Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
actionIsBridged | PLMD::vesselbase::ActionWithVessel | private |
ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
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 | |
addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
addTaskToList(const unsigned &taskCode) | PLMD::vesselbase::ActionWithVessel | 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 |
after | PLMD::Action | private |
allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
AnalysisBase(const ActionOptions &) | PLMD::analysis::AnalysisBase | explicit |
apply() override | PLMD::analysis::AnalysisBase | inlinevirtual |
applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
applyForces() | PLMD::ActionAtomistic | |
arguments | PLMD::ActionWithArguments | private |
atoms | PLMD::ActionAtomistic | protected |
beforeUpdate() | PLMD::Action | inlinevirtual |
bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
buffer | PLMD::vesselbase::ActionWithVessel | private |
buildDataStashes(ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
calculate() override | PLMD::analysis::AnalysisBase | inlinevirtual |
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::analysis::AnalysisBase | inlinevirtual |
changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
charges | PLMD::ActionAtomistic | private |
chargesWereSet | PLMD::ActionAtomistic | private |
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 |
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 |
Dependencies typedef | PLMD::Action | |
der_list | PLMD::vesselbase::ActionWithVessel | private |
derivativesAreRequired() const | PLMD::vesselbase::ActionWithVessel | inline |
dertime | PLMD::vesselbase::ActionWithVessel | protected |
dertime_can_be_off | PLMD::vesselbase::ActionWithVessel | private |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
dissimilaritiesWereSet() const | PLMD::analysis::AnalysisBase | inlinevirtual |
doCheckPoint | PLMD::Action | private |
doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
donotforce | PLMD::ActionAtomistic | private |
doNotForce() | PLMD::ActionAtomistic | inline |
donotretrieve | PLMD::ActionAtomistic | private |
doNotRetrieve() | PLMD::ActionAtomistic | inline |
energy | PLMD::ActionAtomistic | private |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
extraCV | PLMD::ActionAtomistic | private |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
fopen(const char *path, const char *mode) | PLMD::Action | |
forceOnEnergy | PLMD::ActionAtomistic | private |
forceOnExtraCV | PLMD::ActionAtomistic | private |
forces | PLMD::ActionAtomistic | private |
fullTaskList | PLMD::vesselbase::ActionWithVessel | private |
functions | PLMD::vesselbase::ActionWithVessel | private |
getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArgumentList() | PLMD::analysis::AnalysisBase | inlinevirtual |
getArgumentNames() | PLMD::analysis::AnalysisBase | |
getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getAtomIndexes() const | PLMD::analysis::AnalysisBase | inlinevirtual |
getBox() const | PLMD::ActionAtomistic | inline |
getCharge(int i) const | PLMD::ActionAtomistic | inline |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getCurrentNumberOfActiveTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
getDataPointIndexInBase(const unsigned &idata) const override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
getDependencies() const | PLMD::Action | inline |
getDissimilarity(const unsigned &i, const unsigned &j) override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
getDissimilarityInstruction() const | PLMD::analysis::AnalysisBase | inlinevirtual |
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 |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getMass(int i) const | PLMD::ActionAtomistic | inline |
getMetricName() const | PLMD::analysis::AnalysisBase | inlinevirtual |
getName() const | PLMD::Action | inline |
getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getNormalization() const | PLMD::analysis::AnalysisBase | inlinevirtual |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDataPoints() const override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
getNumberOfDerivatives() override | PLMD::analysis::AnalysisBase | inlinevirtual |
getNumberOfQuantities() const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
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 |
getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | 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 |
getPositions() const | PLMD::ActionAtomistic | inline |
getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
getRestart() const | PLMD::Action | inline |
getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
getStep() const | PLMD::Action | |
getStoredData(const unsigned &idat, const bool &calcdist) override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
getStride() const | PLMD::ActionPilot | |
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 | |
getWeight(const unsigned &idata) override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
indexes | PLMD::ActionAtomistic | private |
indexOfTaskInFullList | PLMD::vesselbase::ActionWithVessel | private |
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isPeriodic() override | PLMD::analysis::AnalysisBase | inlinevirtual |
keywords | PLMD::Action | |
