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::FakeFrame | inlinevirtual |
calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const | PLMD::ReferenceConfiguration | |
copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
displaceReferenceConfiguration(const double &weight, Direction &dir) | PLMD::ReferenceConfiguration | |
error(const std::string &msg) | PLMD::ReferenceConfiguration | protected |
extractDisplacementVector(const std::vector< Vector > &pos, const std::vector< Value *> &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const | PLMD::ReferenceConfiguration | |
FakeFrame(const ReferenceConfigurationOptions &ro) | PLMD::FakeFrame | inlineexplicit |
getAbsoluteIndexes() | PLMD::ReferenceConfiguration | inlinevirtual |
getArgumentNames() | PLMD::ReferenceConfiguration | inlinevirtual |
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
getName() const | PLMD::ReferenceConfiguration | |
getNumberOfReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
getNumberOfReferencePositions() const | PLMD::ReferenceConfiguration | inlinevirtual |
getReferenceArgument(const unsigned &i) const | PLMD::ReferenceConfiguration | inlinevirtual |
getReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
getReferenceMetric() | PLMD::ReferenceConfiguration | inlinevirtual |
getReferencePositions() const | PLMD::ReferenceConfiguration | inlinevirtual |
pcaIsEnabledForThisReference() | PLMD::ReferenceConfiguration | 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::FakeFrame | inlinevirtual |
ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | explicit |
setupPCAStorage(ReferenceValuePack &mypack) | PLMD::ReferenceConfiguration | inlinevirtual |
~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |