnArguments(const std::vector< double > &forces)PLMD::ActionWithArguments
addTaskToList(const unsigned &taskCode)PLMD::vesselbase::ActionWithVesselprotected
addVessel(const std::string &name, const std::string &input, const int numlab=0)PLMD::vesselbase::ActionWithVesselprotected
addVessel(Vessel *vv)PLMD::vesselbase::ActionWithVesselprotected
Analysis(const ActionOptions &)PLMD::analysis::Analysis
apply()PLMD::analysis::Analysisinlinevirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
applyForces()PLMD::ActionAtomistic
argument_namesPLMD::analysis::Analysisprivate
atomsPLMD::ActionAtomisticprotected
biasesPLMD::analysis::Analysisprivate
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
bringBackInPbc(int i, double d1) const PLMD::ActionWithArgumentsinline
buildDataStashes()PLMD::vesselbase::ActionWithVesselvirtual
calculate()PLMD::analysis::Analysisvirtual
calculateAllVessels()PLMD::vesselbase::ActionWithVesselprotected
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::analysis::Analysisinlinevirtual
chainRuleForElementDerivatives(const unsigned &, const unsigned &, const double &, Vessel *)PLMD::vesselbase::ActionWithVessel
chainRuleForElementDerivatives(const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)PLMD::vesselbase::ActionWithVessel
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
checkNeedsGradients() const PLMD::Actioninlinevirtual
checkNumericalDerivatives() const PLMD::Actioninlinevirtual
checkRead()PLMD::Action
cite(const std::string &s)PLMD::Action
clearAfterTask()PLMD::vesselbase::ActionWithVesselprotected
clearDependencies()PLMD::Action
clearDerivativesAfterTask(const unsigned &)PLMD::vesselbase::ActionWithVesselvirtual
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::Action
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
current_argsPLMD::analysis::Analysisprivate
dataPLMD::analysis::Analysisprotected
deactivate()PLMD::Actioninlinevirtual
deactivate_task()PLMD::vesselbase::ActionWithVesselvirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
deactivateTasksInRange(const unsigned &lower, const unsigned &upper)PLMD::vesselbase::ActionWithVesselprotected
Dependencies typedefPLMD::Action
derivativesAreRequired() const PLMD::vesselbase::ActionWithVesselinline
difference(int, double, double) const PLMD::ActionWithArgumentsinline
doJobsRequiredBeforeTaskList()PLMD::vesselbase::ActionWithVesselvirtual
doNotForce()PLMD::ActionAtomisticinline
doNotRetrieve()PLMD::ActionAtomisticinline
error(const std::string &msg) const PLMD::Action
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(PDB &pdb)PLMD::ActionWithArgumentsprotected
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
files_iterator typedefPLMD::Action
finalizeWeights(const bool &ignore_weights)PLMD::analysis::Analysisprotected
finishComputations()PLMD::vesselbase::ActionWithVesselvirtual
finishTaskListUpdate()PLMD::vesselbase::ActionWithVesselinlinevirtual
firstAnalysisDonePLMD::analysis::Analysisprivate
fopen(const char *path, const char *mode)PLMD::Action
freqPLMD::analysis::Analysisprivate
getAbsoluteIndex(int i) const PLMD::ActionAtomisticinline
getAbsoluteIndexes() const PLMD::ActionAtomisticinline
getActiveTask(const unsigned &ii) const PLMD::vesselbase::ActionWithVesselinlineprotected
getArgument(const unsigned n) const PLMD::ActionWithArgumentsinline
getArguments()PLMD::analysis::Analysisinlineprotected
getBox() const PLMD::ActionAtomisticinline
getCharge(int i) const PLMD::ActionAtomisticinline
getCurrentNumberOfActiveTasks() const PLMD::vesselbase::ActionWithVesselinlineprotected
getCurrentPositionInTaskList() const PLMD::vesselbase::ActionWithVesselinlineprotected
getCurrentTask() const PLMD::vesselbase::ActionWithVesselinlineprotected
getDataPoint(const unsigned &idata, std::vector< double > &point, double &weight) const PLMD::analysis::Analysisprotected
getDependencies() const PLMD::Actioninline
getDocumentation() const PLMD::Actionvirtual
getElementDerivative(const unsigned &) const PLMD::vesselbase::ActionWithVesselinline
getElementValue(const unsigned &ival) const PLMD::vesselbase::ActionWithVesselinline
getEnergy() const PLMD::ActionAtomisticinline
getExchangeStep() const PLMD::Action
getForcesFromVessels(std::vector< double > &forcesToApply)PLMD::vesselbase::ActionWithVesselprotected
getFullNumberOfTasks() const PLMD::vesselbase::ActionWithVesselinline
getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)PLMD::vesselbase::ActionWithVesselvirtual
getLabel() const PLMD::Actioninline
getMass(int i) const PLMD::ActionAtomisticinline
getMetric() const PLMD::analysis::Analysisprivate
getMetricName() const PLMD::analysis::Analysisinlineprotected
getName() const PLMD::Actioninline
getNLTolerance() const PLMD::vesselbase::ActionWithVesselinlineprotected
getNormalization() const PLMD::analysis::Analysisprotected
getNumberOfArguments() const PLMD::analysis::Analysisinlineprotected
getNumberOfAtoms() const PLMD::ActionAtomisticinline
