Action(const ActionOptions &) | PLMD::Action | explicit |
Action(const Action &a)=delete | PLMD::Action | private |
ActionPilot(const ActionOptions &) | PLMD::ActionPilot | explicit |
ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
activate() | PLMD::Action | virtual |
active | PLMD::Action | private |
addCoeffsSet(const std::vector< std::string > &, const std::vector< unsigned int > &) | PLMD::ves::VesBias | protected |
addCoeffsSet(std::vector< Value * > &, std::vector< BasisFunctions * > &) | PLMD::ves::VesBias | protected |
addCoeffsSet(std::unique_ptr< CoeffsVector >) | PLMD::ves::VesBias | protected |
addComponent(const std::string &name) | PLMD::ActionWithValue | |
addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
addDependency(Action *) | PLMD::Action | |
addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
addToSampledAverages(const std::vector< double > &, const unsigned int c_id=0) | PLMD::ves::VesBias | protected |
addValue() | PLMD::ActionWithValue | |
addValueWithDerivatives() | PLMD::ActionWithValue | |
after | PLMD::Action | private |
all_values_inside | PLMD::ves::VesLinearExpansion | private |
apply() override | PLMD::bias::Bias | virtual |
applyBiasCutoff(double &, std::vector< double > &) const | PLMD::ves::VesBias | inline |
applyBiasCutoff(double &, std::vector< double > &, std::vector< double > &) const | PLMD::ves::VesBias | inline |
arguments | PLMD::ActionWithArguments | private |
aver_counters | PLMD::ves::VesBias | private |
basisf_pntrs_ | PLMD::ves::VesLinearExpansion | private |
beforeUpdate() | PLMD::Action | inlinevirtual |
bf_values | PLMD::ves::VesLinearExpansion | private |
bf_values_set | PLMD::ves::VesLinearExpansion | private |
Bias(const ActionOptions &ao) | PLMD::bias::Bias | explicit |
bias_current_max_value | PLMD::ves::VesBias | private |
bias_cutoff_active_ | PLMD::ves::VesBias | private |
bias_cutoff_swfunc_pntr_ | PLMD::ves::VesBias | private |
bias_cutoff_value_ | PLMD::ves::VesBias | private |
bias_expansion_pntr_ | PLMD::ves::VesLinearExpansion | private |
bias_file_fmt_ | PLMD::ves::VesBias | private |
bias_filename_ | PLMD::ves::VesBias | private |
bias_fileoutput_active_ | PLMD::ves::VesBias | private |
biasCutoffActive() const | PLMD::ves::VesBias | inline |
bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
calc_reweightfactor_ | PLMD::ves::VesBias | private |
calculate() override | PLMD::ves::VesLinearExpansion | virtual |
calculateFromPDB(const PDB &) | PLMD::Action | |
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::Action | virtual |
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) override | PLMD::ActionWithArguments | virtual |
calculateReweightFactor() const override | PLMD::ves::VesLinearExpansion | virtual |
checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
checkNeedsGradients() const | PLMD::Action | inlinevirtual |
PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
PLMD::ActionWithValue::checkNumericalDerivatives() const override | PLMD::ActionWithValue | inlinevirtual |
checkRead() | PLMD::Action | |
checkThatTemperatureIsGiven() | PLMD::ves::VesBias | protected |
checkUpdate() const | PLMD::Action | |
cite(const std::string &s) | PLMD::Action | |
clearCoeffsPntrsVector() | PLMD::ves::VesBias | inlineprotected |
clearDependencies() | PLMD::Action | |
clearDerivatives() | PLMD::ActionWithValue | virtual |
clearGradientAndHessian() | PLMD::ves::VesBias | inline |
clearInputForces() | PLMD::ActionWithValue | |
clearOptions() | PLMD::Action | virtual |
Coeffs(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
coeffs_fnames | PLMD::ves::VesBias | private |
coeffs_id_prefix_ | PLMD::ves::VesBias | private |
coeffs_pntrs_ | PLMD::ves::VesBias | private |
comm | PLMD::Action | |
componentIsNotPeriodic(const std::string &name) | PLMD::ActionWithValue | |
componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
