PLMD::ves::BasisFunctions Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
action_pntr_PLMD::ves::BasisFunctionsprivate
activate()PLMD::Actionvirtual
addDependency(Action *)PLMD::Action
addKeywordToList(const std::string &, const T)PLMD::ves::BasisFunctionsprotected
addKeywordToList(const std::string &, const std::vector< T > &)PLMD::ves::BasisFunctionsprotected
addKeywordToList(const std::string &, const bool)PLMD::ves::BasisFunctionsinlineprotected
apply() overridePLMD::ves::BasisFunctionsinlinevirtual
arePeriodic() constPLMD::ves::BasisFunctionsinline
argT_derivf_PLMD::ves::BasisFunctionsprivate
BasisFunctions(const ActionOptions &ao)PLMD::ves::BasisFunctionsexplicit
beforeUpdate()PLMD::Actioninlinevirtual
bf_keywords_PLMD::ves::BasisFunctionsprivate
bf_label_prefix_PLMD::ves::BasisFunctionsprivate
bf_labels_PLMD::ves::BasisFunctionsprivate
calculate() overridePLMD::ves::BasisFunctionsinlinevirtual
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
checkIfArgumentInsideInterval(const double, bool &) constPLMD::ves::BasisFunctionsinline
checkNeedsGradients() constPLMD::Actioninlinevirtual
checkNumericalDerivatives() constPLMD::Actioninlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearOptions()PLMD::Actionvirtual
commPLMD::Action
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
description_PLMD::ves::BasisFunctionsprivate
error(const std::string &msg) constPLMD::Action
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
fopen(const char *path, const char *mode)PLMD::Action
getAllValues(const double, double &, bool &, std::vector< double > &, std::vector< double > &) const =0PLMD::ves::BasisFunctionspure virtual
getAllValuesNumericalDerivs(const double, double &, bool &, std::vector< double > &, std::vector< double > &) constPLMD::ves::BasisFunctionsprivate
getBasisFunctionLabel(const unsigned int index) constPLMD::ves::BasisFunctionsinline
getBasisFunctionLabels() constPLMD::ves::BasisFunctionsinline
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDescription() constPLMD::ves::BasisFunctionsinline
getDocumentation() constPLMD::Actionvirtual
getExchangeStep() constPLMD::Action
getKeyword(const std::string &key)PLMD::Action
getKeywordList() constPLMD::ves::BasisFunctionsinline
getKeywordString() constPLMD::ves::BasisFunctions
getLabel() constPLMD::Actioninline
getMultipleValue(const std::vector< double > &, std::vector< double > &, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &, const bool numerical_deriv=false) constPLMD::ves::BasisFunctions
getName() constPLMD::Actioninline
getNumberOfBasisFunctions() constPLMD::ves::BasisFunctionsinline
getOrder() constPLMD::ves::BasisFunctionsinline
getPntrToAction() constPLMD::ves::BasisFunctionsinline
getPntrToVesBias() constPLMD::ves::BasisFunctionsinline
getRestart() constPLMD::Actioninline
getSize() constPLMD::ves::BasisFunctionsinline
getStep() constPLMD::Action
getTargetDistributionIntegrals(const TargetDistribution *) constPLMD::ves::BasisFunctions
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getType() constPLMD::ves::BasisFunctionsinline
getUniformIntegrals() constPLMD::ves::BasisFunctionsinline
getValue(const double, const unsigned int, double &, bool &) constPLMD::ves::BasisFunctions
has_been_setPLMD::ves::BasisFunctionsprivate
hasBeenSet() constPLMD::ves::BasisFunctionsinline
interval_bounded_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_max_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_max_str_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_mean_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_min_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_min_str_PLMD::ves::BasisFunctionsprivate
interval_intrinsic_range_PLMD::ves::BasisFunctionsprivate
interval_max_PLMD::ves::BasisFunctionsprivate
interval_max_str_PLMD::ves::BasisFunctionsprivate
interval_mean_PLMD::ves::BasisFunctionsprivate
interval_min_PLMD::ves::BasisFunctionsprivate
interval_min_str_PLMD::ves::BasisFunctionsprivate
interval_range_PLMD::ves::BasisFunctionsprivate
intervalBounded() constPLMD::ves::BasisFunctionsinline
intervalDerivf() constPLMD::ves::BasisFunctionsinline
intervalMax() constPLMD::ves::BasisFunctionsinline
intervalMaxStr() constPLMD::ves::BasisFunctionsinline
