Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
action_pntr_ | PLMD::ves::BasisFunctions | private |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addDependency(Action *) | PLMD::Action | |
addKeywordToList(const std::string &, const T) | PLMD::ves::BasisFunctions | protected |
addKeywordToList(const std::string &, const std::vector< T > &) | PLMD::ves::BasisFunctions | protected |
addKeywordToList(const std::string &, const bool) | PLMD::ves::BasisFunctions | inlineprotected |
after | PLMD::Action | private |
apply() override | PLMD::ves::BasisFunctions | inlinevirtual |
arePeriodic() const | PLMD::ves::BasisFunctions | inline |
argT_derivf_ | PLMD::ves::BasisFunctions | private |
BasisFunctions(const ActionOptions &ao) | PLMD::ves::BasisFunctions | explicit |
beforeUpdate() | PLMD::Action | inlinevirtual |
bf_keywords_ | PLMD::ves::BasisFunctions | private |
bf_label_prefix_ | PLMD::ves::BasisFunctions | private |
bf_labels_ | PLMD::ves::BasisFunctions | private |
calculate() override | PLMD::ves::BasisFunctions | inlinevirtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
castToActionAtomistic() noexcept | PLMD::Action | inlinevirtual |
castToActionForInterface() noexcept | PLMD::Action | inlinevirtual |
castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
castToActionWithValue() noexcept | PLMD::Action | inlinevirtual |
castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
checkForDependency(Action *) | PLMD::Action | |
checkIfArgumentInsideInterval(const double, bool &) const | PLMD::ves::BasisFunctions | inline |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
checkRead() | PLMD::Action | |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearDependencies() | PLMD::Action | |
clearOptions() | PLMD::Action | virtual |
comm | PLMD::Action | |
deactivate() | PLMD::Action | inlinevirtual |
defaults | PLMD::Action | private |
Dependencies typedef | PLMD::Action | |
description_ | PLMD::ves::BasisFunctions | private |
doCheckPoint | PLMD::Action | private |
error(const std::string &msg) const | PLMD::Action | |
exit(int c=0) | PLMD::Action | |
fclose(FILE *fp) | PLMD::Action | |
fflush() | PLMD::Action | |
files | PLMD::Action | |
fopen(const char *path, const char *mode) | PLMD::Action | |
getAllValues(const double, double &, bool &, std::vector< double > &, std::vector< double > &) const =0 | PLMD::ves::BasisFunctions | pure virtual |
getAllValuesNumericalDerivs(const double, double &, bool &, std::vector< double > &, std::vector< double > &) const | PLMD::ves::BasisFunctions | private |
getBasisFunctionLabel(const unsigned int index) const | PLMD::ves::BasisFunctions | inline |
getBasisFunctionLabels() const | PLMD::ves::BasisFunctions | inline |
getCPT() const | PLMD::Action | |
getDefaultString() const | PLMD::Action | inline |
getDependencies() const | PLMD::Action | inline |
getDescription() const | PLMD::ves::BasisFunctions | inline |
getExchangeStep() const | PLMD::Action | |
getKBoltzmann() const | PLMD::Action | protected |
getkBT() | PLMD::Action | |
getKeyword(const std::string &key) | PLMD::Action | |
getKeywordList() const | PLMD::ves::BasisFunctions | inline |
getKeywordString() const | PLMD::ves::BasisFunctions | |
getLabel() const | PLMD::Action | inline |
getMultipleValue(const std::vector< double > &, std::vector< double > &, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &, const bool numerical_deriv=false) const | PLMD::ves::BasisFunctions | |
getName() const | PLMD::Action | inline |
getNumberOfBasisFunctions() const | PLMD::ves::BasisFunctions | inline |
getOrder() const | PLMD::ves::BasisFunctions | inline |
getPntrToAction() const | PLMD::ves::BasisFunctions | inline |
getPntrToVesBias() const | PLMD::ves::BasisFunctions | inline |
getRestart() const | PLMD::Action | inline |
getSize() const | PLMD::ves::BasisFunctions | inline |
getStep() const | PLMD::Action | |
getTargetDistributionIntegrals(const TargetDistribution *) const | PLMD::ves::BasisFunctions | |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
getType() const | PLMD::ves::BasisFunctions | inline |
getUniformIntegrals() const | PLMD::ves::BasisFunctions | inline |
getUnits() const | PLMD::Action | protected |
getValue(const double, const unsigned int, double &, bool &) const | PLMD::ves::BasisFunctions | |
has_been_set | PLMD::ves::BasisFunctions | private |
hasBeenSet() const | PLMD::ves::BasisFunctions | inline |
interval_bounded_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_max_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_max_str_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_mean_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_min_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_min_str_ | PLMD::ves::BasisFunctions | private |
interval_intrinsic_range_ | PLMD::ves::BasisFunctions | private |
interval_max_ | PLMD::ves::BasisFunctions | private |
interval_max_str_ | PLMD::ves::BasisFunctions | private |
interval_mean_ | PLMD::ves::BasisFunctions | private |
interval_min_ | PLMD::ves::BasisFunctions | private |
interval_min_str_ | PLMD::ves::BasisFunctions | private |
