| arg_der_index | PLMD::ReferenceArguments | private |
| arg_names | PLMD::ReferenceArguments | private |
| ArgumentOnlyDistance(const ReferenceConfigurationOptions &ro) | PLMD::ArgumentOnlyDistance | explicit |
| calc(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const override | PLMD::ArgumentOnlyDistance | virtual |
| calculate(const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared) const | PLMD::ArgumentOnlyDistance | |
| PLMD::ReferenceArguments::calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared=false) const | PLMD::ReferenceConfiguration | |
| calculateArgumentDistance(const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const | PLMD::ReferenceArguments | virtual |
| copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
| displaceReferenceArguments(const double &weight, const std::vector< double > &displace) | PLMD::ReferenceArguments | |
| displaceReferenceConfiguration(const double &weight, Direction &dir) | PLMD::ReferenceConfiguration | |
| error(const std::string &msg) | PLMD::ReferenceConfiguration | protected |
| extractArgumentDisplacement(const std::vector< Value * > &vals, const std::vector< double > &arg, std::vector< double > &dirout) const | PLMD::ReferenceArguments | virtual |
| extractDisplacementVector(const std::vector< Vector > &pos, const std::vector< Value * > &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const | PLMD::ReferenceConfiguration | |
| fake_arg_names | PLMD::ReferenceConfiguration | private |
| fake_atom_numbers | PLMD::ReferenceConfiguration | private |
| fake_metric | PLMD::ReferenceConfiguration | private |
| fake_refargs | PLMD::ReferenceConfiguration | private |
| fake_refatoms | PLMD::ReferenceConfiguration | private |
| getAbsoluteIndexes() | PLMD::ReferenceConfiguration | inlinevirtual |
| getArgumentNames() override | PLMD::ReferenceArguments | inlinevirtual |
| getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) override | PLMD::ReferenceArguments | virtual |
| getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
| getName() const | PLMD::ReferenceConfiguration | |
| getNumberOfReferenceArguments() const override | PLMD::ReferenceArguments | inlinevirtual |
| getNumberOfReferencePositions() const | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferenceArgument(const unsigned &i) const override | PLMD::ReferenceArguments | inlinevirtual |
| getReferenceArguments() const override | PLMD::ReferenceArguments | inlinevirtual |
| getReferenceMetric() override | PLMD::ReferenceArguments | virtual |
| getReferencePositions() const | PLMD::ReferenceConfiguration | inlinevirtual |
| hasmetric | PLMD::ReferenceArguments | protected |
| hasweights | PLMD::ReferenceArguments | protected |
| line | PLMD::ReferenceConfiguration | private |
| MahalanobisDistance(const ReferenceConfigurationOptions &ro) | PLMD::MahalanobisDistance | explicit |
| metric | PLMD::ReferenceArguments | private |
| moveReferenceArguments(const std::vector< double > &arg_vals) | PLMD::ReferenceArguments | |
| name | PLMD::ReferenceConfiguration | private |
| pcaIsEnabledForThisReference() override | PLMD::ArgumentOnlyDistance | inlinevirtual |
| projectArgDisplacementOnVector(const std::vector< double > &eigv, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceArguments | |
| projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceConfiguration | |
| read(const PDB &pdb) override | PLMD::ArgumentOnlyDistance | virtual |
| readArgumentsFromPDB(const PDB &pdb) | PLMD::ReferenceArguments | protected |
| reference_args | PLMD::ReferenceArguments | private |
| ReferenceArguments(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceArguments | explicit |
| PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | explicit |
| setReferenceArguments() | PLMD::ReferenceArguments | protected |
| setReferenceArguments(const std::vector< double > &arg_vals, const std::vector< double > &sigma) | PLMD::ReferenceArguments | |
| setupPCAStorage(ReferenceValuePack &mypack) override | PLMD::ArgumentOnlyDistance | inlinevirtual |
| sqrtweight | PLMD::ReferenceArguments | private |
| trig_metric | PLMD::ReferenceArguments | private |
| weights | PLMD::ReferenceArguments | private |
| ~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |
1.8.17