| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| activate() | PLMD::Action | virtual |
| adaptation_ | PLMD::maze::Memetic | protected |
| adaptive_random_search(Member &m, const std::vector< double > ¶ms={1.0, 1.e-5, 2.0, 2.0, 3.0, 3.0}) | PLMD::maze::Memetic | protected |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| annealing(Member &m, const std::vector< double > ¶ms={300.0, 0.95}) | PLMD::maze::Memetic | protected |
| apply() override | PLMD::Colvar | protectedvirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bound_ | PLMD::maze::Memetic | protected |
| calculate() | PLMD::maze::Optimizer | virtual |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionAtomistic | virtual |
| capacity_ | PLMD::maze::Memetic | protected |
| cauchy_mean_alpha_ | PLMD::maze::Memetic | protected |
| cauchy_mean_beta_ | PLMD::maze::Memetic | protected |
| center_of_mass() const | PLMD::maze::Optimizer | |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkIsEnergy() | PLMD::Colvar | inline |
| 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() | PLMD::ActionWithValue | virtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| coding_len_ | PLMD::maze::Memetic | protected |
| Colvar(const ActionOptions &) | PLMD::Colvar | explicit |
| 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 | |
| create_coding() | PLMD::maze::Memetic | private |
| crossover(Member &m1, Member &m2) | PLMD::maze::Memetic | private |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| first_step_ | PLMD::maze::Optimizer | protected |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| get_capacity() const | PLMD::maze::Memetic | inline |
| get_cauchy_mean() const | PLMD::maze::Memetic | inline |
| get_cauchy_spread() const | PLMD::maze::Memetic | inline |
| get_coding_len() const | PLMD::maze::Memetic | inline |
| get_label() const | PLMD::maze::Optimizer | inline |
| get_local_search_rate() const | PLMD::maze::Memetic | inline |
| get_local_search_type() const | PLMD::maze::Memetic | inline |
| get_mating_rate() const | PLMD::maze::Memetic | inline |
| get_mutation_rate() const | PLMD::maze::Memetic | inline |
| get_n_global_iterations() const | PLMD::maze::Memetic | inline |
| get_n_iterations() const | PLMD::maze::Optimizer | inline |
| get_n_local_iterations() const | PLMD::maze::Memetic | inline |
| get_n_threads_openmp() const | PLMD::maze::Optimizer | inline |
| get_nl_cutofff() const | PLMD::maze::Optimizer | inline |
| get_nl_stride() const | PLMD::maze::Optimizer | inline |
| get_opt() const | PLMD::maze::Optimizer | inline |
| get_opt_value() const | PLMD::maze::Optimizer | inline |
| get_optimizer_stride() const | PLMD::maze::Optimizer | inline |
| get_rank_openmp() const | PLMD::maze::Optimizer | inline |
| get_sampling_radius() const | PLMD::maze::Optimizer | inline |
| get_stride_openmp() const | PLMD::maze::Optimizer | inline |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getBox() const | PLMD::ActionAtomistic | inline |
| getBoxDerivatives() const | PLMD::Colvar | protected |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForce() const | PLMD::Colvar | protected |
| getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::Colvar | inlinevirtual |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | protected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getRestart() const | PLMD::Action | inline |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getUniqueLocal() const | PLMD::ActionAtomistic | inline |
| initialize_members() | PLMD::maze::Memetic | private |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| is_local_search_on() const | PLMD::maze::Memetic | inline |
| is_pbc_on() const | PLMD::maze::Optimizer | inline |
| isActive() const | PLMD::Action | inline |
| isEnergy | PLMD::Colvar | protected |
| isExtraCV | PLMD::Colvar | protected |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| keywords | PLMD::Action | |
| label_ | PLMD::maze::Optimizer | protected |
| local_search(std::vector< Member > &members) | PLMD::maze::Memetic | protected |
| local_search_off() | PLMD::maze::Memetic | inline |
| local_search_on() | PLMD::maze::Memetic | inline |
| local_search_on_ | PLMD::maze::Memetic | protected |
| local_search_rate_ | PLMD::maze::Memetic | protected |
| local_search_type_ | PLMD::maze::Memetic | protected |
| lockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| luus_jaakola(Member &m, const std::vector< double > ¶ms) | PLMD::maze::Memetic | protected |
| makeWhole() | PLMD::ActionAtomistic | |
| mating(std::vector< Member > &members) | PLMD::maze::Memetic | private |
| mating_rate_ | PLMD::maze::Memetic | protected |
| member_best_ | PLMD::maze::Memetic | protected |
| members_ | PLMD::maze::Memetic | protected |
| Memetic(const ActionOptions &ao) | PLMD::maze::Memetic | explicit |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
| modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| mutation(Member &m) | PLMD::maze::Memetic | private |
| mutation(std::vector< Member > &members) | PLMD::maze::Memetic | private |
| mutation_rate_ | PLMD::maze::Memetic | protected |
