PLMD::adjmat::ClusteringBase Member List

This is the complete list of members for PLMD::adjmat::ClusteringBase, including all inherited members.

ablocksPLMD::multicolvar::MultiColvarBaseprotected
accumulateSymmetryFunction(const int &ival, const unsigned &iatom, const double &val, const Vector &der, const Tensor &vir, multicolvar::AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBaseprotected
Action(const ActionOptions &)PLMD::Actionexplicit
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionWithInputMatrix(const ActionOptions &)PLMD::adjmat::ActionWithInputMatrixexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
ActionWithVessel(const ActionOptions &ao)PLMD::vesselbase::ActionWithVesselexplicit
activate()PLMD::Actionvirtual
addAtomDerivatives(const int &, const unsigned &, const Vector &, multicolvar::AtomValuePack &) constPLMD::multicolvar::MultiColvarBase
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addConnectionDerivatives(const unsigned &i, const unsigned &j, MultiValue &myvals, MultiValue &myvout) constPLMD::adjmat::ActionWithInputMatrix
addDependency(Action *)PLMD::Action
addTaskToList(const unsigned &taskCode)PLMD::multicolvar::MultiColvarBaseprotected
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::adjmat::ClusteringBaseinlinevirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::vesselbase::ActionWithVesselinlinevirtual
applyForces()PLMD::ActionAtomistic
applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::multicolvar::MultiColvarBase
areConnected(const unsigned &iatom, const unsigned &jatom) constPLMD::adjmat::ClusteringBase
atom_labPLMD::multicolvar::MultiColvarBaseprotected
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
bookeepingPLMD::multicolvar::MultiColvarBaseprotected
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
buildDataStashes(ActionWithVessel *actionThatUses)PLMD::vesselbase::ActionWithVessel
buildSets()PLMD::multicolvar::MultiColvarBaseprotected
calculate() overridePLMD::adjmat::ClusteringBasevirtual
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(ActionWithValue *a=NULL) overridePLMD::multicolvar::MultiColvarBasevirtual
calculateWeight(const unsigned &taskCode, const double &weight, AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBasevirtual
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
cluster_sizesPLMD::adjmat::ClusteringBaseprotected
ClusteringBase(const ActionOptions &)PLMD::adjmat::ClusteringBaseexplicit
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
compute(const unsigned &tindex, multicolvar::AtomValuePack &myatoms) const overridePLMD::adjmat::ActionWithInputMatrixinlinevirtual
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
deactivateAllTasks()PLMD::vesselbase::ActionWithVesselprotected
decodeIndexToAtoms(const unsigned &taskCode, std::vector< unsigned > &atoms) constPLMD::multicolvar::MultiColvarBaseprotected
decoderPLMD::multicolvar::MultiColvarBaseprotected
Dependencies typedefPLMD::Action
derivativesAreRequired() constPLMD::vesselbase::ActionWithVesselinline
dertimePLMD::vesselbase::ActionWithVesselprotected
doJobsRequiredBeforeTaskList()PLMD::vesselbase::ActionWithVesselvirtual
doNotCalculateDerivatives() const overridePLMD::multicolvar::MultiColvarBaseinlinevirtual
doNotCalculateDirector()PLMD::multicolvar::MultiColvarBaseinlinevirtual
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
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
filtersUsedAsInput()PLMD::multicolvar::MultiColvarBaseprotected
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
getAbsoluteIndexOfCentralAtom(const unsigned &i) const overridePLMD::adjmat::ActionWithInputMatrixvirtual
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getAdjacencyVessel() constPLMD::adjmat::ActionWithInputMatrix
getBaseMultiColvar(const unsigned &igrp) constPLMD::adjmat::ActionWithInputMatrixprotected
getBox() constPLMD::ActionAtomisticinline
getCentralAtomPack(const unsigned &basn, const unsigned &curr, CatomPack &mypack)PLMD::multicolvar::MultiColvarBasevirtual
getCentralAtomPos(const unsigned &curr)PLMD::multicolvar::MultiColvarBasevirtual
getCharge(int i) constPLMD::ActionAtomisticinline
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getCurrentNumberOfActiveTasks() constPLMD::vesselbase::ActionWithVesselinline
getCutoffForConnection() constPLMD::adjmat::ClusteringBasevirtual
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
getInputData(const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient0) const overridePLMD::adjmat::ActionWithInputMatrixvirtual
getInputDerivatives(const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms) const overridePLMD::adjmat::ActionWithInputMatrixvirtual
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getLinkCellCutoff() constPLMD::multicolvar::MultiColvarBaseprotected
getMass(int i) constPLMD::ActionAtomisticinline
getName() constPLMD::Actioninline
getNLTolerance() constPLMD::vesselbase::ActionWithVesselinlineprotected
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfAtomsInGroup(const unsigned &igrp) constPLMD::adjmat::ActionWithInputMatrixprotected
getNumberOfBaseMultiColvars() constPLMD::multicolvar::MultiColvarBaseinline
getNumberOfClusters() constPLMD::adjmat::ClusteringBaseinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::adjmat::ActionWithInputMatrixvirtual
getNumberOfNodes() constPLMD::adjmat::ActionWithInputMatrixvirtual
getNumberOfNodeTypes() constPLMD::adjmat::ActionWithInputMatrixprotected
getNumberOfQuantities() const overridePLMD::adjmat::ActionWithInputMatrixvirtual
getNumberOfVessels() constPLMD::vesselbase::ActionWithVesselinline
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
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
getPositionOfAtomForLinkCells(const unsigned &iatom) const overridePLMD::adjmat::ActionWithInputMatrixvirtual
