| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | 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 | |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| anneal_ | PLMD::isdb::EMMI | private |
| apply() override | PLMD::isdb::EMMI | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| arguments | PLMD::ActionWithArguments | private |
| atom_der_ | PLMD::isdb::EMMI | private |
| atoms | PLMD::ActionAtomistic | protected |
| average_weights_ | PLMD::isdb::EMMI | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calculate() override | PLMD::isdb::EMMI | virtual |
| calculate_Gauss() | PLMD::isdb::EMMI | private |
| calculate_Marginal() | PLMD::isdb::EMMI | private |
| calculate_Outliers() | PLMD::isdb::EMMI | private |
| calculate_overlap() | PLMD::isdb::EMMI | private |
| calculate_useful_stuff(double reso) | PLMD::isdb::EMMI | private |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a) override | PLMD::isdb::EMMI | inlinevirtual |
| cfact_ | PLMD::isdb::EMMI | private |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| charges | PLMD::ActionAtomistic | private |
| chargesWereSet | PLMD::ActionAtomistic | private |
| check_GMM_d(const VectorGeneric< 6 > &cov, double w) | PLMD::isdb::EMMI | 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 |
| clearOutputForces() | PLMD::ActionAtomistic | |
| 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 |
| decay_w_ | PLMD::isdb::EMMI | private |
| Dependencies typedef | PLMD::Action | |
| dexp_ | PLMD::isdb::EMMI | private |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| do_reweight_ | PLMD::isdb::EMMI | private |
| doAccept(double oldE, double newE, double kbt) | PLMD::isdb::EMMI | private |
| doMonteCarlo() | PLMD::isdb::EMMI | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| donotforce | PLMD::ActionAtomistic | private |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| donotretrieve | PLMD::ActionAtomistic | private |
| doRegression() | PLMD::isdb::EMMI | private |
| dpcutoff_ | PLMD::isdb::EMMI | private |
| dscale_ | PLMD::isdb::EMMI | private |
| dsigma_ | PLMD::isdb::EMMI | private |
| EMMI(const ActionOptions &) | PLMD::isdb::EMMI | explicit |
| ene_ | PLMD::isdb::EMMI | private |
| energy | PLMD::ActionAtomistic | private |
| 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 |
| extraCV | PLMD::ActionAtomistic | private |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| first_status_ | PLMD::isdb::EMMI | private |
| first_time_ | PLMD::isdb::EMMI | private |
| first_time_w_ | PLMD::isdb::EMMI | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forceOnEnergy | PLMD::ActionAtomistic | private |
| forceOnExtraCV | PLMD::ActionAtomistic | private |
| forces | PLMD::isdb::EMMI | private |
| forcesToApply | PLMD::isdb::EMMI | private |
| get_annealing(long long int step) | PLMD::isdb::EMMI | private |
| get_exp_overlap(const Vector &m_m, const Vector &d_m, const VectorGeneric< 6 > &inv_cov_md) | PLMD::isdb::EMMI | private |
| get_GMM_d(std::string gmm_file) | PLMD::isdb::EMMI | private |
| get_GMM_m(std::vector< AtomNumber > &atoms) | PLMD::isdb::EMMI | private |
| get_median(std::vector< double > &v) | PLMD::isdb::EMMI | private |
| get_overlap(const Vector &m_m, const Vector &d_m, double pre_fact, const VectorGeneric< 6 > &inv_cov_md, Vector &ov_der) | PLMD::isdb::EMMI | private |
| get_prefactor_inverse(const VectorGeneric< 6 > &GMM_cov_0, const VectorGeneric< 6 > &GMM_cov_1, double GMM_w_0, double GMM_w_1, VectorGeneric< 6 > &sum, VectorGeneric< 6 > &inv_sum) | PLMD::isdb::EMMI | private |
| get_self_overlap(unsigned id) | PLMD::isdb::EMMI | private |
| get_weights(double &weight, double &norm, double &neff) | PLMD::isdb::EMMI | private |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| 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 |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| 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 |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::isdb::EMMI | inlinevirtual |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | 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 |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| 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 |
| GMM_d_beta_ | PLMD::isdb::EMMI | private |
| GMM_d_cov_ | PLMD::isdb::EMMI | private |
| GMM_d_grps_ | PLMD::isdb::EMMI | private |