intervalMean() constPLMD::ves::BasisFunctionsinline
intervalMin() constPLMD::ves::BasisFunctionsinline
intervalMinStr() constPLMD::ves::BasisFunctionsinline
intervalRange() constPLMD::ves::BasisFunctionsinline
intrinsicIntervalMax() constPLMD::ves::BasisFunctionsinlineprotected
intrinsicIntervalMaxStr() constPLMD::ves::BasisFunctionsinlineprotected
intrinsicIntervalMin() constPLMD::ves::BasisFunctionsinlineprotected
intrinsicIntervalMinStr() constPLMD::ves::BasisFunctionsinlineprotected
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
keywordsPLMD::Action
linkAction(Action *)PLMD::ves::BasisFunctions
linkVesBias(VesBias *)PLMD::ves::BasisFunctions
lockRequests()PLMD::Actioninlinevirtual
logPLMD::Action
multi_sim_commPLMD::Action
nbasis_PLMD::ves::BasisFunctionsprivate
nbins_PLMD::ves::BasisFunctionsprivate
norder_PLMD::ves::BasisFunctionsprivate
numberOfBasisFunctions() constPLMD::ves::BasisFunctionsinline
numerical_uniform_integrals_PLMD::ves::BasisFunctionsprivate
numericalTargetDistributionIntegralsFromGrid(const Grid *) constPLMD::ves::BasisFunctionsprotected
numericalUniformIntegrals()PLMD::ves::BasisFunctionsprotected
parse(const std::string &key, T &t)PLMD::Action
parseFlag(const std::string &key, bool &t)PLMD::Action
parseNumbered(const std::string &key, const int no, T &t)PLMD::Action
parseNumberedVector(const std::string &key, const int no, std::vector< T > &t)PLMD::Action
parseVector(const std::string &key, std::vector< T > &t)PLMD::Action
periodic_PLMD::ves::BasisFunctionsprivate
plumedPLMD::Action
prepare()PLMD::Actionvirtual
print_debug_info_PLMD::ves::BasisFunctionsprivate
printInfo() constPLMD::ves::BasisFunctions
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
registerKeywords(Keywords &)PLMD::ves::BasisFunctionsstatic
runFinalJobs()PLMD::Actioninlinevirtual
setAllUniformIntegralsToZero()PLMD::ves::BasisFunctionsinlineprotected
setDescription(const std::string &description_in)PLMD::ves::BasisFunctionsinlineprotected
setInterval(const double, const double)PLMD::ves::BasisFunctionsprotected
setInterval(const std::string &, const std::string &)PLMD::ves::BasisFunctionsprotected
setIntervalBounded()PLMD::ves::BasisFunctionsinlineprotected
setIntervalNonBounded()PLMD::ves::BasisFunctionsinlineprotected
setIntrinsicInterval(const double, const double)PLMD::ves::BasisFunctionsprotected
setIntrinsicInterval(const std::string &, const std::string &)PLMD::ves::BasisFunctionsprotected
setLabel(const unsigned int, const std::string &)PLMD::ves::BasisFunctionsinlineprotected
setLabelPrefix(const std::string &)PLMD::ves::BasisFunctionsinlineprotected
setLabels(const std::vector< std::string > &)PLMD::ves::BasisFunctionsinlineprotected
setNonPeriodic()PLMD::ves::BasisFunctionsinlineprotected
setNumberOfBasisFunctions(const unsigned int)PLMD::ves::BasisFunctionsinlineprotected
setNumericalIntegrationBins(const unsigned int nbins)PLMD::ves::BasisFunctionsinlineprotected
setOption(const std::string &s)PLMD::Actionvirtual
setOrder(const unsigned int norder_in)PLMD::ves::BasisFunctionsinlineprotected
setPeriodic()PLMD::ves::BasisFunctionsinlineprotected
setType(const std::string &type_in)PLMD::ves::BasisFunctionsinlineprotected
setUniformIntegral(const unsigned int, const double)PLMD::ves::BasisFunctionsinlineprotected
setUniformIntegrals(const std::vector< double > &)PLMD::ves::BasisFunctionsinlineprotected
setupBF()PLMD::ves::BasisFunctionsprotected
setupInterval()PLMD::ves::BasisFunctionsprotected
setupLabels()PLMD::ves::BasisFunctionsprotectedvirtual
setupUniformIntegrals()PLMD::ves::BasisFunctionsprotectedvirtual
translateArgument(const double, bool &) constPLMD::ves::BasisFunctionsinline
type_PLMD::ves::BasisFunctionsprivate
uniform_integrals_PLMD::ves::BasisFunctionsprivate
unlockRequests()PLMD::Actioninlinevirtual
update()PLMD::Actioninlinevirtual
vesbias_pntr_PLMD::ves::BasisFunctionsprivate
warning(const std::string &msg)PLMD::Action
writeBasisFunctionsToFile(OFile &, OFile &, const std::string &min_in, const std::string &max_in, unsigned int nbins=1000, const bool ignore_periodicity=false, const std::string &output_fmt="%15.8f", const bool numerical_deriv=false) constPLMD::ves::BasisFunctions
~Action()PLMD::Actionvirtual
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