getNumberOfDataPoints() const PLMD::analysis::Analysisinlineprotected
getNumberOfDerivatives()PLMD::analysis::Analysisinlinevirtual
getNumberOfQuantities()PLMD::vesselbase::ActionWithVesselinlinevirtual
getNumberOfVessels() const PLMD::vesselbase::ActionWithVesselinlineprotected
getOutputFormat() const PLMD::analysis::Analysisinlineprotected
getPbc() const PLMD::ActionAtomisticinline
getPeriodicityInformation(const unsigned &i, std::string &dmin, std::string &dmax)PLMD::analysis::Analysisprotected
getPntrToArgument(const unsigned n)PLMD::ActionWithArgumentsinline
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinlineprotected
getPosition(int) const PLMD::ActionAtomisticinline
getPosition(AtomNumber) const PLMD::ActionAtomisticinline
getPositionInFullTaskList(const unsigned &ii) const PLMD::vesselbase::ActionWithVesselinlineprotected
getPositions() const PLMD::ActionAtomisticinline
getProjection(unsigned i, unsigned j) const PLMD::ActionWithArguments
getStep() const PLMD::Action
getStride() const PLMD::ActionPilotprotected
getTemp() const PLMD::analysis::Analysisprotected
getTime() const PLMD::Action
getTimeStep() const PLMD::Action
getTolerance() const PLMD::vesselbase::ActionWithVesselinlineprotected
getTotAtoms() const PLMD::ActionAtomisticinline
getUnique() const PLMD::ActionAtomisticinline
getVesselWithName(const std::string &mynam)PLMD::vesselbase::ActionWithVessel
getWeight(const unsigned &idata) const PLMD::analysis::Analysisprotected
idataPLMD::analysis::Analysisprivate
ignore_reweightPLMD::analysis::Analysisprivate
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)PLMD::ActionWithArguments
isActive() const PLMD::Actioninline
isOptionOn(const std::string &s) const PLMD::Actioninline
isPeriodic()PLMD::analysis::Analysisinlinevirtual
keywordsPLMD::Action
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests()PLMD::analysis::Analysisinlinevirtual
logPLMD::Action
logweightsPLMD::analysis::Analysisprivate
mergeDerivatives(const unsigned &ider, const double &df)PLMD::vesselbase::ActionWithVesselvirtual
metricnamePLMD::analysis::Analysisprivate
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
mydatastashPLMD::analysis::Analysisprivate
ndataPLMD::analysis::Analysisprivate
needengPLMD::analysis::Analysisprivate
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
nomemoryPLMD::analysis::Analysisprivate
normPLMD::analysis::Analysisprivate
ofmtPLMD::analysis::Analysisprivate
old_normPLMD::analysis::Analysisprivate
onStep() const PLMD::ActionPilot
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
parseOutputFile(const std::string &key, std::string &filename)PLMD::analysis::Analysisprotected
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
pbcDistance(const Vector &, const Vector &) const PLMD::ActionAtomistic
performAnalysis()=0PLMD::analysis::Analysispure virtual
performTask()=0PLMD::vesselbase::ActionWithVesselpure virtual
plumedPLMD::Action
prepare()PLMD::analysis::Analysisvirtual
PLMD::readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb)PLMD::ActionAtomisticvirtual
readDataFromFile(const std::string &filename)PLMD::analysis::Analysisprivate
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::analysis::Analysisstatic
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
requestAtoms(const std::vector< AtomNumber > &a)PLMD::ActionAtomistic
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
retrieveAtoms()PLMD::ActionAtomistic
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
retrieveNorm() const PLMD::analysis::Analysisinlineprivate
reusing_dataPLMD::analysis::Analysisprivate
rfilePLMD::analysis::Analysisprivate
rtempPLMD::analysis::Analysisprivate
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runAnalysis()PLMD::analysis::Analysis
runFinalJobs()PLMD::analysis::Analysisvirtual
serialCalculation() const PLMD::vesselbase::ActionWithVesselinlineprotected
setElementDerivative(const unsigned &, const double &)PLMD::vesselbase::ActionWithVesselinline
setElementValue(const unsigned &, const double &)PLMD::vesselbase::ActionWithVesselinline
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setLowMemOption(const bool &)PLMD::vesselbase::ActionWithVesselinlineprotected
setMaximumNumberOfDerivatives(const unsigned &)PLMD::vesselbase::ActionWithVesselprotected
setOption(const std::string &s)PLMD::Actionvirtual
simtempPLMD::analysis::Analysisprivate
single_runPLMD::analysis::Analysisprivate
thisval_wassetPLMD::vesselbase::ActionWithVesselprotected
unlockContributors()PLMD::vesselbase::ActionWithVessel
unlockRequests()PLMD::analysis::Analysisinlinevirtual
update()PLMD::analysis::Analysisvirtual
usingLowMem() const PLMD::vesselbase::ActionWithVesselinlineprotected
usingMemory() const PLMD::analysis::Analysisinlineprotected
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
write_chqPLMD::analysis::Analysisprivate
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
~Analysis()PLMD::analysis::Analysis
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