| GMM_d_m_ | PLMD::isdb::EMMI | private |
| GMM_d_w_ | PLMD::isdb::EMMI | private |
| GMM_m_s_ | PLMD::isdb::EMMI | private |
| GMM_m_type_ | PLMD::isdb::EMMI | private |
| GMM_m_w_ | PLMD::isdb::EMMI | private |
| GMMid_der_ | PLMD::isdb::EMMI | private |
| indexes | PLMD::ActionAtomistic | private |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| inv_cov_md_ | PLMD::isdb::EMMI | private |
| inv_sqrt2_ | PLMD::isdb::EMMI | private |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kanneal_ | PLMD::isdb::EMMI | private |
| kbt_ | PLMD::isdb::EMMI | private |
| keywords | PLMD::Action | |
| lockRequestArguments | PLMD::ActionWithArguments | private |
| lockRequestAtoms | PLMD::ActionAtomistic | private |
| lockRequests() override | PLMD::isdb::EMMI | inlinevirtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| masses | PLMD::ActionAtomistic | private |
| MCaccept_ | PLMD::isdb::EMMI | private |
| MCstride_ | PLMD::isdb::EMMI | private |
| MCtrials_ | PLMD::isdb::EMMI | private |
| 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 | |
| nanneal_ | PLMD::isdb::EMMI | private |
| nexp_ | PLMD::isdb::EMMI | private |
| nl_ | PLMD::isdb::EMMI | private |
| nl_cutoff_ | PLMD::isdb::EMMI | private |
| nl_stride_ | PLMD::isdb::EMMI | private |
| no_aver_ | PLMD::isdb::EMMI | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| noise_ | PLMD::isdb::EMMI | private |
| nregres_ | PLMD::isdb::EMMI | private |
| nrep_ | PLMD::isdb::EMMI | private |
| numericalDerivatives | PLMD::ActionWithValue | private |
| ovdd_ | PLMD::isdb::EMMI | private |
| ovfilename_ | PLMD::isdb::EMMI | private |
| ovmd_ | PLMD::isdb::EMMI | private |
| ovmd_ave_ | PLMD::isdb::EMMI | private |
| ovmd_der_ | PLMD::isdb::EMMI | private |
| ovstride_ | PLMD::isdb::EMMI | 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 | |
| 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::ActionAtomistic | private |
| pbc_ | PLMD::isdb::EMMI | private |
| pbc_fwd | PLMD::ActionAtomistic | private |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| plumed | PLMD::Action | |
| positions | PLMD::ActionAtomistic | private |
| pre_fact_ | PLMD::isdb::EMMI | private |
| prepare() override | PLMD::isdb::EMMI | virtual |
| print_status(long long int step) | PLMD::isdb::EMMI | private |
| prior_ | PLMD::isdb::EMMI | private |
| random_ | PLMD::isdb::EMMI | private |
| rank_ | PLMD::isdb::EMMI | private |
| read_exp_errors(const std::string &errfile) | PLMD::isdb::EMMI | private |
| read_exp_overlaps(const std::string &ovfile) | PLMD::isdb::EMMI | private |
| read_status() | PLMD::isdb::EMMI | private |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::EMMI | static |
| replica_ | PLMD::isdb::EMMI | private |
| requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| scale_ | PLMD::isdb::EMMI | private |
| scale_max_ | PLMD::isdb::EMMI | private |
| scale_min_ | PLMD::isdb::EMMI | private |
| scaleEnergy(double s) | PLMD::isdb::EMMI | private |
| setArgDerivatives(Value *v, const double &d) | PLMD::isdb::EMMI | inline |
| setAtomsDerivatives(Value *v, const unsigned i, const Vector &d) | PLMD::isdb::EMMI | inline |
| setBoxDerivatives(Value *v, const Tensor &d) | PLMD::isdb::EMMI | inline |
| setDerivatives() | PLMD::isdb::EMMI | inline |
| 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 | |
| sigma_ | PLMD::isdb::EMMI | private |
| sigma_max_ | PLMD::isdb::EMMI | private |
| sigma_min_ | PLMD::isdb::EMMI | private |
| size_ | PLMD::isdb::EMMI | private |
| sqrt2_pi_ | PLMD::isdb::EMMI | private |
| statusfile_ | PLMD::isdb::EMMI | private |
| statusfilename_ | PLMD::isdb::EMMI | private |
| statusstride_ | PLMD::isdb::EMMI | private |
| tab_exp_ | PLMD::isdb::EMMI | private |
| turnOnDerivatives() override | PLMD::isdb::EMMI | inlinevirtual |
| unique | PLMD::ActionAtomistic | private |
| unique_local | PLMD::ActionAtomistic | private |
| unlockRequests() override | PLMD::isdb::EMMI | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| update_neighbor_list() | PLMD::isdb::EMMI | private |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| values | PLMD::ActionWithValue | private |
| virial | PLMD::ActionAtomistic | private |
| virial_ | PLMD::isdb::EMMI | private |
| warning(const std::string &msg) | PLMD::Action | |
| write_model_overlap(long long int step) | PLMD::isdb::EMMI | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
1.17.0