PLMD::ves::Optimizer Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
addCoeffsSetIDsToFilenames(std::vector< std::string > &, std::string &)PLMD::ves::Optimizerprotected
addComponent(const std::string &name)PLMD::ActionWithValue
addComponentWithDerivatives(const std::string &name)PLMD::ActionWithValue
addDependency(Action *)PLMD::Action
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
apply()PLMD::ves::Optimizerinlinevirtual
aux_coeffs_pntrs_PLMD::ves::Optimizerprivate
AuxCoeffs(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
aver_gradient_pntrs_PLMD::ves::Optimizerprivate
beforeUpdate()PLMD::Actioninlinevirtual
bias_output_active_PLMD::ves::Optimizerprivate
bias_output_stride_PLMD::ves::Optimizerprivate
bias_pntrs_PLMD::ves::Optimizerprivate
calculate()PLMD::ves::Optimizerinlinevirtual
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() constPLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
Coeffs(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
coeffs_mask_pntrs_PLMD::ves::Optimizerprivate
coeffs_output_fmt_PLMD::ves::Optimizerprivate
coeffs_pntrs_PLMD::ves::Optimizerprivate
coeffs_wstride_PLMD::ves::Optimizerprivate
CoeffsMask(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
coeffsOFiles_PLMD::ves::Optimizerprivate
coeffssetid_prefix_PLMD::ves::Optimizerprivate
coeffsUpdate(const unsigned int coeffs_id=0)=0PLMD::ves::Optimizerprotectedpure virtual
commPLMD::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::ActionWithValuestatic
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
current_stepsizesPLMD::ves::Optimizerprivate
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
description_PLMD::ves::Optimizerprivate
diagonal_hessian_PLMD::ves::Optimizerprivate
diagonalHessian() constPLMD::ves::Optimizerinline
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
dynamic_targetdists_PLMD::ves::Optimizerprivate
dynamicStepSize() constPLMD::ves::Optimizerinline
enableHessian(VesBias *, const bool diagonal_hessian=false)PLMD::ves::Optimizerprotected
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
fclose(FILE *fp)PLMD::Action
fes_output_active_PLMD::ves::Optimizerprivate
fes_output_stride_PLMD::ves::Optimizerprivate
fesproj_output_active_PLMD::ves::Optimizerprivate
fesproj_output_stride_PLMD::ves::Optimizerprivate
fflush()PLMD::Action
filesPLMD::Action
fixed_stepsize_PLMD::ves::Optimizerprivate
fixedStepSize() constPLMD::ves::Optimizerinline
fopen(const char *path, const char *mode)PLMD::Action
getAuxCoeffsPntrs() constPLMD::ves::Optimizerinline
getBiasOutputStride() constPLMD::ves::Optimizerinline
getBiasPntrs() constPLMD::ves::Optimizerinline
getCoeffsMaskPntrs() constPLMD::ves::Optimizerinline
getCoeffsPntrs() constPLMD::ves::Optimizerinline
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getCurrentStepSize(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinline
getCurrentStepSizes() constPLMD::ves::Optimizerinline
getDependencies() constPLMD::Actioninline
getDescription() constPLMD::ves::Optimizerinline
getDocumentation() constPLMD::Actionvirtual
getExchangeStep() constPLMD::Action
getFesOutputStride() constPLMD::ves::Optimizerinline
getFesProjOutputStride() constPLMD::ves::Optimizerinline
getGradientPntrs() constPLMD::ves::Optimizerinline
getHessianPntrs() constPLMD::ves::Optimizerinline
getIterationCounter() constPLMD::ves::Optimizerinline
getIterationCounterDbl() constPLMD::ves::Optimizerinline
