PLMD::MahalanobisDistance Member List

This is the complete list of members for PLMD::MahalanobisDistance, including all inherited members.

arg_der_indexPLMD::ReferenceArgumentsprivate
arg_namesPLMD::ReferenceArgumentsprivate
ArgumentOnlyDistance(const ReferenceConfigurationOptions &ro)PLMD::ArgumentOnlyDistanceexplicit
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 overridePLMD::ArgumentOnlyDistancevirtual
calculate(const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared) constPLMD::ArgumentOnlyDistance
PLMD::ReferenceArguments::calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared=false) constPLMD::ReferenceConfiguration
calculateArgumentDistance(const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) constPLMD::ReferenceArgumentsvirtual
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::ReferenceConfigurationprotected
extractArgumentDisplacement(const std::vector< Value * > &vals, const std::vector< double > &arg, std::vector< double > &dirout) constPLMD::ReferenceArgumentsvirtual
extractDisplacementVector(const std::vector< Vector > &pos, const std::vector< Value * > &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) constPLMD::ReferenceConfiguration
fake_arg_namesPLMD::ReferenceConfigurationprivate
fake_atom_numbersPLMD::ReferenceConfigurationprivate
fake_metricPLMD::ReferenceConfigurationprivate
fake_refargsPLMD::ReferenceConfigurationprivate
fake_refatomsPLMD::ReferenceConfigurationprivate
getAbsoluteIndexes()PLMD::ReferenceConfigurationinlinevirtual
getArgumentNames() overridePLMD::ReferenceArgumentsinlinevirtual
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) overridePLMD::ReferenceArgumentsvirtual
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false)PLMD::ReferenceConfigurationinlinevirtual
getName() constPLMD::ReferenceConfiguration
getNumberOfReferenceArguments() const overridePLMD::ReferenceArgumentsinlinevirtual
getNumberOfReferencePositions() constPLMD::ReferenceConfigurationinlinevirtual
getReferenceArgument(const unsigned &i) const overridePLMD::ReferenceArgumentsinlinevirtual
getReferenceArguments() const overridePLMD::ReferenceArgumentsinlinevirtual
getReferenceMetric() overridePLMD::ReferenceArgumentsvirtual
getReferencePositions() constPLMD::ReferenceConfigurationinlinevirtual
hasmetricPLMD::ReferenceArgumentsprotected
hasweightsPLMD::ReferenceArgumentsprotected
linePLMD::ReferenceConfigurationprivate
MahalanobisDistance(const ReferenceConfigurationOptions &ro)PLMD::MahalanobisDistanceexplicit
metricPLMD::ReferenceArgumentsprivate
moveReferenceArguments(const std::vector< double > &arg_vals)PLMD::ReferenceArguments
namePLMD::ReferenceConfigurationprivate
pcaIsEnabledForThisReference() overridePLMD::ArgumentOnlyDistanceinlinevirtual
projectArgDisplacementOnVector(const std::vector< double > &eigv, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) constPLMD::ReferenceArguments
projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) constPLMD::ReferenceConfiguration
read(const PDB &pdb) overridePLMD::ArgumentOnlyDistancevirtual
readArgumentsFromPDB(const PDB &pdb)PLMD::ReferenceArgumentsprotected
reference_argsPLMD::ReferenceArgumentsprivate
ReferenceArguments(const ReferenceConfigurationOptions &ro)PLMD::ReferenceArgumentsexplicit
PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro)PLMD::ReferenceConfigurationexplicit
setReferenceArguments()PLMD::ReferenceArgumentsprotected
setReferenceArguments(const std::vector< double > &arg_vals, const std::vector< double > &sigma)PLMD::ReferenceArguments
setupPCAStorage(ReferenceValuePack &mypack) overridePLMD::ArgumentOnlyDistanceinlinevirtual
sqrtweightPLMD::ReferenceArgumentsprivate
trig_metricPLMD::ReferenceArgumentsprivate
weightsPLMD::ReferenceArgumentsprivate
~ReferenceConfiguration()PLMD::ReferenceConfigurationvirtual