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 | |
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 |
moveReferenceArguments(const std::vector< double > &arg_vals) | PLMD::ReferenceArguments | |
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 |
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 |
~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |