PLMD::ReferenceAtoms Member List

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

alignPLMD::ReferenceAtomsprivate
atom_der_indexPLMD::ReferenceAtomsprivate
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 =0PLMD::ReferenceConfigurationpure virtual
calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared=false) constPLMD::ReferenceConfiguration
checks_were_disabledPLMD::ReferenceAtomsprivate
copyDerivatives(const ReferenceConfiguration *)PLMD::ReferenceConfiguration
Direction classPLMD::ReferenceAtomsfriend
displacePLMD::ReferenceAtomsprivate
displaceReferenceAtoms(const double &weight, const std::vector< Vector > &dir)PLMD::ReferenceAtoms
displaceReferenceConfiguration(const double &weight, Direction &dir)PLMD::ReferenceConfiguration
error(const std::string &msg)PLMD::ReferenceConfigurationprotected
extractAtomicDisplacement(const std::vector< Vector > &pos, std::vector< Vector > &direction) constPLMD::ReferenceAtomsinlinevirtual
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() overridePLMD::ReferenceAtomsinlinevirtual
getAlign() constPLMD::ReferenceAtomsinline
getArgumentNames()PLMD::ReferenceConfigurationinlinevirtual
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false)PLMD::ReferenceConfigurationinlinevirtual
getAtomIndex(const unsigned &) constPLMD::ReferenceAtomsinline
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) overridePLMD::ReferenceAtomsvirtual
getDisplace() constPLMD::ReferenceAtomsinline
getName() constPLMD::ReferenceConfiguration
getNumberOfAtoms() constPLMD::ReferenceAtomsinline
getNumberOfReferenceArguments() constPLMD::ReferenceConfigurationinlinevirtual
getNumberOfReferencePositions() const overridePLMD::ReferenceAtomsinlinevirtual
getReferenceArgument(const unsigned &i) constPLMD::ReferenceConfigurationinlinevirtual
getReferenceArguments() constPLMD::ReferenceConfigurationinlinevirtual
getReferenceMetric()PLMD::ReferenceConfigurationinlinevirtual
getReferencePosition(const unsigned &iatom) constPLMD::ReferenceAtomsinlineprotected
getReferencePositions() const overridePLMD::ReferenceAtomsinlinevirtual
indicesPLMD::ReferenceAtomsprivate
linePLMD::ReferenceConfigurationprivate
MultiDomainRMSD classPLMD::ReferenceAtomsfriend
namePLMD::ReferenceConfigurationprivate
parseAtomList(const std::string &, std::vector< unsigned > &)PLMD::ReferenceAtomsprotected
pcaIsEnabledForThisReference()PLMD::ReferenceConfigurationinlinevirtual
projectAtomicDisplacementOnVector(const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) constPLMD::ReferenceAtomsinlinevirtual
projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) constPLMD::ReferenceConfiguration
read(const PDB &)=0PLMD::ReferenceConfigurationpure virtual
readAtomsFromPDB(const PDB &, const bool allowblocks=false)PLMD::ReferenceAtomsprotected
reference_atomsPLMD::ReferenceAtomsprivate
ReferenceAtoms(const ReferenceConfigurationOptions &ro)PLMD::ReferenceAtomsexplicit
ReferenceConfiguration classPLMD::ReferenceAtomsfriend
PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro)PLMD::ReferenceConfigurationexplicit
setAtomIndices(const std::vector< AtomNumber > &atomnumbers)PLMD::ReferenceAtomsprotected
setReferenceAtoms(const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)=0PLMD::ReferenceAtomspure virtual
setupPCAStorage(ReferenceValuePack &mypack)PLMD::ReferenceConfigurationinlinevirtual
singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks)PLMD::ReferenceAtomsprotected
SingleDomainRMSD classPLMD::ReferenceAtomsfriend
~ReferenceConfiguration()PLMD::ReferenceConfigurationvirtual