| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
| ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| activate() | PLMD::Action | virtual |
| 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 | |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| apply() | PLMD::bias::Bias | virtual |
| 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() | PLMD::isdb::Metainference | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
| PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionWithArguments | virtual |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::checkNumericalDerivatives() const | 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 |
| 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 |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| deactivate() | PLMD::Action | inlinevirtual |
| 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 vector< double > &mean) | PLMD::isdb::Metainference | private |
| do_reweight_ | PLMD::isdb::Metainference | private |
| Doffset_ | PLMD::isdb::Metainference | private |
| doMonteCarlo(const 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(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| firstTime | PLMD::isdb::Metainference | private |
| firstTimeW | PLMD::isdb::Metainference | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| 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 fact, const double var_fact, const vector< double > &mean) | PLMD::isdb::Metainference | private |
| get_weights(const unsigned iselect, double &fact, double &var_fact) | PLMD::isdb::Metainference | private |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getEnergyForceGJ(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceGJE(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceMIGEN(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceSP(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyForceSPE(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| getEnergyGJ(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergyGJE(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergyMIGEN(const vector< double > &mean, const vector< double > &ftilde, const vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergySP(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getEnergySPE(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::Metainference | private |
| getExchangeStep() const | PLMD::Action | |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getName() const | PLMD::Action | inline |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::bias::Bias | inlinevirtual |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | 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 |
| 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 | |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::isdb::Metainference | private |
| keywords | PLMD::Action | |
| LIKE_GAUSS enum value | PLMD::isdb::Metainference | private |
| LIKE_LOGN enum value | PLMD::isdb::Metainference | private |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::lockRequests() | 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 |
| MCstride_ | 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 |
| multi_sim_comm | PLMD::Action | |
| narg | PLMD::isdb::Metainference | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noise_type_ | PLMD::isdb::Metainference | private |
| nregres_zero_ | PLMD::isdb::Metainference | private |
| nrep_ | PLMD::isdb::Metainference | 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 |
| optsigmamean_stride_ | PLMD::isdb::Metainference | private |
| OUTLIERS enum value | PLMD::isdb::Metainference | 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 fact, std::vector< double > &mean, std::vector< double > &dmean_b) | PLMD::isdb::Metainference | private |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| 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 |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| 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 | |
| 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_mean2_ | PLMD::isdb::Metainference | private |
| sigma_mean2_last_ | PLMD::isdb::Metainference | private |
| sigma_min_ | PLMD::isdb::Metainference | private |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::unlockRequests() | PLMD::ActionWithArguments | inlinevirtual |
| update() | PLMD::isdb::Metainference | virtual |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| valueAccept | PLMD::isdb::Metainference | private |
| valueAcceptFT | PLMD::isdb::Metainference | private |
| valueAcceptScale | PLMD::isdb::Metainference | private |
| valueFtilde | PLMD::isdb::Metainference | private |
| valueOffset | PLMD::isdb::Metainference | 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 |
| writeStatus() | PLMD::isdb::Metainference | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~Metainference() | PLMD::isdb::Metainference | |
1.8.14