getIterationCounterStr(const int offset=0) constPLMD::ves::Optimizer
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getName() constPLMD::Actioninline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::ves::Optimizerinlinevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStepSize(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinline
getStepSizes() constPLMD::ves::Optimizerinline
getStride() constPLMD::ActionPilot
getTargetDistAveragesPntrs() constPLMD::ves::Optimizerinline
getTargetDistOutputStride() constPLMD::ves::Optimizerinline
getTargetDistProjOutputStride() constPLMD::ves::Optimizerinline
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getType() constPLMD::ves::Optimizerinline
Gradient(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
gradient_output_fmt_PLMD::ves::Optimizerprivate
gradient_pntrs_PLMD::ves::Optimizerprivate
gradient_wstride_PLMD::ves::Optimizerprivate
gradientOFiles_PLMD::ves::Optimizerprivate
Hessian(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
hessian_covariance_from_averages_PLMD::ves::Optimizerprivate
hessian_output_fmt_PLMD::ves::Optimizerprivate
hessian_pntrs_PLMD::ves::Optimizerprivate
hessian_wstride_PLMD::ves::Optimizerprivate
hessianOFiles_PLMD::ves::Optimizerprivate
identical_coeffs_shape_PLMD::ves::Optimizerprivate
increaseIterationCounter()PLMD::ves::Optimizerinline
isActive() constPLMD::Actioninline
isBiasOutputActive() constPLMD::ves::Optimizerinline
isFesOutputActive() constPLMD::ves::Optimizerinline
isFesProjOutputActive() constPLMD::ves::Optimizerinline
isFirstStepPLMD::ves::Optimizerprivate
isOptionOn(const std::string &s) constPLMD::Actioninline
isTargetDistOutputActive() constPLMD::ves::Optimizerinline
isTargetDistProjOutputActive() constPLMD::ves::Optimizerinline
iter_counterPLMD::ves::Optimizerprivate
keywordsPLMD::Action
lockRequests()PLMD::Actioninlinevirtual
logPLMD::Action
monitor_instantaneous_gradient_PLMD::ves::Optimizerprivate
multi_sim_commPLMD::Action
mwalkers_mpi_single_files_PLMD::ves::Optimizerprivate
nbiases_PLMD::ves::Optimizerprivate
ncoeffssets_PLMD::ves::Optimizerprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
numberOfBiases() constPLMD::ves::Optimizerinline
numberOfCoeffsSets() constPLMD::ves::Optimizerinline
onStep() constPLMD::ActionPilotvirtual
Optimizer(const ActionOptions &ao)PLMD::ves::Optimizerexplicit
parse(const std::string &key, T &t)PLMD::Action
parseFilenames(const std::string &, std::vector< std::string > &, const std::string &)PLMD::ves::Optimizerinlineprotected
parseFilenames(const std::string &, std::vector< std::string > &)PLMD::ves::Optimizerinlineprotected
parseFlag(const std::string &key, bool &t)PLMD::Action
parseMultipleValues(const std::string &, std::vector< T > &)PLMD::ves::Optimizerprotected
parseMultipleValues(const std::string &, std::vector< T > &, const T &)PLMD::ves::Optimizerprotected
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
plumedPLMD::Action
prepare()PLMD::Actionvirtual
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
readCoeffsFromFiles(const std::vector< std::string > &, const bool)PLMD::ves::Optimizerprivate
registerKeywords(Keywords &)PLMD::ves::Optimizerstatic
runFinalJobs()PLMD::Actioninlinevirtual
setAllCoeffsSetIterationCounters()PLMD::ves::Optimizerprivate
setBiasOutputStride(unsigned int stride)PLMD::ves::Optimizerinline
setCurrentStepSize(const double, const unsigned int i=0)PLMD::ves::Optimizerinlineprotected
