PLMD::Direction Member List

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

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	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
checkRead()	PLMD::ReferenceConfiguration
copyDerivatives(const ReferenceConfiguration *)	PLMD::ReferenceConfiguration
Direction(const ReferenceConfigurationOptions &ro)	PLMD::Direction	explicit
error(const std::string &msg)	PLMD::ReferenceConfiguration	protected
getAbsoluteIndexes()	PLMD::ReferenceAtoms	inlinevirtual
getAlign() const	PLMD::ReferenceAtoms	inlineprotected
PLMD::getArgumentNames()	PLMD::ReferenceConfiguration	inlinevirtual
PLMD::ReferenceArguments::getArgumentNames()	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)	PLMD::ReferenceArguments	virtual
getAtomIndex(const unsigned &) const	PLMD::ReferenceAtoms	inline
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false)	PLMD::ReferenceAtoms	virtual
getDisplace() const	PLMD::ReferenceAtoms	inlineprotected
getName() const	PLMD::ReferenceConfiguration
getNumberOfAtoms() const	PLMD::ReferenceAtoms	inline
PLMD::getNumberOfReferenceArguments() const	PLMD::ReferenceConfiguration	inlinevirtual
PLMD::ReferenceArguments::getNumberOfReferenceArguments() const	PLMD::ReferenceArguments	inlinevirtual
getNumberOfReferencePositions() const	PLMD::ReferenceAtoms	inlinevirtual
PLMD::getReferenceArgument(const unsigned &i) const	PLMD::ReferenceConfiguration	inlinevirtual
PLMD::ReferenceArguments::getReferenceArgument(const unsigned &i) const	PLMD::ReferenceArguments	inlinevirtual
PLMD::getReferenceArguments()	PLMD::ReferenceConfiguration	inlinevirtual
PLMD::ReferenceArguments::getReferenceArguments()	PLMD::ReferenceArguments	inlinevirtual
PLMD::getReferenceMetric()	PLMD::ReferenceConfiguration	inlinevirtual
PLMD::ReferenceArguments::getReferenceMetric()	PLMD::ReferenceArguments	virtual
getReferencePosition(const unsigned &iatom) const	PLMD::ReferenceAtoms	inlineprotected
getReferencePositions() const	PLMD::ReferenceAtoms	inlineprotectedvirtual
getWeight() const	PLMD::ReferenceConfiguration	inline
hasmetric	PLMD::ReferenceArguments	protected
hasweights	PLMD::ReferenceArguments	protected
isDirection() const	PLMD::ReferenceConfiguration
parse(const std::string &key, T &t, bool ignore_missing=false)	PLMD::ReferenceConfiguration
parseAtomList(const std::string &, std::vector< unsigned > &)	PLMD::ReferenceAtoms	protected
parseFlag(const std::string &key, bool &t)	PLMD::ReferenceConfiguration
parseVector(const std::string &key, std::vector< T > &t, bool ignore_missing=false)	PLMD::ReferenceConfiguration
pcaIsEnabledForThisReference()	PLMD::ReferenceConfiguration	inlinevirtual
print(OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)	PLMD::ReferenceConfiguration
print(OFile &ofile, const std::string &fmt, const double &lunits)	PLMD::ReferenceConfiguration
printArguments(OFile &ofile, const std::string &fmt) const	PLMD::ReferenceArguments
printAtoms(OFile &ofile, const double &lunits) const	PLMD::ReferenceAtoms
projectAtomicDisplacementOnVector(const unsigned &i, const Matrix< Vector > &eigv, const std::vector< Vector > &pos, ReferenceValuePack &mypack) const	PLMD::ReferenceConfiguration	inlinevirtual
read(const PDB &)	PLMD::Direction	virtual
readArgumentsFromPDB(const PDB &pdb)	PLMD::ReferenceArguments	protected
readAtomsFromPDB(const PDB &, const bool allowblocks=false)	PLMD::ReferenceAtoms	protected
ReferenceArguments(const ReferenceConfigurationOptions &ro)	PLMD::ReferenceArguments	explicit
ReferenceAtoms(const ReferenceConfigurationOptions &ro)	PLMD::ReferenceAtoms	explicit
ReferenceConfiguration(const ReferenceConfigurationOptions &ro)	PLMD::ReferenceConfiguration	explicit
set(const PDB &)	PLMD::ReferenceConfiguration	virtual
setArgumentNames(const std::vector< std::string > &arg_vals)	PLMD::ReferenceArguments
setAtomIndices(const std::vector< AtomNumber > &atomnumbers)	PLMD::ReferenceAtoms	protected
setAtomNumbers(const std::vector< AtomNumber > &numbers)	PLMD::ReferenceAtoms
setDirection(const std::vector< Vector > &conf, const std::vector< double > &args)	PLMD::Direction
setNamesAndAtomNumbers(const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)	PLMD::ReferenceConfiguration
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)	PLMD::Direction	inlinevirtual
setReferenceConfig(const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)	PLMD::ReferenceConfiguration
setupPCAStorage(ReferenceValuePack &mypack)	PLMD::ReferenceConfiguration	inlinevirtual
setWeight(const double &ww)	PLMD::ReferenceConfiguration	inline
singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks)	PLMD::ReferenceAtoms	protected
~ReferenceConfiguration()	PLMD::ReferenceConfiguration	virtual