PLMD::multicolvar::ActionVolume Member List

This is the complete list of members for PLMD::multicolvar::ActionVolume, 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
ActionVolume(const ActionOptions &)PLMD::multicolvar::ActionVolumeexplicit
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::MultiColvarBaseprotected
addBridgeForces(const std::vector< double > &bb)PLMD::multicolvar::VolumeGradientBase
addBridgingVessel(ActionWithVessel *tome)PLMD::vesselbase::ActionWithVesselprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
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(Vessel *vv)PLMD::vesselbase::ActionWithVesselprotected
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
applyBridgeForces(const std::vector< double > &bb)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
applyForces()PLMD::ActionAtomistic
applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::multicolvar::MultiColvarBase
atom_labPLMD::multicolvar::MultiColvarBaseprotected
atomsPLMD::ActionAtomisticprotected
beforeUpdate()PLMD::Actioninlinevirtual
bookeepingPLMD::multicolvar::MultiColvarBaseprotected
BridgedMultiColvarFunction(const ActionOptions &)PLMD::multicolvar::BridgedMultiColvarFunctionexplicit
bridgeVariablePLMD::vesselbase::ActionWithVesselprotected
buildDataStashes(ActionWithVessel *actionThatUses)PLMD::vesselbase::ActionWithVessel
buildSets()PLMD::multicolvar::MultiColvarBaseprotected
calculate()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)PLMD::vesselbase::ActionWithVesselprotected
calculateAllVolumes(const unsigned &curr, MultiValue &outvals) constPLMD::multicolvar::ActionVolumevirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateCentralAtomPosition()PLMD::multicolvar::BridgedMultiColvarFunctioninline
calculateFromPDB(const PDB &)PLMD::Action
calculateNumberInside(const Vector &cpos, Vector &derivatives, Tensor &vir, std::vector< Vector > &refders) const =0PLMD::multicolvar::ActionVolumepure virtual
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
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() constPLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
clearOutputForces()PLMD::ActionAtomistic
commPLMD::Action
completeTask(const unsigned &curr, MultiValue &invals, MultiValue &outvals) constPLMD::multicolvar::VolumeGradientBasevirtual
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, AtomValuePack &myvals) constPLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
contributorsAreUnlockedPLMD::vesselbase::ActionWithVesselprotected
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
deactivate_task(const unsigned &taskno)PLMD::multicolvar::BridgedMultiColvarFunction
deactivateAllAtoms()PLMD::multicolvar::BridgedMultiColvarFunctionprotected
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::multicolvar::VolumeGradientBasevirtual
doNotCalculateDerivatives() constPLMD::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::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getAbsoluteIndexOfCentralAtom(const unsigned &i) constPLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getActiveTask(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getBaseMultiColvar(const unsigned &icolv) constPLMD::multicolvar::MultiColvarBaseinline
getBox() constPLMD::multicolvar::VolumeGradientBaseinlineprotected
getCentralAtomElementIndex()PLMD::multicolvar::ActionVolumeinline
getCentralAtomPack(const unsigned &basn, const unsigned &curr, CatomPack &mypack)PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
getCentralAtomPos(const unsigned &curr)PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
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
getIndexList(const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)PLMD::multicolvar::BridgedMultiColvarFunction
getInputData(const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient) constPLMD::multicolvar::MultiColvarBasevirtual
getInputDerivatives(const unsigned &iatom, const bool &normed, const multicolvar::AtomValuePack &myatoms) constPLMD::multicolvar::MultiColvarBasevirtual
getKernelType() constPLMD::multicolvar::ActionVolumeinlineprotected
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
getNumberOfBaseMultiColvars() constPLMD::multicolvar::MultiColvarBaseinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getNumberOfQuantities() constPLMD::multicolvar::ActionVolumeinlinevirtual
getNumberOfVessels() constPLMD::vesselbase::ActionWithVesselinline
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::multicolvar::VolumeGradientBaseinlineprotected
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToMultiColvar() constPLMD::multicolvar::BridgedMultiColvarFunctioninline
getPntrToValue()PLMD::ActionWithValueprotected
getPntrToVessel(const unsigned &i)PLMD::vesselbase::ActionWithVesselinline
getPosition(int iatom) constPLMD::multicolvar::VolumeGradientBaseinlineprotected