setCurrentStepSizes(const std::vector< double > &)PLMD::ves::Optimizerinlineprotected
setFesOutputStride(unsigned int stride)PLMD::ves::Optimizerinline
setFesProjOutputStride(unsigned int stride)PLMD::ves::Optimizerinline
setGradientsIfNeeded()PLMD::ActionWithValue
setIterationCounter(const unsigned int)PLMD::ves::Optimizerinline
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setStepSize(const double, const unsigned int coeffs_id=0)PLMD::ves::Optimizerinline
setStepSizes(const std::vector< double > &)PLMD::ves::Optimizerinline
setStride(const int &n)PLMD::ActionPilot
setTargetDistOutputStride(unsigned int stride)PLMD::ves::Optimizerinline
setTargetDistProjOutputStride(unsigned int stride)PLMD::ves::Optimizerinline
setupOFiles(std::vector< std::string > &, std::vector< OFile *> &, const bool multi_sim_single_files=false)PLMD::ves::Optimizerprotected
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
StepSize(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerinlineprotected
stepsizes_PLMD::ves::Optimizerprivate
targetdist_averages_output_fmt_PLMD::ves::Optimizerprivate
targetdist_averages_pntrs_PLMD::ves::Optimizerprivate
targetdist_averages_wstride_PLMD::ves::Optimizerprivate
targetdist_averagesOFiles_PLMD::ves::Optimizerprivate
targetdist_output_active_PLMD::ves::Optimizerprivate
targetdist_output_stride_PLMD::ves::Optimizerprivate
targetdist_proj_output_active_PLMD::ves::Optimizerprivate
targetdist_proj_output_stride_PLMD::ves::Optimizerprivate
TargetDistAverages(const unsigned int coeffs_id=0) constPLMD::ves::Optimizerprotected
turnOffCoeffsOutputFiles()PLMD::ves::Optimizerprotected
turnOffHessian()PLMD::ves::Optimizerprotected
turnOnDerivatives()PLMD::ActionWithValuevirtual
turnOnHessian()PLMD::ves::Optimizerprotected
type_PLMD::ves::Optimizerprivate
unlockRequests()PLMD::Actioninlinevirtual
update()PLMD::ves::Optimizervirtual
updateOutputComponents()PLMD::ves::Optimizerprivate
use_hessian_PLMD::ves::Optimizerprivate
use_mwalkers_mpi_PLMD::ves::Optimizerprivate
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useDynamicStepSizeKeywords(Keywords &)PLMD::ves::Optimizerstatic
useDynamicTargetDistributionKeywords(Keywords &)PLMD::ves::Optimizerstatic
useFixedStepSizeKeywords(Keywords &)PLMD::ves::Optimizerstatic
useHessian() constPLMD::ves::Optimizerinline
useHessianKeywords(Keywords &)PLMD::ves::Optimizerstatic
useMaskKeywords(Keywords &)PLMD::ves::Optimizerstatic
useMonitorAverageGradientKeywords(Keywords &)PLMD::ves::Optimizerstatic
useMultipleWalkers() constPLMD::ves::Optimizerinline
useMultipleWalkersKeywords(Keywords &)PLMD::ves::Optimizerstatic
useNumericalDerivatives()PLMD::ActionWithValueinline
useRestartKeywords(Keywords &)PLMD::ves::Optimizerstatic
useReweightFactorKeywords(Keywords &)PLMD::ves::Optimizerstatic
ustride_reweightfactor_PLMD::ves::Optimizerprivate
ustride_targetdist_PLMD::ves::Optimizerprivate
warning(const std::string &msg)PLMD::Action
writeBiasOutputFiles() constPLMD::ves::Optimizer
writeFesOutputFiles() constPLMD::ves::Optimizer
writeFesProjOutputFiles() constPLMD::ves::Optimizer
writeOutputFiles(const unsigned int coeffs_id=0)PLMD::ves::Optimizerprivate
writeTargetDistOutputFiles() constPLMD::ves::Optimizer
writeTargetDistProjOutputFiles() constPLMD::ves::Optimizer
~Action()PLMD::Actionvirtual
~ActionWithValue()PLMD::ActionWithValue
~Optimizer()PLMD::ves::Optimizer
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