| Action(const ActionOptions &) | PLMD::Action | explicit |
| Action(const Action &a)=delete | PLMD::Action | private |
| ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
| ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | 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 | |
| addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c) | PLMD::ActionWithArguments | |
| 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() override | PLMD::bias::Bias | virtual |
| arguments | PLMD::ActionWithArguments | private |
| average_weights_ | PLMD::isdb::Metainference | private |
| average_weights_stride_ | PLMD::isdb::Metainference | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calculate() override | PLMD::isdb::Metainference | virtual |
| calculateConstantValues(const bool &have_atoms) | PLMD::ActionWithArguments | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
| PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | 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 |
| PLMD::castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::castToActionWithArguments() noexcept final | PLMD::ActionWithArguments | inlinevirtual |
| PLMD::castToActionWithValue() noexcept | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::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 |
| 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(const bool &force=false) | PLMD::ActionWithValue | virtual |
| 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 | |
| Dftilde_ | PLMD::isdb::Metainference | private |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| do_optsigmamean_ | PLMD::isdb::Metainference | private |
| do_regression_zero(const std::vector< double > &mean) | PLMD::isdb::Metainference | private |
| do_reweight_ | PLMD::isdb::Metainference | private |
| doCheckPoint | PLMD::Action | private |
| Doffset_ | PLMD::isdb::Metainference | private |
| doMonteCarlo(const std::vector< double > &mean) | PLMD::isdb::Metainference | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| dooffset_ | PLMD::isdb::Metainference | private |
| doregres_zero_ | PLMD::isdb::Metainference | private |
| doscale_ | PLMD::isdb::Metainference | private |
| Dscale_ | PLMD::isdb::Metainference | private |
| Dsigma_ | PLMD::isdb::Metainference | 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 |
| f | PLMD::bias::Bias | private |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| firststep | PLMD::ActionWithValue | private |
| firstTime | PLMD::isdb::Metainference | private |
| firstTimeW | PLMD::isdb::Metainference | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forces | PLMD::bias::Bias | private |
| forcesForApply | PLMD::ActionWithValue | private |
| ftilde_ | PLMD::isdb::Metainference | private |
| GAUSS enum value | PLMD::isdb::Metainference | private |
| gen_likelihood_ | PLMD::isdb::Metainference | private |
| GENERIC enum value | PLMD::isdb::Metainference | private |
| get_sigma_mean(const unsigned iselect, const double weight, const double norm, const double neff, const std::vector< double > &mean) | PLMD::isdb::Metainference | private |
| get_weights(const unsigned iselect, double &weight, double &norm, double &neff) | PLMD::isdb::Metainference | private |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| 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 |
| getEnergyForceGJ(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceGJE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceMIGEN(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceSP(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceSPE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyGJ(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergyGJE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergyMIGEN(const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergySP(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergySPE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| 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 |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::bias::Bias | 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 |
| getPntrToArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| getRestart() const | PLMD::Action | inline |
| getStep() const | PLMD::Action | |
| getStride() const | PLMD::ActionPilot | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getUnits() const | PLMD::Action | protected |
| interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg) | PLMD::ActionWithArguments | static |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::isdb::Metainference | private |
| keywords | PLMD::Action | |
| label | PLMD::Action | private |
| LIKE_GAUSS enum value | PLMD::isdb::Metainference | private |
| LIKE_LOGN enum value | PLMD::isdb::Metainference | private |
| line | PLMD::Action | private |
| lockRequestArguments | PLMD::ActionWithArguments | private |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| log | PLMD::Action | |
| master | PLMD::isdb::Metainference | private |
| MCaccept_ | PLMD::isdb::Metainference | private |
