| 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 |
| apply() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| average_weights_ | PLMD::isdb::MetainferenceBase | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calc_data_ | PLMD::isdb::MetainferenceBase | private |
| calculate()=0 | PLMD::Action | pure virtual |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a) override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| 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 | |
| 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::MetainferenceBase | private |
| Dependencies typedef | PLMD::Action | |
| Dftilde_ | PLMD::isdb::MetainferenceBase | private |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| do_optsigmamean_ | PLMD::isdb::MetainferenceBase | private |
| do_regression_zero(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| do_reweight_ | PLMD::isdb::MetainferenceBase | private |
| Doffset_ | PLMD::isdb::MetainferenceBase | private |
| doMonteCarlo(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| dooffset_ | PLMD::isdb::MetainferenceBase | private |
| doregres_zero_ | PLMD::isdb::MetainferenceBase | private |
| doscale_ | PLMD::isdb::MetainferenceBase | private |
| doscore_ | PLMD::isdb::MetainferenceBase | private |
| Dscale_ | PLMD::isdb::MetainferenceBase | private |
| Dsigma_ | PLMD::isdb::MetainferenceBase | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| firstTime | PLMD::isdb::MetainferenceBase | private |
| firstTimeW | PLMD::isdb::MetainferenceBase | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forces | PLMD::isdb::MetainferenceBase | private |
| forcesToApply | PLMD::isdb::MetainferenceBase | private |
| ftilde_ | PLMD::isdb::MetainferenceBase | private |
| GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| gen_likelihood_ | PLMD::isdb::MetainferenceBase | private |
| GENERIC enum value | PLMD::isdb::MetainferenceBase | private |
| get_sigma_mean(const double fact, const double var_fact, const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| get_weights(double &fact, double &var_fact) | PLMD::isdb::MetainferenceBase | 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 |
| getCalcData(const unsigned index) | PLMD::isdb::MetainferenceBase | inlineprivate |
| 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 |
| getDoScore() | PLMD::isdb::MetainferenceBase | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getEnergyForceGJ(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceGJE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceMIGEN(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceSP(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceSPE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyGJ(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergyGJE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergyMIGEN(const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergySP(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergySPE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| 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 |
| getMetaDer(const unsigned index) | PLMD::isdb::MetainferenceBase | inline |
| getName() const | PLMD::Action | inline |
| getNarg() | PLMD::isdb::MetainferenceBase | inline |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() override | PLMD::isdb::MetainferenceBase | 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 |
| getScore() | PLMD::isdb::MetainferenceBase | |
| 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 |
| getWstride() | PLMD::isdb::MetainferenceBase | inline |
| Initialise(const unsigned input) | PLMD::isdb::MetainferenceBase | |
| 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 | |
| isActive() const | PLMD::Action | inline |
| iselect | PLMD::isdb::MetainferenceBase | private |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::isdb::MetainferenceBase | private |
| keywords | PLMD::Action | |
| LIKE_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| LIKE_LOGN enum value | PLMD::isdb::MetainferenceBase | private |
| lockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| log | PLMD::Action | |
| makeWhole() | PLMD::ActionAtomistic | |
| master | PLMD::isdb::MetainferenceBase | private |
| MCaccept_ | PLMD::isdb::MetainferenceBase | private |
| MCacceptFT_ | PLMD::isdb::MetainferenceBase | private |
| MCacceptScale_ | PLMD::isdb::MetainferenceBase | private |
| MCchunksize_ | PLMD::isdb::MetainferenceBase | private |
| MCsteps_ | PLMD::isdb::MetainferenceBase | private |
| MCtrial_ | PLMD::isdb::MetainferenceBase | private |
| metader_ | PLMD::isdb::MetainferenceBase | private |
| MetainferenceBase(const ActionOptions &) | PLMD::isdb::MetainferenceBase | explicit |
