PLMD::ves::VesBias Member List

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

Action(const ActionOptions &)PLMD::Actionexplicit
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
addCoeffsSet(const std::vector< std::string > &, const std::vector< unsigned int > &)PLMD::ves::VesBiasprotected
addCoeffsSet(std::vector< Value *> &, std::vector< BasisFunctions *> &)PLMD::ves::VesBiasprotected
addCoeffsSet(CoeffsVector *)PLMD::ves::VesBiasprotected
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::VesBiasprotected
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
apply()PLMD::ves::VesBiasvirtual
applyBiasCutoff(double &, std::vector< double > &) constPLMD::ves::VesBiasinline
applyBiasCutoff(double &, std::vector< double > &, std::vector< double > &) constPLMD::ves::VesBiasinline
aver_countersPLMD::ves::VesBiasprivate
beforeUpdate()PLMD::Actioninlinevirtual
Bias(const ActionOptions &ao)PLMD::bias::Biasexplicit
bias_current_max_valuePLMD::ves::VesBiasprivate
bias_cutoff_active_PLMD::ves::VesBiasprivate
bias_cutoff_swfunc_pntr_PLMD::ves::VesBiasprivate
bias_cutoff_value_PLMD::ves::VesBiasprivate
bias_file_fmt_PLMD::ves::VesBiasprivate
bias_filename_PLMD::ves::VesBiasprivate
bias_fileoutput_active_PLMD::ves::VesBiasprivate
biasCutoffActive() constPLMD::ves::VesBiasinline
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calc_reweightfactor_PLMD::ves::VesBiasprivate
calculate()=0PLMD::Actionpure virtual
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::ActionWithArgumentsvirtual
calculateReweightFactor() constPLMD::ves::VesBiasvirtual
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() constPLMD::ActionWithValueinlinevirtual
checkRead()PLMD::Action
checkThatTemperatureIsGiven()PLMD::ves::VesBiasprotected
checkUpdate() constPLMD::Action
cite(const std::string &s)PLMD::Action
clearCoeffsPntrsVector()PLMD::ves::VesBiasinlineprotected
clearDependencies()PLMD::Action
clearDerivatives()PLMD::ActionWithValuevirtual
clearGradientAndHessian()PLMD::ves::VesBiasinline
clearInputForces()PLMD::ActionWithValue
clearOptions()PLMD::Actionvirtual
Coeffs(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
coeffs_fnamesPLMD::ves::VesBiasprivate
coeffs_id_prefix_PLMD::ves::VesBiasprivate
coeffs_pntrs_PLMD::ves::VesBiasprivate
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
compute_hessian_PLMD::ves::VesBiasprivate
computeCovarianceFromAverages(const unsigned int) constPLMD::ves::VesBiasinlineprivate
computeHessian() constPLMD::ves::VesBiasinline
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
diagonal_hessian_PLMD::ves::VesBiasprivate
diagonalHessian() constPLMD::ves::VesBiasinline
difference(int, double, double) constPLMD::ActionWithArgumentsinline
disableBiasFileOutput()PLMD::ves::VesBiasinline
disableDynamicTargetDistFileOutput()PLMD::ves::VesBiasinline
disableDynamicTargetDistribution()PLMD::ves::VesBiasinline
disableFesFileOutput()PLMD::ves::VesBiasinline
disableFesFileProjOutput()PLMD::ves::VesBiasinline
disableHessian()PLMD::ves::VesBias
disableStaticTargetDistFileOutput()PLMD::ves::VesBiasinline
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
dynamic_targetdist_PLMD::ves::VesBiasprivate
dynamic_targetdist_fileoutput_active_PLMD::ves::VesBiasprivate
dynamicTargetDistribution() constPLMD::ves::VesBiasinline
enableBiasFileOutput()PLMD::ves::VesBiasinline
enableDynamicTargetDistFileOutput()PLMD::ves::VesBiasinline
enableDynamicTargetDistribution()PLMD::ves::VesBiasinline
enableFesFileOutput()PLMD::ves::VesBiasinline
enableFesProjFileOutput()PLMD::ves::VesBiasinline
enableHessian(const bool diagonal_hessian=true)PLMD::ves::VesBias
enableIterationNumberInFilenames()PLMD::ves::VesBiasinline
enableMultipleCoeffsSets()PLMD::ves::VesBiasinline
enableStaticTargetDistFileOutput()PLMD::ves::VesBiasinline
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(PDB &pdb)PLMD::ActionWithArgumentsprotected
fclose(FILE *fp)PLMD::Action
fes_file_fmt_PLMD::ves::VesBiasprivate
fes_filename_PLMD::ves::VesBiasprivate
fes_fileoutput_active_PLMD::ves::VesBiasprivate
fesproj_fileoutput_active_PLMD::ves::VesBiasprivate
fflush()PLMD::Action
filenames_have_iteration_number_PLMD::ves::VesBiasprivate
filenamesIncludeIterationNumber() constPLMD::ves::VesBiasinline
filesPLMD::Action
fopen(const char *path, const char *mode)PLMD::Action
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getBeta() constPLMD::ves::VesBiasinline
getBiasCutoffSwitchingFunction(const double, double &) constPLMD::ves::VesBias
