| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
| actionStride | PLMD::ActionPilot | private |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| activate() | PLMD::Action | virtual |
| adamw_ | PLMD::ves::Opt_Adam | private |
| addCoeffsSetIDsToFilenames(std::vector< std::string > &, std::string &) | PLMD::ves::Optimizer | protected |
| addComponent(const std::string &valname, const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &valname, const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | virtual |
| addDependency(Action *) | PLMD::Action | |
| addValue(const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | |
| addValueWithDerivatives(const std::vector< std::size_t > &shape=std::vector< std::size_t >()) | PLMD::ActionWithValue | virtual |
| amsgrad_ | PLMD::ves::Opt_Adam | private |
| apply() override | PLMD::ves::Optimizer | inlinevirtual |
| aux_coeffs_pntrs_ | PLMD::ves::Optimizer | private |
| AuxCoeffs(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| aver_gradient_pntrs_ | PLMD::ves::Optimizer | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| beta_1_ | PLMD::ves::Opt_Adam | private |
| beta_2_ | PLMD::ves::Opt_Adam | private |
| bias_output_active_ | PLMD::ves::Optimizer | private |
| bias_output_stride_ | PLMD::ves::Optimizer | private |
| bias_pntrs_ | PLMD::ves::Optimizer | private |
| calculate() override | PLMD::ves::Optimizer | inlinevirtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
| calculateOnUpdate() | PLMD::ActionWithValue | virtual |
| castToActionAtomistic() noexcept | PLMD::Action | inlinevirtual |
| castToActionForInterface() noexcept | PLMD::Action | 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) | PLMD::ActionWithValue | virtual |
| clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
| clearOptions() | PLMD::Action | virtual |
| Coeffs(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| coeffs_mask_pntrs_ | PLMD::ves::Optimizer | private |
| coeffs_output_fmt_ | PLMD::ves::Optimizer | private |
| coeffs_pntrs_ | PLMD::ves::Optimizer | private |
| coeffs_wstride_ | PLMD::ves::Optimizer | private |
| CoeffsMask(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| coeffsOFiles_ | PLMD::ves::Optimizer | private |
| coeffssetid_prefix_ | PLMD::ves::Optimizer | private |
| coeffsUpdate(const unsigned int c_id=0) override | PLMD::ves::Opt_Adam | virtual |
| comm | PLMD::Action | |
| componentIsNotPeriodic(const std::string &valname) | PLMD::ActionWithValue | |
| componentIsPeriodic(const std::string &valname, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| copyOutput(const std::string &valname) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| current_stepsizes | PLMD::ves::Optimizer | private |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| description_ | PLMD::ves::Optimizer | private |
| diagonal_hessian_ | PLMD::ves::Optimizer | private |
| diagonalHessian() const | PLMD::ves::Optimizer | inline |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| dynamic_targetdists_ | PLMD::ves::Optimizer | private |
| dynamicStepSize() const | PLMD::ves::Optimizer | inline |
| enableHessian(VesBias *, const bool diagonal_hessian=false) | PLMD::ves::Optimizer | protected |
| epsilon_ | PLMD::ves::Opt_Adam | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &valname) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| fclose(FILE *fp) | PLMD::Action | |
| fes_output_active_ | PLMD::ves::Optimizer | private |
| fes_output_stride_ | PLMD::ves::Optimizer | private |
| fesproj_output_active_ | PLMD::ves::Optimizer | private |
| fesproj_output_stride_ | PLMD::ves::Optimizer | private |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| firststep | PLMD::ActionWithValue | private |
| fixed_stepsize_ | PLMD::ves::Optimizer | private |
| fixedStepSize() const | PLMD::ves::Optimizer | inline |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forcesForApply | PLMD::ActionWithValue | private |
| getAuxCoeffsPntrs() const | PLMD::ves::Optimizer | inline |
| getBiasOutputStride() const | PLMD::ves::Optimizer | inline |
| getBiasPntrs() const | PLMD::ves::Optimizer | inline |
| getCoeffsMaskPntrs() const | PLMD::ves::Optimizer | inline |
| getCoeffsPntrs() const | PLMD::ves::Optimizer | inline |
| getComponent(const std::string &valname) const | PLMD::ActionWithValue | private |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getConstPntrToComponent(unsigned i) const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getCurrentStepSize(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inline |
| getCurrentStepSizes() const | PLMD::ves::Optimizer | inline |
| getDefaultString() const | PLMD::Action | inline |
