| 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 |
| addCoeffsSet(const std::vector< std::string > &, const std::vector< unsigned int > &) | PLMD::ves::VesBias | protected |
| addCoeffsSet(std::vector< Value *> &, std::vector< BasisFunctions *> &) | PLMD::ves::VesBias | protected |
| addCoeffsSet(CoeffsVector *) | PLMD::ves::VesBias | 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::ActionWithArguments | |
| addToSampledAverages(const std::vector< double > &, const unsigned int c_id=0) | PLMD::ves::VesBias | protected |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| apply() | PLMD::ves::VesBias | virtual |
| applyBiasCutoff(double &, std::vector< double > &) const | PLMD::ves::VesBias | inline |
| applyBiasCutoff(double &, std::vector< double > &, std::vector< double > &) const | PLMD::ves::VesBias | inline |
| aver_counters | PLMD::ves::VesBias | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
| bias_current_max_value | PLMD::ves::VesBias | private |
| bias_cutoff_active_ | PLMD::ves::VesBias | private |
| bias_cutoff_swfunc_pntr_ | PLMD::ves::VesBias | private |
| bias_cutoff_value_ | PLMD::ves::VesBias | private |
| bias_file_fmt_ | PLMD::ves::VesBias | private |
| bias_filename_ | PLMD::ves::VesBias | private |
| bias_fileoutput_active_ | PLMD::ves::VesBias | private |
| biasCutoffActive() const | PLMD::ves::VesBias | inline |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calc_reweightfactor_ | PLMD::ves::VesBias | private |
| calculate()=0 | PLMD::Action | pure virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
| PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | virtual |
| calculateReweightFactor() const | PLMD::ves::VesBias | virtual |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
| checkRead() | PLMD::Action | |
| checkThatTemperatureIsGiven() | PLMD::ves::VesBias | protected |
| checkUpdate() const | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearCoeffsPntrsVector() | PLMD::ves::VesBias | inlineprotected |
| clearDependencies() | PLMD::Action | |
| clearDerivatives() | PLMD::ActionWithValue | virtual |
| clearGradientAndHessian() | PLMD::ves::VesBias | inline |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| Coeffs(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| coeffs_fnames | PLMD::ves::VesBias | private |
| coeffs_id_prefix_ | PLMD::ves::VesBias | private |
| coeffs_pntrs_ | PLMD::ves::VesBias | private |
| 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 |
| compute_hessian_ | PLMD::ves::VesBias | private |
| computeCovarianceFromAverages(const unsigned int) const | PLMD::ves::VesBias | inlineprivate |
| computeHessian() const | PLMD::ves::VesBias | inline |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| diagonal_hessian_ | PLMD::ves::VesBias | private |
| diagonalHessian() const | PLMD::ves::VesBias | inline |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| disableBiasFileOutput() | PLMD::ves::VesBias | inline |
| disableDynamicTargetDistFileOutput() | PLMD::ves::VesBias | inline |
| disableDynamicTargetDistribution() | PLMD::ves::VesBias | inline |
| disableFesFileOutput() | PLMD::ves::VesBias | inline |
| disableFesFileProjOutput() | PLMD::ves::VesBias | inline |
| disableHessian() | PLMD::ves::VesBias | |
| disableStaticTargetDistFileOutput() | PLMD::ves::VesBias | inline |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| dynamic_targetdist_ | PLMD::ves::VesBias | private |
| dynamic_targetdist_fileoutput_active_ | PLMD::ves::VesBias | private |
| dynamicTargetDistribution() const | PLMD::ves::VesBias | inline |
| enableBiasFileOutput() | PLMD::ves::VesBias | inline |
| enableDynamicTargetDistFileOutput() | PLMD::ves::VesBias | inline |
| enableDynamicTargetDistribution() | PLMD::ves::VesBias | inline |
| enableFesFileOutput() | PLMD::ves::VesBias | inline |
| enableFesProjFileOutput() | PLMD::ves::VesBias | inline |
| enableHessian(const bool diagonal_hessian=true) | PLMD::ves::VesBias | |
| enableIterationNumberInFilenames() | PLMD::ves::VesBias | inline |
| enableMultipleCoeffsSets() | PLMD::ves::VesBias | inline |
| enableStaticTargetDistFileOutput() | PLMD::ves::VesBias | inline |
| 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 | |
| fes_file_fmt_ | PLMD::ves::VesBias | private |
| fes_filename_ | PLMD::ves::VesBias | private |
| fes_fileoutput_active_ | PLMD::ves::VesBias | private |
| fesproj_fileoutput_active_ | PLMD::ves::VesBias | private |
| fflush() | PLMD::Action | |
| filenames_have_iteration_number_ | PLMD::ves::VesBias | private |
| filenamesIncludeIterationNumber() const | PLMD::ves::VesBias | inline |
| files | PLMD::Action | |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getBeta() const | PLMD::ves::VesBias | inline |
| getBiasCutoffSwitchingFunction(const double, double &) const | PLMD::ves::VesBias | |
| getBiasCutoffSwitchingFunction(const double) const | PLMD::ves::VesBias | inline |
| getBiasCutoffValue() const | PLMD::ves::VesBias | inline |
| getBiasFileFmt() const | PLMD::ves::VesBias | inline |
| getBiasOutputFilename() const | PLMD::ves::VesBias | inline |
| getCoeffsIndex(const std::vector< unsigned int > &indices, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getCoeffsIndices(const size_t index, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getCoeffsPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getCoeffsPntrs() const | PLMD::ves::VesBias | inline |
| getCoeffsSetFilenameSuffix(const unsigned int coeffs_id) const | PLMD::ves::VesBias | |
| getCoeffsSetLabelString(const std::string &, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | protected |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getCurrentBiasMaxValue() const | PLMD::ves::VesBias | inline |
| getCurrentBiasOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | inline |
| getCurrentFesOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | inline |
| getCurrentOutputFilename(const std::string &, const std::string &suffix="") const | PLMD::ves::VesBias | |
| getCurrentTargetDistOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getExchangeStep() const | PLMD::Action | |
| getFesFileFmt() const | PLMD::ves::VesBias | inline |
| getFesOutputFilename() const | PLMD::ves::VesBias | inline |
| getGradientPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getGradientPntrs() const | PLMD::ves::VesBias | inline |
| getGridBins() const | PLMD::ves::VesBias | inline |
| getGridMax() const | PLMD::ves::VesBias | inline |
| getGridMin() const | PLMD::ves::VesBias | inline |
| getHessianIndex(const size_t index1, const size_t index2, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getHessianPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getHessianPntrs() const | PLMD::ves::VesBias | inline |
| getIterationCounter() const | PLMD::ves::VesBias | |
| getIterationFilenameSuffix() const | PLMD::ves::VesBias | |
| getKbT() const | PLMD::ves::VesBias | inline |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getName() const | PLMD::Action | inline |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfArgumentsPerSet() const | PLMD::ves::VesBias | inline |
| getNumberOfArgumentsSets() const | PLMD::ves::VesBias | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::bias::Bias | inlinevirtual |
| getNumberOfProjectionArguments() const | PLMD::ves::VesBias | inline |
| getNumberOfTargetDistributionPntrs() const | PLMD::ves::VesBias | inline |
| getOFile(const std::string &filename, const bool multi_sim_single_file=false, const bool enforce_backup=true) | PLMD::ves::VesBias | |
| getOptimizerPntr() const | PLMD::ves::VesBias | inline |
| 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 | |
| getProjectionArgument(unsigned int i) const | PLMD::ves::VesBias | inline |
| getProjectionArguments() const | PLMD::ves::VesBias | inline |
| getRestart() const | PLMD::Action | inline |
| getStep() const | PLMD::Action | |
| getStride() const | PLMD::ActionPilot | |
| getTargetDistAveragesPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| getTargetDistAveragesPntrs() const | PLMD::ves::VesBias | inline |
| getTargetDistFileFmt() const | PLMD::ves::VesBias | inline |
| getTargetDistOutputFilename() const | PLMD::ves::VesBias | inline |
| getTargetDistRestartFileFmt() const | PLMD::ves::VesBias | inline |
| getTargetDistributionPntrs() const | PLMD::ves::VesBias | inline |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTotalNumberOfArguments() const | PLMD::ves::VesBias | inline |
| Gradient(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| gradient_pntrs_ | PLMD::ves::VesBias | private |
| grid_bins_ | PLMD::ves::VesBias | private |
| grid_max_ | PLMD::ves::VesBias | private |
| grid_min_ | PLMD::ves::VesBias | private |
| Hessian(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| hessian_pntrs_ | PLMD::ves::VesBias | private |
| initializeCoeffs(CoeffsVector *) | PLMD::ves::VesBias | private |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| isActive() const | PLMD::Action | inline |
| isBiasFileOutputActive() const | PLMD::ves::VesBias | inline |
| isDynamicTargetDistFileOutputActive() const | PLMD::ves::VesBias | inline |
| isFesFileOutputActive() const | PLMD::ves::VesBias | inline |
| isFesProjFileOutputActive() const | PLMD::ves::VesBias | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isReweightFactorCalculated() const | PLMD::ves::VesBias | inline |
| isStaticTargetDistFileOutputActive() const | PLMD::ves::VesBias | inline |
| kbt_ | PLMD::ves::VesBias | private |
| keywords | PLMD::Action | |
| linkOptimizer(Optimizer *) | PLMD::ves::VesBias | |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| log | PLMD::Action | |
| multi_sim_comm | PLMD::Action | |
| multiSimSumAverages(const unsigned int, const double walker_weight=1.0) | PLMD::ves::VesBias | private |
| nargs_per_argsset_ | PLMD::ves::VesBias | private |
| nargs_tot_ | PLMD::ves::VesBias | private |
| nargssets_ | PLMD::ves::VesBias | private |
| ncoeffs_total_ | PLMD::ves::VesBias | private |
| ncoeffssets_ | PLMD::ves::VesBias | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| numberOfCoeffs(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| numberOfCoeffsSets() const | PLMD::ves::VesBias | inline |
| onStep() const | PLMD::ActionPilot | virtual |
| optimize_coeffs_ | PLMD::ves::VesBias | private |
| optimizeCoeffs() const | PLMD::ves::VesBias | inline |
| optimizer_pntr_ | PLMD::ves::VesBias | 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 | |
| parseMultipleValues(const std::string &, std::vector< T > &, unsigned int) | PLMD::ves::VesBias | protected |
| parseMultipleValues(const std::string &, std::vector< T > &, unsigned int, const T &) | PLMD::ves::VesBias | 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 |
| projection_args_ | PLMD::ves::VesBias | private |
| readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| readCoeffsFromFiles() | PLMD::ves::VesBias | protected |
| registerKeywords(Keywords &) | PLMD::ves::VesBias | static |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| resetBiasFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| resetFesFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| resetFesProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| resetTargetDistFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| resetTargetDistProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| restartTargetDistributions() | PLMD::ves::VesBias | inlinevirtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| sampled_averages | PLMD::ves::VesBias | private |
| sampled_cross_averages | PLMD::ves::VesBias | private |
| sampledAverages() | PLMD::ves::VesBias | inline |
| sampledCrossAverages() | PLMD::ves::VesBias | inline |
| setBias(double bias) | PLMD::bias::Bias | inlineprotected |
| setCurrentBiasMaxValue(const double max_value) | PLMD::ves::VesBias | inline |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setGridBins(const std::vector< unsigned int > &) | PLMD::ves::VesBias | |
| setGridBins(const unsigned int) | PLMD::ves::VesBias | |
| setGridMax(const std::vector< double > &) | PLMD::ves::VesBias | |
| setGridMin(const std::vector< double > &) | PLMD::ves::VesBias | |
| 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 | |
| setTargetDistAverages(const std::vector< double > &, const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
| setTargetDistAverages(const CoeffsVector &, const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
| setTargetDistAveragesToZero(const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
| setupBiasCutoff(const double, const double) | PLMD::ves::VesBias | |
| setupBiasFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| setupFesFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| setupFesProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| setupOutputForces() | PLMD::bias::Bias | protected |
| setupTargetDistFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| setupTargetDistProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| static_targetdist_fileoutput_active_ | PLMD::ves::VesBias | private |
| targetdist_averages_filename_ | PLMD::ves::VesBias | private |
| targetdist_averages_pntrs_ | PLMD::ves::VesBias | private |
| targetdist_file_fmt_ | PLMD::ves::VesBias | private |
| targetdist_filename_ | PLMD::ves::VesBias | private |
| targetdist_pntrs_ | PLMD::ves::VesBias | private |
| targetdist_restart_file_fmt_ | PLMD::ves::VesBias | private |
| TargetDistAverages(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
| totalNumberOfCoeffs() const | PLMD::ves::VesBias | inline |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| updateGradientAndHessian(const bool) | PLMD::ves::VesBias | |
| updateReweightFactor() | PLMD::ves::VesBias | |
| updateTargetDistributions() | PLMD::ves::VesBias | inlinevirtual |
| use_multiple_coeffssets_ | PLMD::ves::VesBias | private |
| useArgsSetKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useBiasCutoffKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useGridBinKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useGridLimitsKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useInitialCoeffsKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useMultipleTargetDistributionKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useMultipleWalkers() const | PLMD::ves::VesBias | |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| useProjectionArgKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useReweightFactorKeywords(Keywords &) | PLMD::ves::VesBias | static |
| useTargetDistributionKeywords(Keywords &) | PLMD::ves::VesBias | static |
| VesBias(const ActionOptions &ao) | PLMD::ves::VesBias | explicit |
| warning(const std::string &msg) | PLMD::Action | |
| writeBiasToFile() | PLMD::ves::VesBias | inlinevirtual |
| writeFesProjToFile() | PLMD::ves::VesBias | inlinevirtual |
| writeFesToFile() | PLMD::ves::VesBias | inlinevirtual |
| writeTargetDistProjToFile() | PLMD::ves::VesBias | inlinevirtual |
| writeTargetDistToFile() | PLMD::ves::VesBias | inlinevirtual |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~VesBias() | PLMD::ves::VesBias | |
1.8.14