| addDirection(const double &weight, const Direction &dir) | PLMD::Direction | |
| align | PLMD::ReferenceAtoms | private |
| arg_der_index | PLMD::ReferenceArguments | private |
| arg_names | PLMD::ReferenceArguments | private |
| atom_der_index | PLMD::ReferenceAtoms | private |
| calc(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, const std::vector< double > &args, ReferenceValuePack &myder, const bool &squared) const override | PLMD::Direction | virtual |
| 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 |
| checks_were_disabled | PLMD::ReferenceAtoms | private |
| copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
| Direction(const ReferenceConfigurationOptions &ro) | PLMD::Direction | explicit |
| displace | PLMD::ReferenceAtoms | private |
| displaceReferenceArguments(const double &weight, const std::vector< double > &displace) | PLMD::ReferenceArguments | |
| displaceReferenceAtoms(const double &weight, const std::vector< Vector > &dir) | PLMD::ReferenceAtoms | |
| 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 override | PLMD::Direction | virtual |
| extractAtomicDisplacement(const std::vector< Vector > &pos, std::vector< Vector > &dirout) const override | PLMD::Direction | 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() override | PLMD::ReferenceAtoms | inlinevirtual |
| getAlign() const | PLMD::ReferenceAtoms | inline |
| PLMD::getArgumentNames() | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getArgumentNames() override | PLMD::ReferenceArguments | inlinevirtual |
| PLMD::getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) override | PLMD::ReferenceArguments | virtual |
| getAtomIndex(const unsigned &) const | PLMD::ReferenceAtoms | inline |
| getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) override | PLMD::ReferenceAtoms | virtual |
| getDisplace() const | PLMD::ReferenceAtoms | inline |
| getName() const | PLMD::ReferenceConfiguration | |
| getNumberOfAtoms() const | PLMD::ReferenceAtoms | inline |
| PLMD::getNumberOfReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getNumberOfReferenceArguments() const override | PLMD::ReferenceArguments | inlinevirtual |
| getNumberOfReferencePositions() const override | PLMD::ReferenceAtoms | inlinevirtual |
| PLMD::getReferenceArgument(const unsigned &i) const | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getReferenceArgument(const unsigned &i) const override | PLMD::ReferenceArguments | inlinevirtual |
| PLMD::getReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getReferenceArguments() const override | PLMD::ReferenceArguments | inlinevirtual |
| PLMD::getReferenceMetric() | PLMD::ReferenceConfiguration | inlinevirtual |
| PLMD::ReferenceArguments::getReferenceMetric() override | PLMD::ReferenceArguments | virtual |
| getReferencePosition(const unsigned &iatom) const | PLMD::ReferenceAtoms | inlineprotected |
| getReferencePositions() const override | PLMD::ReferenceAtoms | inlinevirtual |
| hasmetric | PLMD::ReferenceArguments | protected |
| hasweights | PLMD::ReferenceArguments | protected |
| indices | PLMD::ReferenceAtoms | private |
| line | PLMD::ReferenceConfiguration | private |
| metric | PLMD::ReferenceArguments | private |
| moveReferenceArguments(const std::vector< double > &arg_vals) | PLMD::ReferenceArguments | |
| name | PLMD::ReferenceConfiguration | private |
| normalized | PLMD::Direction | |
| parseAtomList(const std::string &, std::vector< unsigned > &) | PLMD::ReferenceAtoms | protected |
| pcaIsEnabledForThisReference() | PLMD::ReferenceConfiguration | inlinevirtual |
| projectArgDisplacementOnVector(const std::vector< double > &eigv, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceArguments | |
| projectAtomicDisplacementOnVector(const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const | PLMD::ReferenceAtoms | inlinevirtual |
| projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceConfiguration | |
| read(const PDB &) override | PLMD::Direction | virtual |
| readArgumentsFromPDB(const PDB &pdb) | PLMD::ReferenceArguments | protected |
| readAtomsFromPDB(const PDB &, const bool allowblocks=false) | PLMD::ReferenceAtoms | protected |
| reference_args | PLMD::ReferenceArguments | private |
| reference_atoms | PLMD::ReferenceAtoms | private |
| ReferenceArguments(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceArguments | explicit |
| ReferenceAtoms(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceAtoms | explicit |
| PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | explicit |
| setAtomIndices(const std::vector< AtomNumber > &atomnumbers) | PLMD::ReferenceAtoms | protected |
| setDirection(const std::vector< Vector > &conf, const std::vector< double > &args) | PLMD::Direction | |
| setReferenceArguments() | PLMD::ReferenceArguments | protected |
| setReferenceArguments(const std::vector< double > &arg_vals, const std::vector< double > &sigma) | PLMD::ReferenceArguments | |
| setReferenceAtoms(const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override | PLMD::Direction | inlinevirtual |
| setupPCAStorage(ReferenceValuePack &mypack) | PLMD::ReferenceConfiguration | inlinevirtual |
| singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks) | PLMD::ReferenceAtoms | protected |
| sqrtweight | PLMD::ReferenceArguments | private |
| trig_metric | PLMD::ReferenceArguments | private |
| weights | PLMD::ReferenceArguments | private |
| zeroDirection() | PLMD::Direction | |
| ~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |
1.8.17