| acc | PLMD::bias::MetaD | private |
| acc_restart_mean_ | PLMD::bias::MetaD | private |
| acceleration | PLMD::bias::MetaD | private |
| 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 |
| adaptive_ | PLMD::bias::MetaD | private |
| 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 | |
| addGaussian(const Gaussian &) | PLMD::bias::MetaD | private |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| apply() | PLMD::bias::Bias | virtual |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
| biasf_ | PLMD::bias::MetaD | private |
| BiasGrid_ | PLMD::bias::MetaD | private |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calc_max_bias_ | PLMD::bias::MetaD | private |
| calc_rct_ | PLMD::bias::MetaD | private |
| calc_transition_bias_ | PLMD::bias::MetaD | private |
| calculate() | PLMD::bias::MetaD | 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::bias::MetaD | virtual |
| 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 |
| computeReweightingFactor() | PLMD::bias::MetaD | private |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| current_stride | PLMD::bias::MetaD | private |
| dampfactor_ | PLMD::bias::MetaD | private |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doInt_ | PLMD::bias::MetaD | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| dp_ | PLMD::bias::MetaD | private |
| error(const std::string &msg) const | PLMD::Action | |
| evaluateGaussian(const vector< double > &, const Gaussian &, double *der=NULL) | PLMD::bias::MetaD | private |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fa_max_stride_ | PLMD::bias::MetaD | private |
| fa_min_acceleration_ | PLMD::bias::MetaD | private |
| fa_update_frequency_ | PLMD::bias::MetaD | private |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| flexbin | PLMD::bias::MetaD | private |
| flying | PLMD::bias::MetaD | private |
| fmt | PLMD::bias::MetaD | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| freq_adaptive_ | PLMD::bias::MetaD | private |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getBiasAndDerivatives(const vector< double > &, double *der=NULL) | PLMD::bias::MetaD | private |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getExchangeStep() const | PLMD::Action | |
| getGaussianNormalization(const Gaussian &) | PLMD::bias::MetaD | private |
| getGaussianSupport(const Gaussian &) | PLMD::bias::MetaD | private |
| getHeight(const vector< double > &) | PLMD::bias::MetaD | private |
| 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 | |
| getTransitionBarrierBias() | PLMD::bias::MetaD | private |
| grid_ | PLMD::bias::MetaD | private |
| gridfile_ | PLMD::bias::MetaD | private |
| height0_ | PLMD::bias::MetaD | private |
| hills_ | PLMD::bias::MetaD | private |
| hillsOfile_ | PLMD::bias::MetaD | private |
| ifiles | PLMD::bias::MetaD | private |
| ifilesnames | PLMD::bias::MetaD | private |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| isActive() const | PLMD::Action | inline |
| isFirstStep | PLMD::bias::MetaD | private |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::bias::MetaD | private |
| keywords | PLMD::Action | |
| last_step_warn_grid | PLMD::bias::MetaD | private |
| PLMD::lockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::lockRequests() | PLMD::ActionWithArguments | inlinevirtual |
| log | PLMD::Action | |
| logTemperingSpecs(const TemperingSpecs &t_specs) | PLMD::bias::MetaD | private |
| lowI_ | PLMD::bias::MetaD | private |
| max_bias_ | PLMD::bias::MetaD | private |
| MetaD(const ActionOptions &) | PLMD::bias::MetaD | explicit |
| mpi_mw_ | PLMD::bias::MetaD | private |
| mpi_nw_ | PLMD::bias::MetaD | private |
| multi_sim_comm | PLMD::Action | |
| mw_dir_ | PLMD::bias::MetaD | private |
| mw_id_ | PLMD::bias::MetaD | private |
| mw_n_ | PLMD::bias::MetaD | private |
| mw_rstride_ | PLMD::bias::MetaD | private |
| n_tempering_options_ | PLMD::bias::MetaD | privatestatic |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| onStep() const | PLMD::ActionPilot | virtual |
| 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 |
| rct_ustride_ | PLMD::bias::MetaD | private |
| readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| readGaussians(IFile *) | PLMD::bias::MetaD | private |
| readTemperingSpecs(TemperingSpecs &t_specs) | PLMD::bias::MetaD | private |
| registerKeywords(Keywords &keys) | PLMD::bias::MetaD | static |
| registerTemperingKeywords(const std::string &name_stem, const std::string &name, Keywords &keys) | PLMD::bias::MetaD | privatestatic |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| reweight_factor_ | PLMD::bias::MetaD | private |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| scanOneHill(IFile *ifile, vector< Value > &v, vector< double > ¢er, vector< double > &sigma, double &height, bool &multivariate) | PLMD::bias::MetaD | 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 | |
| sigma0_ | PLMD::bias::MetaD | private |
| sigma0max_ | PLMD::bias::MetaD | private |
| sigma0min_ | PLMD::bias::MetaD | private |
| storeOldGrids_ | PLMD::bias::MetaD | private |
| stride_ | PLMD::bias::MetaD | private |
| targetfilename_ | PLMD::bias::MetaD | private |
| TargetGrid_ | PLMD::bias::MetaD | private |
| temperHeight(double &height, const TemperingSpecs &t_specs, const double tempering_bias) | PLMD::bias::MetaD | private |
| tempering_names_ | PLMD::bias::MetaD | privatestatic |
| transition_bias_ | PLMD::bias::MetaD | private |
| transitionwells_ | PLMD::bias::MetaD | private |
| tt_specs_ | PLMD::bias::MetaD | private |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::unlockRequests() | PLMD::ActionWithArguments | inlinevirtual |
| update() | PLMD::bias::MetaD | virtual |
| updateFrequencyAdaptiveStride() | PLMD::bias::MetaD | private |
| uppI_ | PLMD::bias::MetaD | private |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| walkers_mpi | PLMD::bias::MetaD | private |
| warning(const std::string &msg) | PLMD::Action | |
| welltemp_ | PLMD::bias::MetaD | private |
| wgridstride_ | PLMD::bias::MetaD | private |
| work_ | PLMD::bias::MetaD | private |
| writeGaussian(const Gaussian &, OFile &) | PLMD::bias::MetaD | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
1.8.14