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getSeparation(const Vector &vec1, const Vector &vec2) constPLMD::multicolvar::MultiColvarBase
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
hasDifferentiableOrientation() constPLMD::multicolvar::MultiColvarBaseinlinevirtual
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
isActive() constPLMD::Actioninline
isCurrentlyActive(const unsigned &code)PLMD::multicolvar::MultiColvarBaseinlinevirtual
isDensity() constPLMD::multicolvar::MultiColvarBaseinlinevirtual
isOptionOn(const std::string &s) constPLMD::Actioninline
isPeriodic() overridePLMD::adjmat::ActionWithInputMatrixinlinevirtual
keywordsPLMD::Action
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests() overridePLMD::ActionAtomisticinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
matsumsPLMD::multicolvar::MultiColvarBaseprotected
mergeInputDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBaseprotected
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
MultiColvarBase(const ActionOptions &)PLMD::multicolvar::MultiColvarBaseexplicit
mybasedataPLMD::multicolvar::MultiColvarBaseprotected
mybasemulticolvarsPLMD::multicolvar::MultiColvarBaseprotected
mydataPLMD::vesselbase::ActionWithVesselprotected
mymatrixPLMD::adjmat::ActionWithInputMatrixprotected
nblockPLMD::multicolvar::MultiColvarBaseprotected
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
normalizeVector(std::vector< double > &vals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::vesselbase::ActionWithVesselinlinevirtual
number_of_clusterPLMD::adjmat::ClusteringBaseprotected
parse(const std::string &key, T &t)PLMD::Action
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
parseMultiColvarAtomList(const std::string &key, const int &num, std::vector< AtomNumber > &t)PLMD::multicolvar::MultiColvarBaseprotected
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
performClustering()=0PLMD::adjmat::ClusteringBasepure virtual
performTask(const unsigned &, const unsigned &, MultiValue &) const overridePLMD::multicolvar::MultiColvarBasevirtual
plumedPLMD::Action
prepare() overridePLMD::multicolvar::MultiColvarBasevirtual
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
readAtomsLikeKeyword(const std::string &key, const int &natoms, std::vector< AtomNumber > &all_atoms)PLMD::multicolvar::MultiColvarBaseprotected
readGroupKeywords(const std::string &key0, const std::string &key1, const std::string &key2, const std::string &key3, const bool &no_third_dim_accum, const bool &symmetric, std::vector< AtomNumber > &all_atoms)PLMD::multicolvar::MultiColvarBaseprotected
readThreeGroups(const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2, const bool &no_third_dim_accum, std::vector< AtomNumber > &all_atoms)PLMD::multicolvar::MultiColvarBaseprotected
readTwoGroups(const std::string &key0, const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms)PLMD::multicolvar::MultiColvarBaseprotected
readVesselKeywords()PLMD::vesselbase::ActionWithVesselprotected
registerKeywords(Keywords &keys)PLMD::adjmat::ClusteringBasestatic
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
resizeBookeepingArray(const unsigned &num1, const unsigned &num2)PLMD::multicolvar::MultiColvarBaseprotected
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
retrieveAtoms() overridePLMD::multicolvar::MultiColvarBasevirtual
retrieveAtomsInCluster(const unsigned &clust, std::vector< unsigned > &myatoms) constPLMD::adjmat::ClusteringBasevirtual
retrieveConnectionValue(const unsigned &i, const unsigned &j, std::vector< double > &vals) constPLMD::adjmat::ActionWithInputMatrix
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setAtomsForCentralAtom(const std::vector< bool > &catom_ind)PLMD::multicolvar::MultiColvarBaseprotected
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setLinkCellCutoff(const double &lcut, double tcut=-1.0)PLMD::multicolvar::MultiColvarBaseprotected
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
setupActiveTaskSet(std::vector< unsigned > &active_tasks, const std::string &input_label)PLMD::multicolvar::MultiColvarBaseprotected
setupCurrentAtomList(const unsigned &taskCode, AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBaseprotected
setupLinkCells()PLMD::multicolvar::MultiColvarBaseprotected
setupMultiColvarBase(const std::vector< AtomNumber > &atoms)PLMD::multicolvar::MultiColvarBaseprotected
setupNonUseSpeciesLinkCells(const unsigned &)PLMD::multicolvar::MultiColvarBaseprotected
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
splitInputDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBaseprotected
storedValueIsActive(const unsigned &iatom)PLMD::multicolvar::MultiColvarBase
taskFlagsPLMD::vesselbase::ActionWithVesselprotected
taskIsCurrentlyActive(const unsigned &index) constPLMD::vesselbase::ActionWithVessel
threadSafe() const overridePLMD::multicolvar::MultiColvarBaseinlinevirtual
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::vesselbase::ActionWithVesselvirtual
turnOnDerivatives() overridePLMD::adjmat::ClusteringBasevirtual
unlockRequests() overridePLMD::ActionAtomisticinlinevirtual
update()PLMD::Actioninlinevirtual
updateActiveAtoms(AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBasevirtual
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
usesPbc() constPLMD::multicolvar::MultiColvarBaseinline
usespeciesPLMD::multicolvar::MultiColvarBaseprotected
usingLowMem() constPLMD::vesselbase::ActionWithVesselinlineprotected
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
which_clusterPLMD::adjmat::ClusteringBaseprotected
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
~MultiColvarBase()PLMD::multicolvar::MultiColvarBaseinline
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