PLMD::bias::MetaD Member List

This is the complete list of members for PLMD::bias::MetaD, including all inherited members.

accPLMD::bias::MetaDprivate
acc_restart_mean_PLMD::bias::MetaDprivate
accelerationPLMD::bias::MetaDprivate
Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionPilot(const ActionOptions &)PLMD::ActionPilotexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
adaptive_PLMD::bias::MetaDprivate
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
addGaussian(const Gaussian &)PLMD::bias::MetaDprivate
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
afterPLMD::Actionprivate
apply() overridePLMD::bias::Biasvirtual
argumentsPLMD::ActionWithArgumentsprivate
beforeUpdate()PLMD::Actioninlinevirtual
Bias(const ActionOptions &ao)PLMD::bias::Biasexplicit
biasf_PLMD::bias::MetaDprivate
BiasGrid_PLMD::bias::MetaDprivate
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calc_max_bias_PLMD::bias::MetaDprivate
calc_rct_PLMD::bias::MetaDprivate
calc_transition_bias_PLMD::bias::MetaDprivate
calculate() overridePLMD::bias::MetaDvirtual
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionWithArgumentsvirtual
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() const overridePLMD::bias::MetaDvirtual
PLMD::checkNumericalDerivatives() constPLMD::Actioninlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const overridePLMD::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
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
computeReweightingFactor()PLMD::bias::MetaDprivate
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
current_stridePLMD::bias::MetaDprivate
dampfactor_PLMD::bias::MetaDprivate
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
difference(int, double, double) constPLMD::ActionWithArgumentsinline
doCheckPointPLMD::Actionprivate
doInt_PLMD::bias::MetaDprivate
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
dp_PLMD::bias::MetaDprivate
error(const std::string &msg) constPLMD::Action
evaluateGaussian(const vector< double > &, const Gaussian &, double *der=NULL)PLMD::bias::MetaDprivate
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(PDB &pdb)PLMD::ActionWithArgumentsprotected
fa_max_stride_PLMD::bias::MetaDprivate
fa_min_acceleration_PLMD::bias::MetaDprivate
fa_update_frequency_PLMD::bias::MetaDprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
flexbinPLMD::bias::MetaDprivate
flyingPLMD::bias::MetaDprivate
fmtPLMD::bias::MetaDprivate
fopen(const char *path, const char *mode)PLMD::Action
freq_adaptive_PLMD::bias::MetaDprivate
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getBiasAndDerivatives(const vector< double > &, double *der=NULL)PLMD::bias::MetaDprivate
getComponent(const std::string &name) constPLMD::ActionWithValueprivate
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getExchangeStep() constPLMD::Action
getGaussianNormalization(const Gaussian &)PLMD::bias::MetaDprivate
getGaussianSupport(const Gaussian &)PLMD::bias::MetaDprivate
getHeight(const vector< double > &)PLMD::bias::MetaDprivate
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getName() constPLMD::Actioninline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::bias::Biasinlinevirtual
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
getRestart() constPLMD::Actioninline
getStep() constPLMD::Action
getStride() constPLMD::ActionPilot
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTransitionBarrierBias()PLMD::bias::MetaDprivate
grid_PLMD::bias::MetaDprivate
gridfile_PLMD::bias::MetaDprivate
height0_PLMD::bias::MetaDprivate
hills_PLMD::bias::MetaDprivate
hillsOfile_PLMD::bias::MetaDprivate
ifilesPLMD::bias::MetaDprivate
ifilesnamesPLMD::bias::MetaDprivate
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)PLMD::ActionWithArguments
isActive() constPLMD::Actioninline
isFirstStepPLMD::bias::MetaDprivate
isOptionOn(const std::string &s) constPLMD::Actioninline
kbt_PLMD::bias::MetaDprivate
keywordsPLMD::Action
labelPLMD::Actionprivate
last_step_warn_gridPLMD::bias::MetaDprivate
linePLMD::Actionprivate
lockRequestArgumentsPLMD::ActionWithArgumentsprivate
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::lockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
logPLMD::Action
logTemperingSpecs(const TemperingSpecs &t_specs)PLMD::bias::MetaDprivate
lowI_PLMD::bias::MetaDprivate
max_bias_PLMD::bias::MetaDprivate
MetaD(const ActionOptions &)PLMD::bias::MetaDexplicit
mpi_mw_PLMD::bias::MetaDprivate
mpi_nw_PLMD::bias::MetaDprivate
multi_sim_commPLMD::Action
mw_dir_PLMD::bias::MetaDprivate
mw_id_PLMD::bias::MetaDprivate
mw_n_PLMD::bias::MetaDprivate
mw_rstride_PLMD::bias::MetaDprivate
n_tempering_options_PLMD::bias::MetaDprivatestatic
namePLMD::Actionprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noderivPLMD::ActionWithValueprivate
numericalDerivativesPLMD::ActionWithValueprivate
onStep() constPLMD::ActionPilotvirtual
operator=(const Action &a)=deletePLMD::Actionprivate
optionsPLMD::Actionprivate
outputForcesPLMD::bias::Biasprivate
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
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
rct_ustride_PLMD::bias::MetaDprivate
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
readGaussians(IFile *)PLMD::bias::MetaDprivate
readTemperingSpecs(TemperingSpecs &t_specs)PLMD::bias::MetaDprivate
registerKeywords(Keywords &keys)PLMD::bias::MetaDstatic
registerTemperingKeywords(const std::string &name_stem, const std::string &name, Keywords &keys)PLMD::bias::MetaDprivatestatic
replica_indexPLMD::Actionprivate
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
restartPLMD::Actionprivate
reweight_factor_PLMD::bias::MetaDprivate
runFinalJobs()PLMD::Actioninlinevirtual
scanOneHill(IFile *ifile, vector< Value > &v, vector< double > &center, vector< double > &sigma, double &height, bool &multivariate)PLMD::bias::MetaDprivate
setBias(double bias)PLMD::bias::Biasinlineprotected
setGradientsIfNeeded()PLMD::ActionWithValue
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
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
sigma0_PLMD::bias::MetaDprivate
sigma0max_PLMD::bias::MetaDprivate
sigma0min_PLMD::bias::MetaDprivate
storeOldGrids_PLMD::bias::MetaDprivate
stridePLMD::ActionPilotprivate
stride_PLMD::bias::MetaDprivate
targetfilename_PLMD::bias::MetaDprivate
TargetGrid_PLMD::bias::MetaDprivate
temperHeight(double &height, const TemperingSpecs &t_specs, const double tempering_bias)PLMD::bias::MetaDprivate
tempering_names_PLMD::bias::MetaDprivatestatic
transition_bias_PLMD::bias::MetaDprivate
transitionwells_PLMD::bias::MetaDprivate
tt_specs_PLMD::bias::MetaDprivate
turnOnDerivatives()PLMD::ActionWithValuevirtual
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::unlockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
update() overridePLMD::bias::MetaDvirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateFrequencyAdaptiveStride()PLMD::bias::MetaDprivate
uppI_PLMD::bias::MetaDprivate
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
valueBiasPLMD::bias::Biasprivate
valuesPLMD::ActionWithValueprivate
walkers_mpiPLMD::bias::MetaDprivate
warning(const std::string &msg)PLMD::Action
welltemp_PLMD::bias::MetaDprivate
wgridstride_PLMD::bias::MetaDprivate
work_PLMD::bias::MetaDprivate
writeGaussian(const Gaussian &, OFile &)PLMD::bias::MetaDprivate
~Action()PLMD::Actionvirtual
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue