ablocks | PLMD::multicolvar::MultiColvarBase | protected |
accumulateSymmetryFunction(const int &ival, const unsigned &iatom, const double &val, const Vector &der, const Tensor &vir, multicolvar::AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
Action(const ActionOptions &) | PLMD::Action | explicit |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
activate() | PLMD::Action | virtual |
addAtomDerivatives(const int &, const unsigned &, const Vector &, multicolvar::AtomValuePack &) const | PLMD::multicolvar::MultiColvarBase | |
addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
addComponent(const std::string &name) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
addDependency(Action *) | PLMD::Action | |
addTaskToList(const unsigned &taskCode) | PLMD::multicolvar::MultiColvarBase | protected |
addValue() | PLMD::ActionWithValue | |
addValueWithDerivatives() | PLMD::ActionWithValue | |
addVessel(const std::string &name, const std::string &input, const int numlab=0) | PLMD::vesselbase::ActionWithVessel | protected |
addVessel(std::unique_ptr< Vessel > vv) | PLMD::vesselbase::ActionWithVessel | protected |
allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
apply() override | PLMD::multicolvar::MultiColvarBase | virtual |
applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
applyForces() | PLMD::ActionAtomistic | |
applyPbc(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::multicolvar::MultiColvarBase | |
atom_lab | PLMD::multicolvar::MultiColvarBase | protected |
atoms | PLMD::ActionAtomistic | protected |
beforeUpdate() | PLMD::Action | inlinevirtual |
bookeeping | PLMD::multicolvar::MultiColvarBase | protected |
bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
buildDataStashes(ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
buildSets() | PLMD::multicolvar::MultiColvarBase | protected |
calculate() override | PLMD::multicolvar::MultiColvarBase | virtual |
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) | PLMD::vesselbase::ActionWithVessel | protected |
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::multicolvar::MultiColvarBase | virtual |
calculateWeight(const unsigned &taskCode, const double &weight, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | virtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
PLMD::ActionWithValue::checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearDerivatives() | PLMD::ActionWithValue | virtual |
clearInputForces() | PLMD::ActionWithValue | |
clearOptions() | PLMD::Action | virtual |
clearOutputForces() | PLMD::ActionAtomistic | |
comm | PLMD::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::ActionWithValue | static |
compute(const unsigned &tindex, AtomValuePack &myatoms) const override | PLMD::multicolvar::LocalAverage | virtual |
contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | protected |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
deactivate() | PLMD::Action | inlinevirtual |
deactivateAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
decodeIndexToAtoms(const unsigned &taskCode, std::vector< unsigned > &atoms) const | PLMD::multicolvar::MultiColvarBase | protected |
decoder | PLMD::multicolvar::MultiColvarBase | protected |
Dependencies typedef | PLMD::Action | |
derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
dertime | PLMD::vesselbase::ActionWithVessel | protected |
doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
doNotCalculateDerivatives() const override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
doNotCalculateDirector() | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
doNotForce() | PLMD::ActionAtomistic | inline |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
filtersUsedAsInput() | PLMD::multicolvar::MultiColvarBase | protected |
finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
fopen(const char *path, const char *mode) | PLMD::Action | |
getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
getAbsoluteIndexOfCentralAtom(const unsigned &i) const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getBaseMultiColvar(const unsigned &icolv) const | PLMD::multicolvar::MultiColvarBase | inline |
getBox() const | PLMD::ActionAtomistic | inline |
getCentralAtomPack(const unsigned &basn, const unsigned &curr, CatomPack &mypack) | PLMD::multicolvar::MultiColvarBase | virtual |
getCentralAtomPos(const unsigned &curr) | PLMD::multicolvar::MultiColvarBase | virtual |
getCharge(int i) const | PLMD::ActionAtomistic | inline |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getEnergy() const | PLMD::ActionAtomistic | inline |
getExchangeStep() const | PLMD::Action | |
getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
getInputData(const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient) const | PLMD::multicolvar::MultiColvarBase | virtual |
getInputDerivatives(const unsigned &iatom, const bool &normed, const multicolvar::AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | virtual |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getLinkCellCutoff() const | PLMD::multicolvar::MultiColvarBase | protected |
getMass(int i) const | PLMD::ActionAtomistic | inline |
getName() const | PLMD::Action | inline |
getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
getNumberOfBaseMultiColvars() const | PLMD::multicolvar::MultiColvarBase | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
getNumberOfQuantities() const override | PLMD::multicolvar::LocalAverage | virtual |
getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inline |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPbc() const | PLMD::ActionAtomistic | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | protected |
getPntrToVessel(const unsigned &i) | PLMD::vesselbase::ActionWithVessel | inline |
getPosition(int) const | PLMD::ActionAtomistic | inline |
getPositionInCurrentTaskList(const unsigned &myind) const | PLMD::vesselbase::ActionWithVessel | inline |
getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getPositionOfAtomForLinkCells(const unsigned &iatom) const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