PLMD::multicolvar::BridgedMultiColvarFunction::getPosition(AtomNumber) constPLMD::ActionAtomisticinline
getPositionInCurrentTaskList(const unsigned &myind) constPLMD::vesselbase::ActionWithVesselinline
getPositionInFullTaskList(const unsigned &ii) constPLMD::vesselbase::ActionWithVesselinline
getPositionOfAtomForLinkCells(const unsigned &iatom) constPLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
getPositions() constPLMD::ActionAtomisticinline
getRestart() constPLMD::Actioninline
getSeparation(const Vector &vec1, const Vector &vec2) constPLMD::multicolvar::MultiColvarBaseprotected
getSigma() constPLMD::multicolvar::ActionVolumeinlineprotected
getSizeOfAtomsWithDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctioninline
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
inVolumeOfInterest(const unsigned &curr) constPLMD::multicolvar::ActionVolume
isActive() constPLMD::Actioninline
isCurrentlyActive(const unsigned &)PLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
isDensity() constPLMD::multicolvar::MultiColvarBaseinlinevirtual
isOptionOn(const std::string &s) constPLMD::Actioninline
isPeriodic()PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
kerneltypePLMD::multicolvar::ActionVolumeprivate
keywordsPLMD::Action
lockContributors()PLMD::vesselbase::ActionWithVessel
lockRequests()PLMD::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
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
multi_sim_commPLMD::Action
PLMD::multicolvar::MultiColvarBase::MultiColvarBase(const ActionOptions &)PLMD::multicolvar::MultiColvarBaseexplicit
mybasedataPLMD::multicolvar::MultiColvarBaseprotected
mybasemulticolvarsPLMD::multicolvar::MultiColvarBaseprotected
mydataPLMD::vesselbase::ActionWithVesselprotected
nblockPLMD::multicolvar::MultiColvarBaseprotected
needsDerivatives()PLMD::vesselbase::ActionWithVesselprotected
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
normalizeVector(std::vector< double > &vals) constPLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
normalizeVectorDerivatives(MultiValue &myvals) constPLMD::multicolvar::BridgedMultiColvarFunctioninlinevirtual
not_inPLMD::multicolvar::ActionVolumeprivate
nquantitiesPLMD::multicolvar::ActionVolumeprivate
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 &v1, const Vector &v2) constPLMD::multicolvar::VolumeGradientBaseinlineprotected
performTask(const unsigned &, const unsigned &, MultiValue &) constPLMD::multicolvar::BridgedMultiColvarFunctionvirtual
plumedPLMD::Action
prepare()PLMD::multicolvar::MultiColvarBasevirtual
readAtomsFromPDB(const PDB &pdb)PLMD::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::multicolvar::ActionVolumestatic
requestAtoms(const std::vector< AtomNumber > &atoms)PLMD::multicolvar::VolumeGradientBaseprotected
resizeBookeepingArray(const unsigned &num1, const unsigned &num2)PLMD::multicolvar::MultiColvarBaseprotected
resizeFunctions()PLMD::vesselbase::ActionWithVesselprotected
retrieveAtoms()PLMD::multicolvar::MultiColvarBasevirtual
retrieveCentralAtomPos()PLMD::multicolvar::BridgedMultiColvarFunction
retrieveDomain(std::string &min, std::string &max)PLMD::vesselbase::ActionWithVesselvirtual
runAllTasks()PLMD::vesselbase::ActionWithVesselprotected
runFinalJobs()PLMD::Actioninlinevirtual
serialCalculation() constPLMD::vesselbase::ActionWithVesselinlineprotected
setAtomActive(const unsigned &n)PLMD::multicolvar::BridgedMultiColvarFunctionprotected
setAtomsForCentralAtom(const std::vector< bool > &catom_ind)PLMD::multicolvar::MultiColvarBaseprotected
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
setNumberInVolume(const unsigned &, const unsigned &, const double &, const Vector &, const Tensor &, const std::vector< Vector > &, MultiValue &) constPLMD::multicolvar::VolumeGradientBaseprotected
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
setupRegions()=0PLMD::multicolvar::VolumeGradientBasepure virtual
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
sigmaPLMD::multicolvar::ActionVolumeprivate
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() constPLMD::multicolvar::MultiColvarBaseinlinevirtual
transformBridgedDerivatives(const unsigned &current, MultiValue &invals, MultiValue &outvals) constPLMD::multicolvar::BridgedMultiColvarFunctionvirtual
turnOnDerivatives()PLMD::multicolvar::BridgedMultiColvarFunctionvirtual
unlockRequests()PLMD::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
VolumeGradientBase(const ActionOptions &)PLMD::multicolvar::VolumeGradientBaseexplicit
warning(const std::string &msg)PLMD::Action
weightHasDerivativesPLMD::vesselbase::ActionWithVesselprotected
weightWithDerivatives() constPLMD::vesselbase::ActionWithVesselinline
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithValue()PLMD::ActionWithValue
~ActionWithVessel()PLMD::vesselbase::ActionWithVessel
~MultiColvarBase()PLMD::multicolvar::MultiColvarBaseinline
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