PLMD::MahalanobisDistance Member List

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

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
MahalanobisDistance(const ReferenceConfigurationOptions &ro)	PLMD::MahalanobisDistance	explicit
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