| 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 | |
| alpha_vector_ | PLMD::eds::EDS | private |
| alpha_vector_2_ | PLMD::eds::EDS | private |
| apply() override | PLMD::bias::Bias | virtual |
| apply_bias() | PLMD::eds::EDS | private |
| arguments | PLMD::ActionWithArguments | private |
| avg_coupling_count_ | PLMD::eds::EDS | private |
| b_adaptive_ | PLMD::eds::EDS | private |
| b_c_values_ | PLMD::eds::EDS | private |
| b_covar_ | PLMD::eds::EDS | private |
| b_equil_ | PLMD::eds::EDS | private |
| b_freeze_ | PLMD::eds::EDS | private |
| b_lm_ | PLMD::eds::EDS | private |
| b_ramp_ | PLMD::eds::EDS | private |
| b_restart_ | PLMD::eds::EDS | private |
| b_update_virial_ | PLMD::eds::EDS | private |
| b_virial_ | PLMD::eds::EDS | private |
| b_weights_ | PLMD::eds::EDS | private |
| b_write_restart_ | PLMD::eds::EDS | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calc_covar_step_size() | PLMD::eds::EDS | private |
| calc_lm_step_size() | PLMD::eds::EDS | private |
| calc_ssd_step_size() | PLMD::eds::EDS | private |
| calculate() | PLMD::eds::EDS | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | virtual |
| center_ | PLMD::eds::EDS | private |
| center_values_ | PLMD::eds::EDS | private |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| 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() | 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 | |
| coupling_accum_ | PLMD::eds::EDS | private |
| coupling_rate_ | PLMD::eds::EDS | private |
| covar2_ | PLMD::eds::EDS | private |
| covar_ | PLMD::eds::EDS | private |
| current_coupling_ | PLMD::eds::EDS | private |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| differences_ | PLMD::eds::EDS | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| EDS(const ActionOptions &) | PLMD::eds::EDS | explicit |
| 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 |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| fmt_ | PLMD::eds::EDS | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| 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 | |
| getCPT() const | PLMD::Action | |
| getDefaultString() const | PLMD::Action | inline |
| getDependencies() const | PLMD::Action | inline |
| 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() override | 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 | |
| in_restart_ | PLMD::eds::EDS | private |
| in_restart_name_ | PLMD::eds::EDS | private |
| 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::eds::EDS | private |
| keywords | PLMD::Action | |
| lm_inv_ | PLMD::eds::EDS | private |
| lm_mixing_par_ | PLMD::eds::EDS | private |
| lockRequestArguments | PLMD::ActionWithArguments | private |
| lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| log | PLMD::Action | |
| logweights_ | PLMD::eds::EDS | private |
| max_coupling_grad_ | PLMD::eds::EDS | private |
| max_coupling_range_ | PLMD::eds::EDS | private |
| max_logweight_ | PLMD::eds::EDS | private |
| means_ | PLMD::eds::EDS | private |
| multi_prop_ | PLMD::eds::EDS | private |
| multi_sim_comm | PLMD::Action | |
| ncvs_ | PLMD::eds::EDS | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| numericalDerivatives | PLMD::ActionWithValue | private |
| onStep() const | PLMD::ActionPilot | virtual |
| out_coupling_ | PLMD::eds::EDS | private |
| out_restart_ | PLMD::eds::EDS | private |
| out_restart_name_ | PLMD::eds::EDS | private |
| outputForces | PLMD::bias::Bias | 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 |
| pseudo_virial_ | PLMD::eds::EDS | private |
| pseudo_virial_sum_ | PLMD::eds::EDS | private |
| rand_ | PLMD::eds::EDS | private |
| readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
| readInRestart(const bool b_mean) | PLMD::eds::EDS | private |
| registerKeywords(Keywords &keys) | PLMD::eds::EDS | static |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
| reset_statistics() | PLMD::eds::EDS | private |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| scale_ | PLMD::eds::EDS | private |
| seed_ | PLMD::eds::EDS | private |
| set_coupling_ | PLMD::eds::EDS | 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 | |
| setupOutRestart() | PLMD::eds::EDS | private |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| ssds_ | PLMD::eds::EDS | private |
| step_size_ | PLMD::eds::EDS | private |
| stride | PLMD::ActionPilot | private |
| target_coupling_ | PLMD::eds::EDS | private |
| turnOnDerivatives() | PLMD::eds::EDS | virtual |
| unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
| update() | PLMD::eds::EDS | virtual |
| update_bias() | PLMD::eds::EDS | private |
| update_calls_ | PLMD::eds::EDS | private |
| update_period_ | PLMD::eds::EDS | private |
| update_pseudo_virial() | PLMD::eds::EDS | private |
| update_statistics() | PLMD::eds::EDS | private |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| value_force2_ | PLMD::eds::EDS | private |
| value_pressure_ | PLMD::eds::EDS | private |
| valueBias | PLMD::bias::Bias | private |
| values | PLMD::ActionWithValue | private |
| virial_scaling_ | PLMD::eds::EDS | private |
| warning(const std::string &msg) | PLMD::Action | |
| writeOutRestart() | PLMD::eds::EDS | private |
| wsum_ | PLMD::eds::EDS | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~EDS() | PLMD::eds::EDS | |
1.17.0