| MGAUSS enum value | PLMD::isdb::MetainferenceBase | 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 |
| MOUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
| moveScaleOffset(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
| moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow) | PLMD::isdb::MetainferenceBase | private |
| moveTilde(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
| multi_sim_comm | PLMD::Action | |
| narg | PLMD::isdb::MetainferenceBase | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noise_type_ | PLMD::isdb::MetainferenceBase | private |
| nregres_zero_ | PLMD::isdb::MetainferenceBase | private |
| nrep_ | PLMD::isdb::MetainferenceBase | private |
| nsel_ | PLMD::isdb::MetainferenceBase | private |
| offset_ | PLMD::isdb::MetainferenceBase | private |
| offset_max_ | PLMD::isdb::MetainferenceBase | private |
| offset_min_ | PLMD::isdb::MetainferenceBase | private |
| offset_mu_ | PLMD::isdb::MetainferenceBase | private |
| offset_prior_ | PLMD::isdb::MetainferenceBase | private |
| optsigmamean_stride_ | PLMD::isdb::MetainferenceBase | private |
| OUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
| parameters | PLMD::isdb::MetainferenceBase | 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 | |
| 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::Action | virtual |
| random | PLMD::isdb::MetainferenceBase | private |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::MetainferenceBase | static |
| replica_ | PLMD::isdb::MetainferenceBase | private |
| replica_averaging(const double fact, std::vector< double > &mean, std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| SC_FLAT enum value | PLMD::isdb::MetainferenceBase | private |
| SC_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| scale_ | PLMD::isdb::MetainferenceBase | private |
| scale_max_ | PLMD::isdb::MetainferenceBase | private |
| scale_min_ | PLMD::isdb::MetainferenceBase | private |
| scale_mu_ | PLMD::isdb::MetainferenceBase | private |
| scale_prior_ | PLMD::isdb::MetainferenceBase | private |
| Selector() | PLMD::isdb::MetainferenceBase | |
| selector_ | PLMD::isdb::MetainferenceBase | private |
| setArgDerivatives(Value *v, const double &d) | PLMD::isdb::MetainferenceBase | inline |
| setAtomsDerivatives(Value *v, const unsigned i, const Vector &d) | PLMD::isdb::MetainferenceBase | inline |
| setBoxDerivatives(Value *v, const Tensor &d) | PLMD::isdb::MetainferenceBase | inline |
| setCalcData(const unsigned index, const double datum) | PLMD::isdb::MetainferenceBase | inline |
| setCalcData(const std::vector< double > &data) | PLMD::isdb::MetainferenceBase | inline |
| setDerivatives() | PLMD::isdb::MetainferenceBase | inline |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setMetaDer(const unsigned index, const double der) | PLMD::isdb::MetainferenceBase | inlineprivate |
| setNarg(const unsigned input) | PLMD::isdb::MetainferenceBase | inline |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setParameter(const double input) | PLMD::isdb::MetainferenceBase | inline |
| setParameters(const std::vector< double > &input) | PLMD::isdb::MetainferenceBase | inline |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setScore(const double score) | PLMD::isdb::MetainferenceBase | inline |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| sfile_ | PLMD::isdb::MetainferenceBase | private |
| sigma_ | PLMD::isdb::MetainferenceBase | private |
| sigma_max_ | PLMD::isdb::MetainferenceBase | private |
| sigma_mean2_ | PLMD::isdb::MetainferenceBase | private |
| sigma_mean2_last_ | PLMD::isdb::MetainferenceBase | private |
| sigma_min_ | PLMD::isdb::MetainferenceBase | private |
| status_file_name_ | PLMD::isdb::MetainferenceBase | private |
| turnOnDerivatives() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| unlockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| valueAccept | PLMD::isdb::MetainferenceBase | private |
| valueAcceptFT | PLMD::isdb::MetainferenceBase | private |
| valueAcceptScale | PLMD::isdb::MetainferenceBase | private |
| valueFtilde | PLMD::isdb::MetainferenceBase | private |
| valueOffset | PLMD::isdb::MetainferenceBase | private |
| valueScale | PLMD::isdb::MetainferenceBase | private |
| valueScore | PLMD::isdb::MetainferenceBase | private |
| valueSigma | PLMD::isdb::MetainferenceBase | private |
| valueSigmaMean | PLMD::isdb::MetainferenceBase | private |
| warning(const std::string &msg) | PLMD::Action | |
| write_stride_ | PLMD::isdb::MetainferenceBase | private |
| writeStatus() | PLMD::isdb::MetainferenceBase | |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~MetainferenceBase() | PLMD::isdb::MetainferenceBase | |
1.8.14