PLMD::EuclideanDistance Member List

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

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) constPLMD::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
checkRead()PLMD::ReferenceConfiguration
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
EuclideanDistance(const ReferenceConfigurationOptions &ro)PLMD::EuclideanDistanceexplicit
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
getAbsoluteIndexes()PLMD::ReferenceConfigurationinlinevirtual
getArgumentNames()PLMD::ReferenceArgumentsinlinevirtual
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false)PLMD::ReferenceArgumentsvirtual
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false)PLMD::ReferenceConfigurationinlinevirtual
getName() constPLMD::ReferenceConfiguration
getNumberOfReferenceArguments() constPLMD::ReferenceArgumentsinlinevirtual
getNumberOfReferencePositions() constPLMD::ReferenceConfigurationinlinevirtual
getReferenceArgument(const unsigned &i) constPLMD::ReferenceArgumentsinlinevirtual
getReferenceArguments() constPLMD::ReferenceArgumentsinlinevirtual
getReferenceMetric()PLMD::ReferenceArgumentsvirtual
getReferencePositions() constPLMD::ReferenceConfigurationinlinevirtual
getWeight() constPLMD::ReferenceConfigurationinline
hasmetricPLMD::ReferenceArgumentsprotected
hasweightsPLMD::ReferenceArgumentsprotected
moveReferenceArguments(const std::vector< double > &arg_vals)PLMD::ReferenceArguments
parse(const std::string &key, T &t, bool ignore_missing=false)PLMD::ReferenceConfiguration
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::ArgumentOnlyDistanceinlinevirtual
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) constPLMD::ReferenceArguments
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)PLMD::ArgumentOnlyDistancevirtual
readArgumentsFromPDB(const PDB &pdb)PLMD::ReferenceArgumentsprotected
ReferenceArguments(const ReferenceConfigurationOptions &ro)PLMD::ReferenceArgumentsexplicit
PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro)PLMD::ReferenceConfigurationexplicit
set(const PDB &)PLMD::ReferenceConfigurationvirtual
setArgumentNames(const std::vector< std::string > &arg_vals)PLMD::ReferenceArguments
setNamesAndAtomNumbers(const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)PLMD::ReferenceConfiguration
setReferenceArguments()PLMD::ReferenceArgumentsprotected
setReferenceArguments(const std::vector< double > &arg_vals, const std::vector< double > &sigma)PLMD::ReferenceArguments
setReferenceConfig(const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)PLMD::ReferenceConfiguration
setupPCAStorage(ReferenceValuePack &mypack)PLMD::ArgumentOnlyDistanceinlinevirtual
setWeight(const double &ww)PLMD::ReferenceConfigurationinline
~ReferenceConfiguration()PLMD::ReferenceConfigurationvirtual