| MCacceptFT_ | PLMD::isdb::Metainference | private |
| MCacceptScale_ | PLMD::isdb::Metainference | private |
| MCchunksize_ | PLMD::isdb::Metainference | private |
| MCsteps_ | PLMD::isdb::Metainference | private |
| MCtrial_ | PLMD::isdb::Metainference | private |
| Metainference(const ActionOptions &) | PLMD::isdb::Metainference | explicit |
| MGAUSS enum value | PLMD::isdb::Metainference | private |
| MOUTLIERS enum value | PLMD::isdb::Metainference | private |
| moveScaleOffset(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::Metainference | private |
| moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow) | PLMD::isdb::Metainference | private |
| moveTilde(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::Metainference | private |
| multi_sim_comm | PLMD::Action | |
| N_optimized_step_ | PLMD::isdb::Metainference | private |
| name | PLMD::Action | private |
| narg | PLMD::isdb::Metainference | private |
| never_activate | PLMD::Action | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| noise_type_ | PLMD::isdb::Metainference | private |
| nregres_zero_ | PLMD::isdb::Metainference | private |
| nrep_ | PLMD::isdb::Metainference | private |
| numericalDerivatives | PLMD::ActionWithValue | private |
| offset_ | PLMD::isdb::Metainference | private |
| offset_max_ | PLMD::isdb::Metainference | private |
| offset_min_ | PLMD::isdb::Metainference | private |
| offset_mu_ | PLMD::isdb::Metainference | private |
| offset_prior_ | PLMD::isdb::Metainference | private |
| onStep() const | PLMD::ActionPilot | virtual |
| operator=(const Action &a)=delete | PLMD::Action | private |
| optimized_step_ | PLMD::isdb::Metainference | private |
| options | PLMD::Action | private |
| optsigmamean_stride_ | PLMD::isdb::Metainference | private |
| OUTLIERS enum value | PLMD::isdb::Metainference | private |
| outputForces | PLMD::bias::Bias | private |
| parameters | PLMD::isdb::Metainference | 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 | |
| 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 | |
| prepare() | PLMD::Action | virtual |
| random | PLMD::isdb::Metainference | private |
| readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::Metainference | static |
| replica_ | PLMD::isdb::Metainference | private |
| replica_averaging(const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| replica_index | PLMD::Action | private |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
| resetStoredTimestep() | PLMD::Action | |
| restart | PLMD::Action | private |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| SC_FLAT enum value | PLMD::isdb::Metainference | private |
| SC_GAUSS enum value | PLMD::isdb::Metainference | private |
| scale_ | PLMD::isdb::Metainference | private |
| scale_max_ | PLMD::isdb::Metainference | private |
| scale_min_ | PLMD::isdb::Metainference | private |
| scale_mu_ | PLMD::isdb::Metainference | private |
| scale_prior_ | PLMD::isdb::Metainference | private |
| selector_ | PLMD::isdb::Metainference | private |
| setBias(double bias) | PLMD::bias::Bias | inlineprotected |
| setGradients(Value *myval, unsigned &start) const | PLMD::ActionWithArguments | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | virtual |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setOutputForce(int i, double f) | PLMD::bias::Bias | inlineprotected |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setStride(const int &n) | PLMD::ActionPilot | |
| setupConstantValues(const bool &have_atoms) | PLMD::Action | |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| sfile_ | PLMD::isdb::Metainference | private |
| sigma_ | PLMD::isdb::Metainference | private |
| sigma_max_ | PLMD::isdb::Metainference | private |
| sigma_max_est_ | PLMD::isdb::Metainference | private |
| sigma_mean2_ | PLMD::isdb::Metainference | private |
| sigma_mean2_last_ | PLMD::isdb::Metainference | private |
| sigma_min_ | PLMD::isdb::Metainference | private |
| sigmamax_opt_done_ | PLMD::isdb::Metainference | private |
| stride | PLMD::ActionPilot | private |
| timestep | PLMD::Action | private |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| update() override | PLMD::isdb::Metainference | virtual |
| 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 |
| valueAccept | PLMD::isdb::Metainference | private |
| valueAcceptFT | PLMD::isdb::Metainference | private |
| valueAcceptScale | PLMD::isdb::Metainference | private |
| valueBias | PLMD::bias::Bias | private |
| valueFtilde | PLMD::isdb::Metainference | private |
| valueOffset | PLMD::isdb::Metainference | private |
| values | PLMD::ActionWithValue | private |
| valueScale | PLMD::isdb::Metainference | private |
| valueSigma | PLMD::isdb::Metainference | private |
| valueSigmaMean | PLMD::isdb::Metainference | private |
| warning(const std::string &msg) | PLMD::Action | |
| write_stride_ | PLMD::isdb::Metainference | private |
| writeInGraph() const | PLMD::Action | virtual |
| writeStatus() | PLMD::isdb::Metainference | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~Metainference() | PLMD::isdb::Metainference | |
1.8.17