componentsAreNotOptional(Keywords &keys) | PLMD::ActionWithValue | static |
compute_hessian_ | PLMD::ves::VesBias | private |
computeCovarianceFromAverages(const unsigned int) const | PLMD::ves::VesBias | inlineprivate |
computeHessian() const | PLMD::ves::VesBias | inline |
copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
deactivate() | PLMD::Action | inlinevirtual |
Dependencies typedef | PLMD::Action | |
diagonal_hessian_ | PLMD::ves::VesBias | private |
diagonalHessian() const | PLMD::ves::VesBias | inline |
difference(int, double, double) const | PLMD::ActionWithArguments | inline |
disableBiasFileOutput() | PLMD::ves::VesBias | inline |
disableDynamicTargetDistFileOutput() | PLMD::ves::VesBias | inline |
disableDynamicTargetDistribution() | PLMD::ves::VesBias | inline |
disableFesFileOutput() | PLMD::ves::VesBias | inline |
disableFesFileProjOutput() | PLMD::ves::VesBias | inline |
disableHessian() | PLMD::ves::VesBias | |
disableStaticTargetDistFileOutput() | PLMD::ves::VesBias | inline |
doCheckPoint | PLMD::Action | private |
doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
dynamic_targetdist_ | PLMD::ves::VesBias | private |
dynamic_targetdist_fileoutput_active_ | PLMD::ves::VesBias | private |
dynamicTargetDistribution() const | PLMD::ves::VesBias | inline |
enableBiasFileOutput() | PLMD::ves::VesBias | inline |
enableDynamicTargetDistFileOutput() | PLMD::ves::VesBias | inline |
enableDynamicTargetDistribution() | PLMD::ves::VesBias | inline |
enableFesFileOutput() | PLMD::ves::VesBias | inline |
enableFesProjFileOutput() | PLMD::ves::VesBias | inline |
enableHessian(const bool diagonal_hessian=true) | PLMD::ves::VesBias | |
enableIterationNumberInFilenames() | PLMD::ves::VesBias | inline |
enableMultipleCoeffsSets() | PLMD::ves::VesBias | inline |
enableStaticTargetDistFileOutput() | PLMD::ves::VesBias | inline |
error(const std::string &msg) const | PLMD::Action | |
exists(const std::string &name) const | PLMD::ActionWithValue | |
exit(int c=0) | PLMD::Action | |
expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
fclose(FILE *fp) | PLMD::Action | |
fes_file_fmt_ | PLMD::ves::VesBias | private |
fes_filename_ | PLMD::ves::VesBias | private |
fes_fileoutput_active_ | PLMD::ves::VesBias | private |
fesproj_fileoutput_active_ | PLMD::ves::VesBias | private |
fflush() | PLMD::Action | |
filenames_have_iteration_number_ | PLMD::ves::VesBias | private |
filenamesIncludeIterationNumber() const | PLMD::ves::VesBias | inline |
files | PLMD::Action | |
fopen(const char *path, const char *mode) | PLMD::Action | |
getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
getArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getBeta() const | PLMD::ves::VesBias | inline |
getBiasCutoffSwitchingFunction(const double, double &) const | PLMD::ves::VesBias | |
getBiasCutoffSwitchingFunction(const double) const | PLMD::ves::VesBias | inline |
getBiasCutoffValue() const | PLMD::ves::VesBias | inline |
getBiasFileFmt() const | PLMD::ves::VesBias | inline |
getBiasOutputFilename() const | PLMD::ves::VesBias | inline |
getCoeffsIndex(const std::vector< unsigned int > &indices, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getCoeffsIndices(const size_t index, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getCoeffsPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getCoeffsPntrs() const | PLMD::ves::VesBias | inline |
getCoeffsSetFilenameSuffix(const unsigned int coeffs_id) const | PLMD::ves::VesBias | |
getCoeffsSetLabelString(const std::string &, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | protected |
getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
getComponentsList() const | PLMD::ActionWithValue | |
getComponentsVector() const | PLMD::ActionWithValue | |
getCPT() const | PLMD::Action | |
getCurrentBiasMaxValue() const | PLMD::ves::VesBias | inline |
getCurrentBiasOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | inline |
getCurrentFesOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | inline |
getCurrentOutputFilename(const std::string &, const std::string &suffix="") const | PLMD::ves::VesBias | |
getCurrentTargetDistOutputFilename(const std::string &suffix="") const | PLMD::ves::VesBias | |
getDependencies() const | PLMD::Action | inline |
getDocumentation() const | PLMD::Action | virtual |
getExchangeStep() const | PLMD::Action | |
getFesFileFmt() const | PLMD::ves::VesBias | inline |
getFesOutputFilename() const | PLMD::ves::VesBias | inline |
getGradientPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getGradientPntrs() const | PLMD::ves::VesBias | inline |
getGridBins() const | PLMD::ves::VesBias | inline |
getGridMax() const | PLMD::ves::VesBias | inline |
getGridMin() const | PLMD::ves::VesBias | inline |
getHessianIndex(const size_t index1, const size_t index2, const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getHessianPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getHessianPntrs() const | PLMD::ves::VesBias | inline |
getIterationCounter() const | PLMD::ves::VesBias | |
getIterationFilenameSuffix() const | PLMD::ves::VesBias | |
getKbT() const | PLMD::ves::VesBias | inline |
getKeyword(const std::string &key) | PLMD::Action | |
getLabel() const | PLMD::Action | inline |
getName() const | PLMD::Action | inline |
getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
getNumberOfComponents() const | PLMD::ActionWithValue | inline |
getNumberOfDerivatives() override | PLMD::bias::Bias | inlinevirtual |
getNumberOfProjectionArguments() const | PLMD::ves::VesBias | inline |
getNumberOfTargetDistributionPntrs() const | PLMD::ves::VesBias | inline |
getOFile(const std::string &filename, const bool multi_sim_single_file=false, const bool enforce_backup=true) | PLMD::ves::VesBias | |
getOptimizerPntr() const | PLMD::ves::VesBias | inline |
getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | inline |
getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
getPntrToValue() | PLMD::ActionWithValue | protected |
getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
getProjectionArgument(unsigned int i) const | PLMD::ves::VesBias | inline |
getProjectionArguments() const | PLMD::ves::VesBias | inline |
getRestart() const | PLMD::Action | inline |
getStep() const | PLMD::Action | |
getStride() const | PLMD::ActionPilot | |
getTargetDistAveragesPntr(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
getTargetDistAveragesPntrs() const | PLMD::ves::VesBias | inline |
getTargetDistFileFmt() const | PLMD::ves::VesBias | inline |
getTargetDistOutputFilename() const | PLMD::ves::VesBias | inline |
getTargetDistRestartFileFmt() const | PLMD::ves::VesBias | inline |
getTargetDistributionPntrs() const | PLMD::ves::VesBias | inline |
getTime() const | PLMD::Action | |
getTimeStep() const | PLMD::Action | |
Gradient(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
gradient_pntrs_ | PLMD::ves::VesBias | private |
grid_bins_ | PLMD::ves::VesBias | private |
grid_max_ | PLMD::ves::VesBias | private |
grid_min_ | PLMD::ves::VesBias | private |
Hessian(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
hessian_pntrs_ | PLMD::ves::VesBias | private |
initializeCoeffs(std::unique_ptr< CoeffsVector >) | PLMD::ves::VesBias | private |
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
isActive() const | PLMD::Action | inline |
isBiasFileOutputActive() const | PLMD::ves::VesBias | inline |
isDynamicTargetDistFileOutputActive() const | PLMD::ves::VesBias | inline |
isFesFileOutputActive() const | PLMD::ves::VesBias | inline |
isFesProjFileOutputActive() const | PLMD::ves::VesBias | inline |
isOptionOn(const std::string &s) const | PLMD::Action | inline |
isReweightFactorCalculated() const | PLMD::ves::VesBias | inline |