interval_range_ | PLMD::ves::BasisFunctions | private |
intervalBounded() const | PLMD::ves::BasisFunctions | inline |
intervalDerivf() const | PLMD::ves::BasisFunctions | inline |
intervalMax() const | PLMD::ves::BasisFunctions | inline |
intervalMaxStr() const | PLMD::ves::BasisFunctions | inline |
intervalMean() const | PLMD::ves::BasisFunctions | inline |
intervalMin() const | PLMD::ves::BasisFunctions | inline |
intervalMinStr() const | PLMD::ves::BasisFunctions | inline |
intervalRange() const | PLMD::ves::BasisFunctions | inline |
intrinsicIntervalMax() const | PLMD::ves::BasisFunctions | inlineprotected |
intrinsicIntervalMaxStr() const | PLMD::ves::BasisFunctions | inlineprotected |
intrinsicIntervalMin() const | PLMD::ves::BasisFunctions | inlineprotected |
intrinsicIntervalMinStr() const | PLMD::ves::BasisFunctions | inlineprotected |
isActive() const | PLMD::Action | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
linkAction(Action *) | PLMD::ves::BasisFunctions | |
linkVesBias(VesBias *) | PLMD::ves::BasisFunctions | |
lockRequests() | PLMD::Action | inlinevirtual |
log | PLMD::Action | |
multi_sim_comm | PLMD::Action | |
name | PLMD::Action | private |
nbasis_ | PLMD::ves::BasisFunctions | private |
nbins_ | PLMD::ves::BasisFunctions | private |
never_activate | PLMD::Action | private |
norder_ | PLMD::ves::BasisFunctions | private |
numberOfBasisFunctions() const | PLMD::ves::BasisFunctions | inline |
numerical_uniform_integrals_ | PLMD::ves::BasisFunctions | private |
numericalTargetDistributionIntegralsFromGrid(const Grid *) const | PLMD::ves::BasisFunctions | protected |
numericalUniformIntegrals() | PLMD::ves::BasisFunctions | protected |
operator=(const Action &a)=delete | PLMD::Action | private |
options | PLMD::Action | private |
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::BasisFunctions | private |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
print_debug_info_ | PLMD::ves::BasisFunctions | private |
printInfo() const | PLMD::ves::BasisFunctions | |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
registerKeywords(Keywords &) | PLMD::ves::BasisFunctions | static |
replica_index | PLMD::Action | private |
resetStoredTimestep() | PLMD::Action | |
restart | PLMD::Action | private |
runFinalJobs() | PLMD::Action | inlinevirtual |
setAllUniformIntegralsToZero() | PLMD::ves::BasisFunctions | inlineprotected |
setDescription(const std::string &description_in) | PLMD::ves::BasisFunctions | inlineprotected |
setInterval(const double, const double) | PLMD::ves::BasisFunctions | protected |
setInterval(const std::string &, const std::string &) | PLMD::ves::BasisFunctions | protected |
setIntervalBounded() | PLMD::ves::BasisFunctions | inlineprotected |
setIntervalNonBounded() | PLMD::ves::BasisFunctions | inlineprotected |
setIntrinsicInterval(const double, const double) | PLMD::ves::BasisFunctions | protected |
setIntrinsicInterval(const std::string &, const std::string &) | PLMD::ves::BasisFunctions | protected |
setLabel(const unsigned int, const std::string &) | PLMD::ves::BasisFunctions | inlineprotected |
setLabelPrefix(const std::string &) | PLMD::ves::BasisFunctions | inlineprotected |
setLabels(const std::vector< std::string > &) | PLMD::ves::BasisFunctions | inlineprotected |
setNonPeriodic() | PLMD::ves::BasisFunctions | inlineprotected |
setNumberOfBasisFunctions(const unsigned int) | PLMD::ves::BasisFunctions | inlineprotected |
setNumericalIntegrationBins(const unsigned int nbins) | PLMD::ves::BasisFunctions | inlineprotected |
setOption(const std::string &s) | PLMD::Action | virtual |
setOrder(const unsigned int norder_in) | PLMD::ves::BasisFunctions | inlineprotected |
setPeriodic() | PLMD::ves::BasisFunctions | inlineprotected |
setType(const std::string &type_in) | PLMD::ves::BasisFunctions | inlineprotected |
setUniformIntegral(const unsigned int, const double) | PLMD::ves::BasisFunctions | inlineprotected |
setUniformIntegrals(const std::vector< double > &) | PLMD::ves::BasisFunctions | inlineprotected |
setupBF() | PLMD::ves::BasisFunctions | protected |
setupConstantValues(const bool &have_atoms) | PLMD::Action | |
setupInterval() | PLMD::ves::BasisFunctions | protected |
setupLabels() | PLMD::ves::BasisFunctions | protectedvirtual |
setupUniformIntegrals() | PLMD::ves::BasisFunctions | protectedvirtual |
timestep | PLMD::Action | private |
translateArgument(const double, bool &) const | PLMD::ves::BasisFunctions | inline |
type_ | PLMD::ves::BasisFunctions | private |
uniform_integrals_ | PLMD::ves::BasisFunctions | private |
unlockRequests() | PLMD::Action | inlinevirtual |
update() | PLMD::Action | inlinevirtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
usingNaturalUnits() const | PLMD::Action | protected |
vesbias_pntr_ | PLMD::ves::BasisFunctions | private |
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_values="%15.8f", const std::string &output_fmt_derivs="%15.8f", const bool numerical_deriv=false) const | PLMD::ves::BasisFunctions | |
writeInGraph() const | PLMD::Action | virtual |
~Action() | PLMD::Action | virtual |