| getDependencies() const | PLMD::Action | inline |
| getDescription() const | PLMD::ves::Optimizer | inline |
| getExchangeStep() const | PLMD::Action | |
| getFesOutputStride() const | PLMD::ves::Optimizer | inline |
| getFesProjOutputStride() const | PLMD::ves::Optimizer | inline |
| getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
| getGradientPntrs() const | PLMD::ves::Optimizer | inline |
| getHessianPntrs() const | PLMD::ves::Optimizer | inline |
| getIterationCounter() const | PLMD::ves::Optimizer | inline |
| getIterationCounterDbl() const | PLMD::ves::Optimizer | inline |
| getIterationCounterStr(const int offset=0) const | PLMD::ves::Optimizer | |
| 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::ves::Optimizer | 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 &valname) const | PLMD::ActionWithValue | inline |
| getPntrToComponent(unsigned i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &valname) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
| getRestart() const | PLMD::Action | inline |
| getStep() const | PLMD::Action | |
| getStepSize(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inline |
| getStepSizes() const | PLMD::ves::Optimizer | inline |
| getStride() const | PLMD::ActionPilot | |
| getTargetDistAveragesPntrs() const | PLMD::ves::Optimizer | inline |
| getTargetDistOutputStride() const | PLMD::ves::Optimizer | inline |
| getTargetDistProjOutputStride() const | PLMD::ves::Optimizer | inline |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getType() const | PLMD::ves::Optimizer | inline |
| getUnits() const | PLMD::Action | protected |
| Gradient(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| gradient_output_fmt_ | PLMD::ves::Optimizer | private |
| gradient_pntrs_ | PLMD::ves::Optimizer | private |
| gradient_wstride_ | PLMD::ves::Optimizer | private |
| gradientOFiles_ | PLMD::ves::Optimizer | private |
| Hessian(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| hessian_covariance_from_averages_ | PLMD::ves::Optimizer | private |
| hessian_output_fmt_ | PLMD::ves::Optimizer | private |
| hessian_pntrs_ | PLMD::ves::Optimizer | private |
| hessian_wstride_ | PLMD::ves::Optimizer | private |
| hessianOFiles_ | PLMD::ves::Optimizer | private |
| identical_coeffs_shape_ | PLMD::ves::Optimizer | private |
| increaseIterationCounter() | PLMD::ves::Optimizer | inline |
| isActive() const | PLMD::Action | inline |
| isBiasOutputActive() const | PLMD::ves::Optimizer | inline |
| isFesOutputActive() const | PLMD::ves::Optimizer | inline |
| isFesProjOutputActive() const | PLMD::ves::Optimizer | inline |
| isFirstStep | PLMD::ves::Optimizer | private |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isTargetDistOutputActive() const | PLMD::ves::Optimizer | inline |
| isTargetDistProjOutputActive() const | PLMD::ves::Optimizer | inline |
| iter_counter | PLMD::ves::Optimizer | private |
| keywords | PLMD::Action | |
| lockRequests() | PLMD::Action | inlinevirtual |
| log | PLMD::Action | |
| monitor_instantaneous_gradient_ | PLMD::ves::Optimizer | private |
| multi_sim_comm | PLMD::Action | |
| mwalkers_mpi_single_files_ | PLMD::ves::Optimizer | private |
| nbiases_ | PLMD::ves::Optimizer | private |
| ncoeffssets_ | PLMD::ves::Optimizer | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| numberOfBiases() const | PLMD::ves::Optimizer | inline |
| numberOfCoeffsSets() const | PLMD::ves::Optimizer | inline |
| numericalDerivatives | PLMD::ActionWithValue | private |
| one_minus_weight_decay_ | PLMD::ves::Opt_Adam | private |
| onStep() const | PLMD::ActionPilot | virtual |
| Opt_Adam(const ActionOptions &) | PLMD::ves::Opt_Adam | explicit |
| Optimizer(const ActionOptions &ao) | PLMD::ves::Optimizer | explicit |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseFilenames(const std::string &, std::vector< std::string > &, const std::string &) | PLMD::ves::Optimizer | inlineprotected |
| parseFilenames(const std::string &, std::vector< std::string > &) | PLMD::ves::Optimizer | inlineprotected |
| parseFlag(const std::string &key, bool &t) | PLMD::Action | |
| parseMultipleValues(const std::string &, std::vector< T > &) | PLMD::ves::Optimizer | protected |
| parseMultipleValues(const std::string &, std::vector< T > &, const T &) | PLMD::ves::Optimizer | 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 | |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| readCoeffsFromFiles(const std::vector< std::string > &, const bool) | PLMD::ves::Optimizer | private |
| registerKeywords(Keywords &) | PLMD::ves::Opt_Adam | static |
| resetStoredTimestep() | PLMD::Action | |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| setAllCoeffsSetIterationCounters() | PLMD::ves::Optimizer | private |