isStaticTargetDistFileOutputActive() const | PLMD::ves::VesBias | inline |
kbt_ | PLMD::ves::VesBias | private |
keywords | PLMD::Action | |
label | PLMD::Action | private |
line | PLMD::Action | private |
linkOptimizer(Optimizer *) | PLMD::ves::VesBias | |
lockRequestArguments | PLMD::ActionWithArguments | private |
PLMD::lockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::lockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
log | PLMD::Action | |
multi_sim_comm | PLMD::Action | |
multiSimSumAverages(const unsigned int, const double walker_weight=1.0) | PLMD::ves::VesBias | private |
name | PLMD::Action | private |
nargs_ | PLMD::ves::VesLinearExpansion | private |
ncoeffs_ | PLMD::ves::VesLinearExpansion | private |
ncoeffs_total_ | PLMD::ves::VesBias | private |
ncoeffssets_ | PLMD::ves::VesBias | private |
noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
noderiv | PLMD::ActionWithValue | private |
numberOfCoeffs(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
numberOfCoeffsSets() const | PLMD::ves::VesBias | inline |
numericalDerivatives | PLMD::ActionWithValue | private |
onStep() const | PLMD::ActionPilot | virtual |
operator=(const Action &a)=delete | PLMD::Action | private |
optimization_threshold_ | PLMD::ves::VesBias | private |
optimize_coeffs_ | PLMD::ves::VesBias | private |
optimizeCoeffs() const | PLMD::ves::VesBias | inline |
optimizer_pntr_ | PLMD::ves::VesBias | private |
options | PLMD::Action | private |
outputForces | PLMD::bias::Bias | private |
parse(const std::string &key, T &t) | PLMD::Action | |
parseArgumentList(const std::string &key, std::vector< Value * > &args) | PLMD::ActionWithArguments | |
parseArgumentList(const std::string &key, int i, std::vector< Value * > &args) | PLMD::ActionWithArguments | |
parseFlag(const std::string &key, bool &t) | PLMD::Action | |
parseMultipleValues(const std::string &, std::vector< T > &, unsigned int) | PLMD::ves::VesBias | protected |
parseMultipleValues(const std::string &, std::vector< T > &, unsigned int, const T &) | PLMD::ves::VesBias | protected |
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 | |
plumed | PLMD::Action | |
prepare() | PLMD::Action | virtual |
projection_args_ | PLMD::ves::VesBias | private |
readAtomsFromPDB(const PDB &) | PLMD::Action | inlinevirtual |
readCoeffsFromFiles() | PLMD::ves::VesBias | protected |
registerKeywords(Keywords &keys) | PLMD::ves::VesLinearExpansion | static |
replica_index | PLMD::Action | private |
requestArguments(const std::vector< Value * > &arg) | PLMD::ActionWithArguments | |
requestExtraDependencies(const std::vector< Value * > &extra) | PLMD::ActionWithArguments | |
resetBiasFileOutput() override | PLMD::ves::VesLinearExpansion | virtual |
resetFesFileOutput() override | PLMD::ves::VesLinearExpansion | virtual |
resetFesProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
resetTargetDistFileOutput() | PLMD::ves::VesBias | inlinevirtual |
resetTargetDistProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
restart | PLMD::Action | private |
restartTargetDistributions() override | PLMD::ves::VesLinearExpansion | virtual |
runFinalJobs() | PLMD::Action | inlinevirtual |
sampled_averages | PLMD::ves::VesBias | private |
sampled_cross_averages | PLMD::ves::VesBias | private |
setBias(double bias) | PLMD::bias::Bias | inlineprotected |
setCurrentBiasMaxValue(const double max_value) | PLMD::ves::VesBias | inline |
setGradientsIfNeeded() | PLMD::ActionWithValue | |
setGridBins(const std::vector< unsigned int > &) | PLMD::ves::VesBias | |
setGridBins(const unsigned int) | PLMD::ves::VesBias | |
setGridMax(const std::vector< double > &) | PLMD::ves::VesBias | |
setGridMin(const std::vector< double > &) | PLMD::ves::VesBias | |
setNotPeriodic() | PLMD::ActionWithValue | |
setOption(const std::string &s) | PLMD::Action | virtual |
setOutputForce(int i, double f) | PLMD::bias::Bias | inlineprotected |
setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
setStride(const int &n) | PLMD::ActionPilot | |
setTargetDistAverages(const std::vector< double > &, const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
setTargetDistAverages(const CoeffsVector &, const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
setTargetDistAveragesToZero(const unsigned int coeffs_id=0) | PLMD::ves::VesBias | protected |
setupBiasCutoff(const double, const double) | PLMD::ves::VesBias | |
setupBiasFileOutput() override | PLMD::ves::VesLinearExpansion | virtual |
setupFesFileOutput() override | PLMD::ves::VesLinearExpansion | virtual |
setupFesProjFileOutput() override | PLMD::ves::VesLinearExpansion | virtual |
setupTargetDistFileOutput() | PLMD::ves::VesBias | inlinevirtual |
setupTargetDistProjFileOutput() | PLMD::ves::VesBias | inlinevirtual |
setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
setValue(Value *, double) | PLMD::ActionWithValue | |
static_targetdist_fileoutput_active_ | PLMD::ves::VesBias | private |
stride | PLMD::ActionPilot | private |
targetdist_averages_filename_ | PLMD::ves::VesBias | private |
targetdist_averages_pntrs_ | PLMD::ves::VesBias | private |
targetdist_file_fmt_ | PLMD::ves::VesBias | private |
targetdist_filename_ | PLMD::ves::VesBias | private |
targetdist_pntrs_ | PLMD::ves::VesBias | private |
targetdist_restart_file_fmt_ | PLMD::ves::VesBias | private |
TargetDistAverages(const unsigned int coeffs_id=0) const | PLMD::ves::VesBias | inline |
totalNumberOfCoeffs() const | PLMD::ves::VesBias | inline |
turnOnDerivatives() | PLMD::ActionWithValue | virtual |
PLMD::unlockRequests() | PLMD::Action | inlinevirtual |
PLMD::ActionWithArguments::unlockRequests() override | PLMD::ActionWithArguments | inlinevirtual |
update() override | PLMD::ves::VesLinearExpansion | virtual |
update_from | PLMD::Action | private |
update_until | PLMD::Action | private |
updateGradientAndHessian(const bool) | PLMD::ves::VesBias | |
updateReweightFactor() | PLMD::ves::VesBias | |
updateTargetDistributions() override | PLMD::ves::VesLinearExpansion | virtual |
use_multiple_coeffssets_ | PLMD::ves::VesBias | private |
useBiasCutoffKeywords(Keywords &) | PLMD::ves::VesBias | static |
useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
useGridBinKeywords(Keywords &) | PLMD::ves::VesBias | static |
useGridLimitsKeywords(Keywords &) | PLMD::ves::VesBias | static |
useInitialCoeffsKeywords(Keywords &) | PLMD::ves::VesBias | static |
useMultipleTargetDistributionKeywords(Keywords &) | PLMD::ves::VesBias | static |
useMultipleWalkers() const | PLMD::ves::VesBias | |
useNumericalDerivatives() | PLMD::ActionWithValue | inline |
useProjectionArgKeywords(Keywords &) | PLMD::ves::VesBias | static |
useReweightFactorKeywords(Keywords &) | PLMD::ves::VesBias | static |
useTargetDistributionKeywords(Keywords &) | PLMD::ves::VesBias | static |
valueBias | PLMD::bias::Bias | private |
valueForce2_ | PLMD::ves::VesLinearExpansion | private |
values | PLMD::ActionWithValue | private |
VesBias(const ActionOptions &ao) | PLMD::ves::VesBias | explicit |
VesLinearExpansion(const ActionOptions &) | PLMD::ves::VesLinearExpansion | explicit |
warning(const std::string &msg) | PLMD::Action | |
writeBiasToFile() override | PLMD::ves::VesLinearExpansion | virtual |
writeFesProjToFile() override | PLMD::ves::VesLinearExpansion | virtual |
writeFesToFile() override | PLMD::ves::VesLinearExpansion | virtual |
writeTargetDistProjToFile() override | PLMD::ves::VesLinearExpansion | virtual |
writeTargetDistToFile() override | PLMD::ves::VesLinearExpansion | virtual |
~Action() | PLMD::Action | virtual |
~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
~ActionWithValue() | PLMD::ActionWithValue | |
~VesBias() | PLMD::ves::VesBias | |
~VesLinearExpansion() | PLMD::ves::VesLinearExpansion | |