| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | 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 | |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| analysis_ | PLMD::isdb::EMMI | private |
| apply() | PLMD::Colvar | protectedvirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atom_der_ | PLMD::isdb::EMMI | private |
| atom_der_b_ | PLMD::isdb::EMMI | private |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| calculate() | PLMD::isdb::EMMI | virtual |
| calculate_overlap() | PLMD::isdb::EMMI | private |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionAtomistic | virtual |
| cfact_ | PLMD::isdb::EMMI | private |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| check_GMM_d(VectorGeneric< 6 > &cov, double w) | PLMD::isdb::EMMI | private |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkIsEnergy() | PLMD::Colvar | inline |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| 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 |
| clearOutputForces() | PLMD::ActionAtomistic | |
| 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 | |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| Devfile_ | PLMD::isdb::EMMI | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| EMMI(const ActionOptions &) | PLMD::isdb::EMMI | explicit |
| err_f_ | PLMD::isdb::EMMI | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| fact_md_ | PLMD::isdb::EMMI | private |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| first_time_ | PLMD::isdb::EMMI | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| get_auxiliary_stuff() | PLMD::isdb::EMMI | private |
| get_cutoff_ov() | PLMD::isdb::EMMI | private |
| get_GMM_d(string gmm_file) | PLMD::isdb::EMMI | private |
| get_GMM_m(vector< AtomNumber > &atoms) | PLMD::isdb::EMMI | private |
| get_overlap(const Vector &m_m, const Vector &d_m, double &fact_md, const VectorGeneric< 6 > &inv_cov_md, Vector &ov_der) | PLMD::isdb::EMMI | private |
| get_overlap(const Vector &m_m, const Vector &d_m, double &fact_md, const VectorGeneric< 6 > &inv_cov_md) | 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 |
| 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 |
| 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() | 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 |
| getPosition(AtomNumber) 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 |
| GMM_d_beta_ | PLMD::isdb::EMMI | private |
| GMM_d_cov_ | PLMD::isdb::EMMI | private |
| GMM_d_m_ | PLMD::isdb::EMMI | private |
| GMM_d_w_ | PLMD::isdb::EMMI | private |
| GMM_m_type_ | PLMD::isdb::EMMI | private |
| GMM_m_w_ | PLMD::isdb::EMMI | private |
| 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 |
| isEnergy | PLMD::Colvar | protected |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::isdb::EMMI | private |
| keywords | PLMD::Action | |
| lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| nframe_ | 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 |
| normalize_GMM(vector< double > &w) | PLMD::isdb::EMMI | private |
| nrep_ | PLMD::isdb::EMMI | private |
| ov_cut_ | PLMD::isdb::EMMI | private |
| ovdd_ | PLMD::isdb::EMMI | private |
| ovdd_cut_ | PLMD::isdb::EMMI | private |
| ovmd_ | PLMD::isdb::EMMI | private |
| ovmd_ave_ | PLMD::isdb::EMMI | private |
| ovmd_der_ | PLMD::isdb::EMMI | private |
| 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::isdb::EMMI | private |
| 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::isdb::EMMI | virtual |
| rank_ | PLMD::isdb::EMMI | private |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::EMMI | static |
| replica_ | PLMD::isdb::EMMI | private |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::Colvar | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| s_map_ | PLMD::isdb::EMMI | private |
| 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 |
| 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_mean_ | PLMD::isdb::EMMI | private |
| size_ | PLMD::isdb::EMMI | private |
| sqrt2_pi_ | PLMD::isdb::EMMI | private |
| turnOnDerivatives() | PLMD::ActionWithValue | virtual |
| unlockRequests() | PLMD::ActionAtomistic | 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 |
| warning(const std::string &msg) | PLMD::Action | |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~Colvar() | PLMD::Colvar | inline |
1.8.14