Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
actionIsBridged | PLMD::vesselbase::ActionWithVessel | private |
ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
ActionWithInputVessel(const ActionOptions &) | PLMD::vesselbase::ActionWithInputVessel | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithInputVessel | inlinevirtual |
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::vesselbase::ActionWithInputVessel | protected |
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 |
apply() override | PLMD::manyrestraints::ManyRestraintsBase | virtual |
applyBridgeForces(const std::vector< double > &bb) override | PLMD::manyrestraints::ManyRestraintsBase | inlinevirtual |
arguments | PLMD::vesselbase::ActionWithInputVessel | private |
aves | PLMD::manyrestraints::ManyRestraintsBase | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
buffer | PLMD::vesselbase::ActionWithVessel | private |
buildDataStashes(ActionWithVessel *actionThatUses) | PLMD::vesselbase::ActionWithVessel | |
calcPotential(const double &val, double &df) const =0 | PLMD::manyrestraints::ManyRestraintsBase | pure virtual |
calculate() override | PLMD::manyrestraints::ManyRestraintsBase | inlinevirtual |
calculateAllVessels(const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) | PLMD::vesselbase::ActionWithVessel | protected |
calculateFromPDB(const PDB &) | PLMD::Action | |
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
PLMD::vesselbase::ActionWithInputVessel::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::vesselbase::ActionWithInputVessel | virtual |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearDerivatives() override | PLMD::manyrestraints::ManyRestraintsBase | inlinevirtual |
clearInputForces() | PLMD::ActionWithValue | |
clearOptions() | PLMD::Action | virtual |
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 |
deactivate_task(const unsigned &task_index) | PLMD::manyrestraints::ManyRestraintsBase | inline |
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 |
doCheckPoint | PLMD::Action | private |
doJobsRequiredBeforeTaskList() override | PLMD::manyrestraints::ManyRestraintsBase | virtual |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
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 | |
finishComputations(const std::vector< double > &buffer) | PLMD::vesselbase::ActionWithVessel | virtual |
fopen(const char *path, const char *mode) | PLMD::Action | |
fullTaskList | PLMD::vesselbase::ActionWithVessel | private |
functions | PLMD::vesselbase::ActionWithVessel | private |
getActiveTask(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | 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 |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
getFullNumberOfTasks() const | PLMD::vesselbase::ActionWithVessel | inline |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getName() const | PLMD::Action | inline |
getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::manyrestraints::ManyRestraintsBase | 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 |
getPntrToArgument() | PLMD::vesselbase::ActionWithInputVessel | inlineprotected |
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 |
getPositionInCurrentTaskList(const unsigned &myind) const | PLMD::vesselbase::ActionWithVessel | inline |
getPositionInFullTaskList(const unsigned &ii) const | PLMD::vesselbase::ActionWithVessel | inline |
getRestart() const | PLMD::Action | inline |
getSizeOfBuffer(unsigned &bufsize) | PLMD::vesselbase::ActionWithVessel | protected |
getStep() const | PLMD::Action | |
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 |
getVesselWithName(const std::string &mynam) | PLMD::vesselbase::ActionWithVessel | |
indexOfTaskInFullList | PLMD::vesselbase::ActionWithVessel | private |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isPeriodic() override | PLMD::manyrestraints::ManyRestraintsBase | inlinevirtual |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
lockContributors() | PLMD::vesselbase::ActionWithVessel | |
lockRequests() | PLMD::Action | inlinevirtual |
log | PLMD::Action | |
lowmem | PLMD::vesselbase::ActionWithVessel | private |
ManyRestraintsBase(const ActionOptions &) | PLMD::manyrestraints::ManyRestraintsBase | explicit |
maxderivatives | PLMD::vesselbase::ActionWithVessel | private |
multi_sim_comm | PLMD::Action | |
myBridgeVessel | PLMD::vesselbase::ActionWithInputVessel | private |
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 |
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 |
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 | |
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 |
performTask(const unsigned &, const unsigned &, MultiValue &) const override | PLMD::manyrestraints::ManyRestraintsBase | inlinevirtual |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
readArgument(const std::string &type) | PLMD::vesselbase::ActionWithInputVessel | protected |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
registerKeywords(Keywords &keys) | PLMD::manyrestraints::ManyRestraintsBase | static |
replica_index | PLMD::Action | private |
resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
restart | PLMD::Action | private |
retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
runFinalJobs() | PLMD::Action | inlinevirtual |
serial | PLMD::vesselbase::ActionWithVessel | private |
serialCalculation() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
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 override | PLMD::manyrestraints::ManyRestraintsBase | virtual |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
unlockRequests() | PLMD::Action | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
usingLowMem() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
values | PLMD::ActionWithValue | private |
warning(const std::string &msg) | PLMD::Action | |
weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
weightWithDerivatives() const | PLMD::vesselbase::ActionWithVessel | inline |
~Action() | PLMD::Action | virtual |
~ActionWithInputVessel() | PLMD::vesselbase::ActionWithInputVessel | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |