Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionForInterface(const ActionOptions &ao) | PLMD::ActionForInterface | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addComponent(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | virtual |
addDependency(Action *) | PLMD::Action | |
addValue(const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | |
addValueWithDerivatives(const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | virtual |
after | PLMD::Action | private |
apply()=0 | PLMD::Action | pure virtual |
Atoms class | PLMD::ActionForInterface | friend |
beforeUpdate() | PLMD::Action | inlinevirtual |
calculate() override | PLMD::ActionForInterface | inlinevirtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
calculateOnUpdate() | PLMD::ActionWithValue | virtual |
castToActionAtomistic() noexcept | PLMD::Action | inlinevirtual |
castToActionForInterface() noexcept final | PLMD::ActionForInterface | inlinevirtual |
castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
castToActionWithValue() noexcept final | PLMD::ActionWithValue | inlinevirtual |
castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkForDependency(Action *) | PLMD::Action | |
checkForForces() | PLMD::ActionWithValue | protected |
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(const bool &force=false) override | PLMD::ActionForInterface | inlinevirtual |
clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
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 | |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
deactivate() | PLMD::Action | inlinevirtual |
defaults | PLMD::Action | private |
Dependencies typedef | PLMD::Action | |
doCheckPoint | PLMD::Action | private |
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 | |
firststep | PLMD::ActionForInterface | protected |
fopen(const char *path, const char *mode) | PLMD::Action | |
forcesForApply | PLMD::ActionWithValue | private |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getConstPntrToComponent(int i) const | PLMD::ActionWithValue | protected |
getCPT() const | PLMD::Action | |
getDefaultString() const | PLMD::Action | inline |
getDependencies() const | PLMD::Action | inline |
getExchangeStep() const | PLMD::Action | |
getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
getKBoltzmann() const | PLMD::Action | protected |
getkBT() | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getMatrixColumnTitles(std::vector< std::string > &argnames) const | PLMD::ActionWithValue | virtual |
getName() const | PLMD::Action | inline |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::ActionForInterface | inlinevirtual |
getNumberOfForcesToRescale() const | PLMD::ActionForInterface | inlinevirtual |
getOutputComponentDescription(const std::string &cname, const Keywords &keys) const | PLMD::ActionWithValue | virtual |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
getRestart() const | PLMD::Action | inline |
getRole() const | PLMD::ActionForInterface | |
getStep() const | PLMD::Action | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getUnits() const | PLMD::Action | protected |
hasBeenSet() const | PLMD::ActionForInterface | inline |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
lockRequests() | PLMD::Action | inlinevirtual |
log | PLMD::Action | |
multi_sim_comm | PLMD::Action | |
name | PLMD::Action | private |
never_activate | PLMD::Action | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
numericalDerivatives | PLMD::ActionWithValue | private |
onStep() const =0 | PLMD::ActionForInterface | pure 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 | |
plumed | PLMD::Action | |
PlumedMain class | PLMD::ActionForInterface | friend |
prepare() | PLMD::Action | virtual |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readBinary(std::istream &i)=0 | PLMD::ActionForInterface | pure virtual |
registerKeywords(Keywords &keys) | PLMD::ActionForInterface | static |
replica_index | PLMD::Action | private |
reset() | PLMD::ActionForInterface | inlinevirtual |
resetForStepStart()=0 | PLMD::ActionForInterface | pure virtual |
resetStoredTimestep() | PLMD::Action | |
restart | PLMD::Action | private |
role | PLMD::ActionForInterface | protected |
runFinalJobs() | PLMD::Action | inlinevirtual |
Set_comm(Communicator &comm)=0 | PLMD::ActionForInterface | pure virtual |
setForcePointer(const std::string &name, const TypesafePtr &)=0 | PLMD::ActionForInterface | pure virtual |
setGradientsIfNeeded() override | PLMD::ActionForInterface | inlinevirtual |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setStart(const std::string &name, const unsigned &sss)=0 | PLMD::ActionForInterface | pure virtual |
setStride(const std::string &name, const unsigned &sss)=0 | PLMD::ActionForInterface | pure virtual |
setupConstantValues(const bool &have_atoms) | PLMD::Action | |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
setValuePointer(const std::string &name, const TypesafePtr &)=0 | PLMD::ActionForInterface | pure virtual |
share()=0 | PLMD::ActionForInterface | pure virtual |
shareAll()=0 | PLMD::ActionForInterface | pure virtual |
timestep | PLMD::Action | private |
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 |
usingNaturalUnits() const | PLMD::Action | protected |
valsToForce | PLMD::ActionWithValue | private |
values | PLMD::ActionWithValue | private |
wait()=0 | PLMD::ActionForInterface | pure virtual |
warning(const std::string &msg) | PLMD::Action | |
wasscaled | PLMD::ActionForInterface | protected |
wasset | PLMD::ActionForInterface | protected |
writeBinary(std::ostream &o)=0 | PLMD::ActionForInterface | pure virtual |
writeInGraph() const | PLMD::Action | virtual |
~Action() | PLMD::Action | virtual |
~ActionWithValue() | PLMD::ActionWithValue | |