| setBiasOutputStride(unsigned int stride) | PLMD::ves::Optimizer | inline |
| setCurrentStepSize(const double, const unsigned int i=0) | PLMD::ves::Optimizer | inlineprotected |
| setCurrentStepSizes(const std::vector< double > &) | PLMD::ves::Optimizer | inlineprotected |
| setFesOutputStride(unsigned int stride) | PLMD::ves::Optimizer | inline |
| setFesProjOutputStride(unsigned int stride) | PLMD::ves::Optimizer | inline |
| setGradientsIfNeeded() | PLMD::ActionWithValue | virtual |
| setIterationCounter(const unsigned int) | PLMD::ves::Optimizer | inline |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setStepSize(const double, const unsigned int coeffs_id=0) | PLMD::ves::Optimizer | inline |
| setStepSizes(const std::vector< double > &) | PLMD::ves::Optimizer | inline |
| setStride(unsigned n) | PLMD::ActionPilot | |
| setTargetDistOutputStride(unsigned int stride) | PLMD::ves::Optimizer | inline |
| setTargetDistProjOutputStride(unsigned int stride) | PLMD::ves::Optimizer | inline |
| setupConstantValues(const bool &have_atoms) | PLMD::Action | |
| setupOFiles(std::vector< std::string > &, std::vector< std::unique_ptr< OFile > > &, const bool multi_sim_single_files=false) | PLMD::ves::Optimizer | protected |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| StepSize(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | inlineprotected |
| stepsizes_ | PLMD::ves::Optimizer | private |
| targetdist_averages_output_fmt_ | PLMD::ves::Optimizer | private |
| targetdist_averages_pntrs_ | PLMD::ves::Optimizer | private |
| targetdist_averages_wstride_ | PLMD::ves::Optimizer | private |
| targetdist_averagesOFiles_ | PLMD::ves::Optimizer | private |
| targetdist_output_active_ | PLMD::ves::Optimizer | private |
| targetdist_output_stride_ | PLMD::ves::Optimizer | private |
| targetdist_proj_output_active_ | PLMD::ves::Optimizer | private |
| targetdist_proj_output_stride_ | PLMD::ves::Optimizer | private |
| TargetDistAverages(const unsigned int coeffs_id=0) const | PLMD::ves::Optimizer | protected |
| time_ | PLMD::ves::Opt_Adam | private |
| turnOffCoeffsOutputFiles() | PLMD::ves::Optimizer | protected |
| turnOffHessian() | PLMD::ves::Optimizer | protected |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| turnOnHessian() | PLMD::ves::Optimizer | protected |
| type_ | PLMD::ves::Optimizer | private |
| unlockRequests() | PLMD::Action | inlinevirtual |
| update() override | PLMD::ves::Optimizer | virtual |
| updateOutputComponents() | PLMD::ves::Optimizer | private |
| use_hessian_ | PLMD::ves::Optimizer | private |
| use_mwalkers_mpi_ | PLMD::ves::Optimizer | private |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useDynamicStepSizeKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useDynamicTargetDistributionKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useFixedStepSizeKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useHessian() const | PLMD::ves::Optimizer | inline |
| useHessianKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useMaskKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useMonitorAverageGradientKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useMultipleWalkers() const | PLMD::ves::Optimizer | inline |
| useMultipleWalkersKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| useRestartKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| useReweightFactorKeywords(Keywords &) | PLMD::ves::Optimizer | static |
| usingNaturalUnits() const | PLMD::Action | protected |
| ustride_reweightfactor_ | PLMD::ves::Optimizer | private |
| ustride_targetdist_ | PLMD::ves::Optimizer | private |
| valsToForce | PLMD::ActionWithValue | private |
| values | PLMD::ActionWithValue | private |
| var_coeffs_pntrs_ | PLMD::ves::Opt_Adam | private |
| VarCoeffs(const unsigned int coeffs_id=0) const | PLMD::ves::Opt_Adam | inlineprotected |
| varmax_coeffs_pntrs_ | PLMD::ves::Opt_Adam | private |
| VarmaxCoeffs(const unsigned int coeffs_id=0) const | PLMD::ves::Opt_Adam | inlineprotected |
| warning(const std::string &msg) | PLMD::Action | |
| writeBiasOutputFiles() const | PLMD::ves::Optimizer | |
| writeFesOutputFiles() const | PLMD::ves::Optimizer | |
| writeFesProjOutputFiles() const | PLMD::ves::Optimizer | |
| writeInGraph() const | PLMD::Action | virtual |
| writeOutputFiles(const unsigned int coeffs_id=0) | PLMD::ves::Optimizer | private |
| writeTargetDistOutputFiles() const | PLMD::ves::Optimizer | |
| writeTargetDistProjOutputFiles() const | PLMD::ves::Optimizer | |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~Optimizer() | PLMD::ves::Optimizer | |
1.13.2