getBiasCutoffSwitchingFunction(const double) constPLMD::ves::VesBiasinline
getBiasCutoffValue() constPLMD::ves::VesBiasinline
getBiasFileFmt() constPLMD::ves::VesBiasinline
getBiasOutputFilename() constPLMD::ves::VesBiasinline
getCoeffsIndex(const std::vector< unsigned int > &indices, const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getCoeffsIndices(const size_t index, const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getCoeffsPntr(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getCoeffsPntrs() constPLMD::ves::VesBiasinline
getCoeffsSetFilenameSuffix(const unsigned int coeffs_id) constPLMD::ves::VesBias
getCoeffsSetLabelString(const std::string &, const unsigned int coeffs_id=0) constPLMD::ves::VesBiasprotected
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getCurrentBiasMaxValue() constPLMD::ves::VesBiasinline
getCurrentBiasOutputFilename(const std::string &suffix="") constPLMD::ves::VesBiasinline
getCurrentFesOutputFilename(const std::string &suffix="") constPLMD::ves::VesBiasinline
getCurrentOutputFilename(const std::string &, const std::string &suffix="") constPLMD::ves::VesBias
getCurrentTargetDistOutputFilename(const std::string &suffix="") constPLMD::ves::VesBias
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getExchangeStep() constPLMD::Action
getFesFileFmt() constPLMD::ves::VesBiasinline
getFesOutputFilename() constPLMD::ves::VesBiasinline
getGradientPntr(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getGradientPntrs() constPLMD::ves::VesBiasinline
getGridBins() constPLMD::ves::VesBiasinline
getGridMax() constPLMD::ves::VesBiasinline
getGridMin() constPLMD::ves::VesBiasinline
getHessianIndex(const size_t index1, const size_t index2, const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getHessianPntr(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getHessianPntrs() constPLMD::ves::VesBiasinline
getIterationCounter() constPLMD::ves::VesBias
getIterationFilenameSuffix() constPLMD::ves::VesBias
getKbT() constPLMD::ves::VesBiasinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getName() constPLMD::Actioninline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives()PLMD::bias::Biasinlinevirtual
getNumberOfProjectionArguments() constPLMD::ves::VesBiasinline
getNumberOfTargetDistributionPntrs() constPLMD::ves::VesBiasinline
getOFile(const std::string &filename, const bool multi_sim_single_file=false, const bool enforce_backup=true)PLMD::ves::VesBias
getOptimizerPntr() constPLMD::ves::VesBiasinline
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPntrToArgument(const unsigned n)PLMD::ActionWithArgumentsinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
getProjectionArgument(unsigned int i) constPLMD::ves::VesBiasinline
getProjectionArguments() constPLMD::ves::VesBiasinline
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
getTargetDistAveragesPntr(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
getTargetDistAveragesPntrs() constPLMD::ves::VesBiasinline
getTargetDistFileFmt() constPLMD::ves::VesBiasinline
getTargetDistOutputFilename() constPLMD::ves::VesBiasinline
getTargetDistRestartFileFmt() constPLMD::ves::VesBiasinline
getTargetDistributionPntrs() constPLMD::ves::VesBiasinline
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
Gradient(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
gradient_pntrs_PLMD::ves::VesBiasprivate
grid_bins_PLMD::ves::VesBiasprivate
grid_max_PLMD::ves::VesBiasprivate
grid_min_PLMD::ves::VesBiasprivate
Hessian(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
hessian_pntrs_PLMD::ves::VesBiasprivate
initializeCoeffs(CoeffsVector *)PLMD::ves::VesBiasprivate
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg)PLMD::ActionWithArguments
isActive() constPLMD::Actioninline
isBiasFileOutputActive() constPLMD::ves::VesBiasinline
isDynamicTargetDistFileOutputActive() constPLMD::ves::VesBiasinline
isFesFileOutputActive() constPLMD::ves::VesBiasinline
isFesProjFileOutputActive() constPLMD::ves::VesBiasinline
isOptionOn(const std::string &s) constPLMD::Actioninline
isReweightFactorCalculated() constPLMD::ves::VesBiasinline
isStaticTargetDistFileOutputActive() constPLMD::ves::VesBiasinline
kbt_PLMD::ves::VesBiasprivate
keywordsPLMD::Action
linkOptimizer(Optimizer *)PLMD::ves::VesBias
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::lockRequests()PLMD::ActionWithArgumentsinlinevirtual
logPLMD::Action
multi_sim_commPLMD::Action
multiSimSumAverages(const unsigned int, const double walker_weight=1.0)PLMD::ves::VesBiasprivate
ncoeffs_total_PLMD::ves::VesBiasprivate
ncoeffssets_PLMD::ves::VesBiasprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
numberOfCoeffs(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
numberOfCoeffsSets() constPLMD::ves::VesBiasinline
onStep() constPLMD::ActionPilotvirtual
optimize_coeffs_PLMD::ves::VesBiasprivate
optimizeCoeffs() constPLMD::ves::VesBiasinline
optimizer_pntr_PLMD::ves::VesBiasprivate
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::VesBiasprotected
parseMultipleValues(const std::string &, std::vector< T > &, unsigned int, const T &)PLMD::ves::VesBiasprotected
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
projection_args_PLMD::ves::VesBiasprivate
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
readCoeffsFromFiles()PLMD::ves::VesBiasprotected
registerKeywords(Keywords &)PLMD::ves::VesBiasstatic
requestArguments(const std::vector< Value *> &arg)PLMD::ActionWithArguments
resetBiasFileOutput()PLMD::ves::VesBiasinlinevirtual
resetFesFileOutput()PLMD::ves::VesBiasinlinevirtual
resetFesProjFileOutput()PLMD::ves::VesBiasinlinevirtual
resetTargetDistFileOutput()PLMD::ves::VesBiasinlinevirtual
resetTargetDistProjFileOutput()PLMD::ves::VesBiasinlinevirtual
restartTargetDistributions()PLMD::ves::VesBiasinlinevirtual
runFinalJobs()PLMD::Actioninlinevirtual
sampled_averagesPLMD::ves::VesBiasprivate
sampled_cross_averagesPLMD::ves::VesBiasprivate
setBias(double bias)PLMD::bias::Biasinlineprotected
setCurrentBiasMaxValue(const double max_value)PLMD::ves::VesBiasinline
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::Actionvirtual
setOutputForce(int i, double f)PLMD::bias::Biasinlineprotected
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::VesBiasprotected
setTargetDistAverages(const CoeffsVector &, const unsigned int coeffs_id=0)PLMD::ves::VesBiasprotected
setTargetDistAveragesToZero(const unsigned int coeffs_id=0)PLMD::ves::VesBiasprotected
setupBiasCutoff(const double, const double)PLMD::ves::VesBias
setupBiasFileOutput()PLMD::ves::VesBiasinlinevirtual
setupFesFileOutput()PLMD::ves::VesBiasinlinevirtual
setupFesProjFileOutput()PLMD::ves::VesBiasinlinevirtual
setupTargetDistFileOutput()PLMD::ves::VesBiasinlinevirtual
setupTargetDistProjFileOutput()PLMD::ves::VesBiasinlinevirtual
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
static_targetdist_fileoutput_active_PLMD::ves::VesBiasprivate
targetdist_averages_filename_PLMD::ves::VesBiasprivate
targetdist_averages_pntrs_PLMD::ves::VesBiasprivate
targetdist_file_fmt_PLMD::ves::VesBiasprivate
targetdist_filename_PLMD::ves::VesBiasprivate
targetdist_pntrs_PLMD::ves::VesBiasprivate
targetdist_restart_file_fmt_PLMD::ves::VesBiasprivate
TargetDistAverages(const unsigned int coeffs_id=0) constPLMD::ves::VesBiasinline
totalNumberOfCoeffs() constPLMD::ves::VesBiasinline
turnOnDerivatives()PLMD::ActionWithValuevirtual
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::unlockRequests()PLMD::ActionWithArgumentsinlinevirtual
update()PLMD::Actioninlinevirtual
updateGradientAndHessian(const bool)PLMD::ves::VesBias
updateReweightFactor()PLMD::ves::VesBias
updateTargetDistributions()PLMD::ves::VesBiasinlinevirtual
use_multiple_coeffssets_PLMD::ves::VesBiasprivate
useBiasCutoffKeywords(Keywords &)PLMD::ves::VesBiasstatic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useGridBinKeywords(Keywords &)PLMD::ves::VesBiasstatic
useGridLimitsKeywords(Keywords &)PLMD::ves::VesBiasstatic
useInitialCoeffsKeywords(Keywords &)PLMD::ves::VesBiasstatic
useMultipleTargetDistributionKeywords(Keywords &)PLMD::ves::VesBiasstatic
useMultipleWalkers() constPLMD::ves::VesBias
useNumericalDerivatives()PLMD::ActionWithValueinline
useProjectionArgKeywords(Keywords &)PLMD::ves::VesBiasstatic
useReweightFactorKeywords(Keywords &)PLMD::ves::VesBiasstatic
useTargetDistributionKeywords(Keywords &)PLMD::ves::VesBiasstatic
VesBias(const ActionOptions &ao)PLMD::ves::VesBiasexplicit
warning(const std::string &msg)PLMD::Action
writeBiasToFile()PLMD::ves::VesBiasinlinevirtual
writeFesProjToFile()PLMD::ves::VesBiasinlinevirtual
writeFesToFile()PLMD::ves::VesBiasinlinevirtual
writeTargetDistProjToFile()PLMD::ves::VesBiasinlinevirtual
writeTargetDistToFile()PLMD::ves::VesBiasinlinevirtual
~Action()PLMD::Actionvirtual
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
~VesBias()PLMD::ves::VesBias
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