getPositions() const | PLMD::ActionAtomistic | inline |
getRestart() const | PLMD::Action | inline |
getSeparation(const Vector &vec1, const Vector &vec2) const | PLMD::multicolvar::MultiColvarBase | |
getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
getStep() const | PLMD::Action | |
getTaskCode(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getTotAtoms() const | PLMD::ActionAtomistic | inline |
getUnique() const | PLMD::ActionAtomistic | inline |
getUniqueLocal() const | PLMD::ActionAtomistic | inline |
getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
hasDifferentiableOrientation() const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
isActive() const | PLMD::Action | inline |
isCurrentlyActive(const unsigned &code) | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
isDensity() const | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isPeriodic() override | PLMD::multicolvar::LocalAverage | inlinevirtual |
keywords | PLMD::Action | |
LocalAverage(const ActionOptions &) | PLMD::multicolvar::LocalAverage | explicit |
lockContributors() | PLMD::vesselbase::ActionWithVessel | |
lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
log | PLMD::Action | |
makeWhole() | PLMD::ActionAtomistic | |
matsums | PLMD::multicolvar::MultiColvarBase | protected |
mergeInputDerivatives(const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
modifyForces() | PLMD::ActionAtomistic | inline |
modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
modifyVirial() | PLMD::ActionAtomistic | inline |
multi_sim_comm | PLMD::Action | |
MultiColvarBase(const ActionOptions &) | PLMD::multicolvar::MultiColvarBase | explicit |
mybasedata | PLMD::multicolvar::MultiColvarBase | protected |
mybasemulticolvars | PLMD::multicolvar::MultiColvarBase | protected |
mydata | PLMD::vesselbase::ActionWithVessel | protected |
nblock | PLMD::multicolvar::MultiColvarBase | protected |
needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
normalizeVector(std::vector< double > &vals) const override | PLMD::multicolvar::LocalAverage | inlinevirtual |
normalizeVectorDerivatives(MultiValue &myvals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
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::MultiColvarBase | protected |
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) const | PLMD::ActionAtomistic | |
pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
performTask(const unsigned &, const unsigned &, MultiValue &) const override | PLMD::multicolvar::MultiColvarBase | virtual |
plumed | PLMD::Action | |
prepare() override | PLMD::multicolvar::MultiColvarBase | virtual |
rcut2 | PLMD::multicolvar::LocalAverage | private |
readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
readAtomsLikeKeyword(const std::string &key, const int &natoms, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
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::MultiColvarBase | protected |
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::MultiColvarBase | protected |
readTwoGroups(const std::string &key0, const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms) | PLMD::multicolvar::MultiColvarBase | protected |
readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
registerKeywords(Keywords &keys) | PLMD::multicolvar::LocalAverage | static |
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
resizeBookeepingArray(const unsigned &num1, const unsigned &num2) | PLMD::multicolvar::MultiColvarBase | protected |
resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
retrieveAtoms() override | PLMD::multicolvar::MultiColvarBase | virtual |
retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
runFinalJobs() | PLMD::Action | inlinevirtual |
serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
setAtomsForCentralAtom(const std::vector< bool > &catom_ind) | PLMD::multicolvar::MultiColvarBase | protected |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
setLinkCellCutoff(const double &lcut, double tcut=-1.0) | PLMD::multicolvar::MultiColvarBase | protected |
setLowMemOption(const bool &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setupActiveTaskSet(std::vector< unsigned > &active_tasks, const std::string &input_label) | PLMD::multicolvar::MultiColvarBase | protected |
setupCurrentAtomList(const unsigned &taskCode, AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | protected |
setupLinkCells() | PLMD::multicolvar::MultiColvarBase | protected |
setupMultiColvarBase(const std::vector< AtomNumber > &atoms) | PLMD::multicolvar::MultiColvarBase | protected |
setupNonUseSpeciesLinkCells(const unsigned &) | PLMD::multicolvar::MultiColvarBase | protected |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
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) const | PLMD::multicolvar::MultiColvarBase | protected |
storedValueIsActive(const unsigned &iatom) | PLMD::multicolvar::MultiColvarBase | |
switchingFunction | PLMD::multicolvar::LocalAverage | private |
taskFlags | PLMD::vesselbase::ActionWithVessel | protected |
taskIsCurrentlyActive(const unsigned &index) const | PLMD::vesselbase::ActionWithVessel | |
threadSafe() const override | PLMD::multicolvar::MultiColvarBase | inlinevirtual |
transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
turnOnDerivatives() override | PLMD::multicolvar::MultiColvarBase | virtual |
unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
updateActiveAtoms(AtomValuePack &myatoms) const | PLMD::multicolvar::MultiColvarBase | virtual |
updateUniqueLocal() | PLMD::ActionAtomistic | |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
usesPbc() const | PLMD::multicolvar::MultiColvarBase | inline |
usespecies | PLMD::multicolvar::MultiColvarBase | protected |
usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
warning(const std::string &msg) | PLMD::Action | |
weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
~Action() | PLMD::Action | virtual |
~ActionAtomistic() | PLMD::ActionAtomistic | |
~ActionWithValue() | PLMD::ActionWithValue | |
~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
~MultiColvarBase() | PLMD::multicolvar::MultiColvarBase | inline |