| n_global_iterations_ | PLMD::maze::Memetic | protected |
| n_iter_ | PLMD::maze::Optimizer | protected |
| n_local_iterations_ | PLMD::maze::Memetic | protected |
| n_threads_ | PLMD::maze::Optimizer | protected |
| neighbor_list_ | PLMD::maze::Optimizer | protected |
| nl_cutoff_ | PLMD::maze::Optimizer | protected |
| nl_stride_ | PLMD::maze::Optimizer | protected |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| opt_ | PLMD::maze::Optimizer | protected |
| opt_value_ | PLMD::maze::Optimizer | protected |
| optimize() override | PLMD::maze::Memetic | virtual |
| Optimizer(const ActionOptions &) | PLMD::maze::Optimizer | explicit |
| optimizer_stride_ | PLMD::maze::Optimizer | protected |
| out_of_bounds(double v) | PLMD::maze::Memetic | private |
| pairing(double distance) const | PLMD::maze::Optimizer | virtual |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseAtomList(const std::string &key, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| 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 | |
| pbc_ | PLMD::maze::Optimizer | protected |
| pbc_off() | PLMD::maze::Optimizer | inline |
| pbc_on() | PLMD::maze::Optimizer | inline |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| plumed | PLMD::Action | |
| prepare() | PLMD::maze::Optimizer | virtual |
| print_status() const | PLMD::maze::Memetic | private |
| random_restart_hill_climbing(Member &m, const std::vector< double > ¶ms={10}) | PLMD::maze::Memetic | protected |
| rank_ | PLMD::maze::Optimizer | protected |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::maze::Memetic | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::Colvar | protected |
| PLMD::ActionAtomistic::requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| sampling_r_ | PLMD::maze::Optimizer | protected |
| sampling_radius() | PLMD::maze::Optimizer | |
| score() | PLMD::maze::Optimizer | |
| score_best_ | PLMD::maze::Memetic | protected |
| score_mean() | PLMD::maze::Memetic | private |
| score_member(const Vector &v) | PLMD::maze::Memetic | private |
| score_members() | PLMD::maze::Memetic | private |
| score_worst_ | PLMD::maze::Memetic | protected |
| selection_roulette() | PLMD::maze::Memetic | private |
| set_capacity(unsigned int) | PLMD::maze::Memetic | inline |
| set_cauchy_mean(double) | PLMD::maze::Memetic | inline |
| set_cauchy_spread(double) | PLMD::maze::Memetic | inline |
| set_coding_len(unsigned int) | PLMD::maze::Memetic | inline |
| set_label(const std::string &) | PLMD::maze::Optimizer | inline |
| set_local_search_rate(double) | PLMD::maze::Memetic | inline |
| set_local_search_type(const std::string &) | PLMD::maze::Memetic | inline |
| set_mating_rate(double) | PLMD::maze::Memetic | inline |
| set_mutation_rate(double) | PLMD::maze::Memetic | inline |
| set_n_global_iterations(unsigned int) | PLMD::maze::Memetic | inline |
| set_n_iterations(unsigned int) | PLMD::maze::Optimizer | inline |
| set_n_local_iterations(unsigned int) | PLMD::maze::Memetic | inline |
| set_n_threads_openmp(unsigned int) | PLMD::maze::Optimizer | inline |
| set_nl_cutoff(double) | PLMD::maze::Optimizer | inline |
| set_nl_stride(unsigned int) | PLMD::maze::Optimizer | inline |
| set_opt(Vector) | PLMD::maze::Optimizer | inline |
| set_opt_value(double) | PLMD::maze::Optimizer | inline |
| set_optimizer_stride(unsigned int) | PLMD::maze::Optimizer | inline |
| set_rank_openmp(unsigned int) | PLMD::maze::Optimizer | inline |
| set_sampling_radius(double) | PLMD::maze::Optimizer | inline |
| set_stride_openmp(unsigned int) | PLMD::maze::Optimizer | inline |
| setAtomsDerivatives(int, const Vector &) | PLMD::Colvar | inlineprotected |
| setAtomsDerivatives(Value *, int, const Vector &) | PLMD::Colvar | inlineprotected |
| setBoxDerivatives(const Tensor &) | PLMD::Colvar | inlineprotected |
| setBoxDerivatives(Value *, const Tensor &) | PLMD::Colvar | inlineprotected |
| setBoxDerivativesNoPbc() | PLMD::Colvar | inlineprotected |
| setBoxDerivativesNoPbc(Value *) | PLMD::Colvar | protected |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| solve() | PLMD::maze::Memetic | protected |
| sort_members() | PLMD::maze::Memetic | private |
| start_step_0() | PLMD::maze::Optimizer | inline |
| start_step_stride() | PLMD::maze::Optimizer | inline |
| stochastic_hill_climbing(Member &m, const std::vector< double > ¶ms={}) | PLMD::maze::Memetic | protected |
| stride_ | PLMD::maze::Optimizer | protected |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| unlockRequests() override | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| update_nl() | PLMD::maze::Optimizer | |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| value_action_ | PLMD::maze::Optimizer | |
| value_sampling_radius_ | PLMD::maze::Optimizer | |
| value_x_ | PLMD::maze::Optimizer | |
| value_y_ | PLMD::maze::Optimizer | |
| value_z_ | PLMD::maze::Optimizer | |
| warning(const std::string &msg) | PLMD::Action | |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~Colvar() | PLMD::Colvar | inline |
| ~Memetic() | PLMD::maze::Memetic | |
| ~Optimizer() | PLMD::maze::Optimizer | inline |
1.8.14