label | PLMD::Action | private |
landmark_indices | PLMD::analysis::LandmarkSelectionBase | private |
LandmarkSelectionBase(const ActionOptions &ao) | PLMD::analysis::LandmarkSelectionBase | explicit |
line | PLMD::Action | private |
lockContributors() | PLMD::vesselbase::ActionWithVessel | |
lockRequestArguments | PLMD::ActionWithArguments | private |
lockRequestAtoms | PLMD::ActionAtomistic | private |
lockRequests() override | PLMD::analysis::AnalysisBase | inlinevirtual |
log | PLMD::Action | |
lowmem | PLMD::vesselbase::ActionWithVessel | private |
lweights | PLMD::analysis::LandmarkSelectionBase | private |
makeWhole() | PLMD::ActionAtomistic | |
masses | PLMD::ActionAtomistic | private |
maxderivatives | PLMD::vesselbase::ActionWithVessel | private |
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 | |
my_input_data | PLMD::analysis::AnalysisBase | protected |
mydata | PLMD::vesselbase::ActionWithVessel | protected |
nactive_tasks | PLMD::vesselbase::ActionWithVessel | private |
name | PLMD::Action | private |
needsDerivatives() | PLMD::vesselbase::ActionWithVessel | protected |
nl_tolerance | PLMD::vesselbase::ActionWithVessel | private |
nlandmarks | PLMD::analysis::LandmarkSelectionBase | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
PLMD::noderiv | PLMD::ActionWithValue | private |
normalizeVector(std::vector< double > &vals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
normalizeVectorDerivatives(MultiValue &myvals) const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
novoronoi | PLMD::analysis::LandmarkSelectionBase | private |
noweights | PLMD::analysis::LandmarkSelectionBase | private |
numericalDerivatives | PLMD::ActionWithValue | private |
onStep() const | PLMD::ActionPilot | virtual |
operator=(const Action &a)=delete | PLMD::Action | private |
options | PLMD::Action | private |
parse(const std::string &key, T &t) | PLMD::Action | |
parseArgumentList(const std::string &key, std::vector< Value * > &args) | PLMD::ActionWithArguments | |
parseArgumentList(const std::string &key, int i, 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 | |
parseVector(const std::string &key, std::vector< T > &t) | PLMD::Action | |
partialTaskList | PLMD::vesselbase::ActionWithVessel | private |
pbc | PLMD::ActionAtomistic | private |
pbc_fwd | PLMD::ActionAtomistic | private |
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
performAnalysis() override | PLMD::analysis::LandmarkSelectionBase | virtual |
performTask(const unsigned &, const unsigned &, MultiValue &) const override | PLMD::analysis::LandmarkSelectionBase | inlinevirtual |
plumed | PLMD::Action | |
positions | PLMD::ActionAtomistic | private |
prepare() | PLMD::Action | virtual |
PLMD::readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
PLMD::ActionAtomistic::readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
registerKeywords(Keywords &keys) | PLMD::analysis::LandmarkSelectionBase | static |
replica_index | PLMD::Action | private |
requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
ReselectLandmarks class | PLMD::analysis::LandmarkSelectionBase | friend |
resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
restart | PLMD::Action | private |
retrieveAtoms() | PLMD::ActionAtomistic | virtual |
retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
runFinalJobs() override | PLMD::analysis::AnalysisBase | virtual |
selectFrame(const unsigned &) | PLMD::analysis::LandmarkSelectionBase | protected |
selectLandmarks()=0 | PLMD::analysis::LandmarkSelectionBase | pure virtual |
serial | PLMD::vesselbase::ActionWithVessel | private |
serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
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 | |
setStride(const int &n) | PLMD::ActionPilot | |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
stopwatch | PLMD::vesselbase::ActionWithVessel | private |
stopwatch_fwd | PLMD::vesselbase::ActionWithVessel | private |
stride | PLMD::ActionPilot | private |
taskFlags | PLMD::vesselbase::ActionWithVessel | protected |
taskIsCurrentlyActive(const unsigned &index) const | PLMD::vesselbase::ActionWithVessel | |
threadSafe() const | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
timers | PLMD::vesselbase::ActionWithVessel | private |
tmpforces | PLMD::vesselbase::ActionWithVessel | private |
tolerance | PLMD::vesselbase::ActionWithVessel | private |
transformBridgedDerivatives(const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const | PLMD::vesselbase::ActionWithVessel | virtual |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
unique | PLMD::ActionAtomistic | private |
unique_local | PLMD::ActionAtomistic | private |
unlockRequests() override | PLMD::analysis::AnalysisBase | inlinevirtual |
update() override | PLMD::analysis::AnalysisBase | virtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateUniqueLocal() | PLMD::ActionAtomistic | |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
usingMemory() const | PLMD::analysis::AnalysisBase | inlinevirtual |
values | PLMD::ActionWithValue | private |
virial | PLMD::ActionAtomistic | private |
voronoiAnalysis(const std::vector< unsigned > &myindices, std::vector< double > &lweights, std::vector< unsigned > &assignments) const | PLMD::analysis::LandmarkSelectionBase | protected |
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 | |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |