PLMD::isdb::Metainference Member List

This is the complete list of members for PLMD::isdb::Metainference, 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
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
addValue()PLMD::ActionWithValue
addValueWithDerivatives()PLMD::ActionWithValue
apply() overridePLMD::bias::Biasvirtual
average_weights_PLMD::isdb::Metainferenceprivate
average_weights_stride_PLMD::isdb::Metainferenceprivate
beforeUpdate()PLMD::Actioninlinevirtual
Bias(const ActionOptions &ao)PLMD::bias::Biasexplicit
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calculate() overridePLMD::isdb::Metainferencevirtual
calculateFromPDB(const PDB &)PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)PLMD::Actionvirtual
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL) overridePLMD::ActionWithArgumentsvirtual
checkFieldsAllowed()PLMD::ActionWithValueinlinevirtual
checkNeedsGradients() constPLMD::Actioninlinevirtual
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
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
Dependencies typedefPLMD::Action
Dftilde_PLMD::isdb::Metainferenceprivate
difference(int, double, double) constPLMD::ActionWithArgumentsinline
do_optsigmamean_PLMD::isdb::Metainferenceprivate
do_regression_zero(const vector< double > &mean)PLMD::isdb::Metainferenceprivate
do_reweight_PLMD::isdb::Metainferenceprivate
Doffset_PLMD::isdb::Metainferenceprivate
doMonteCarlo(const vector< double > &mean)PLMD::isdb::Metainferenceprivate
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
dooffset_PLMD::isdb::Metainferenceprivate
doregres_zero_PLMD::isdb::Metainferenceprivate
doscale_PLMD::isdb::Metainferenceprivate
Dscale_PLMD::isdb::Metainferenceprivate
Dsigma_PLMD::isdb::Metainferenceprivate
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
fflush()PLMD::Action
filesPLMD::Action
firstTimePLMD::isdb::Metainferenceprivate
firstTimeWPLMD::isdb::Metainferenceprivate
fopen(const char *path, const char *mode)PLMD::Action
ftilde_PLMD::isdb::Metainferenceprivate
GAUSS enum valuePLMD::isdb::Metainferenceprivate
gen_likelihood_PLMD::isdb::Metainferenceprivate
GENERIC enum valuePLMD::isdb::Metainferenceprivate
get_sigma_mean(const unsigned iselect, const double fact, const double var_fact, const vector< double > &mean)PLMD::isdb::Metainferenceprivate
get_weights(const unsigned iselect, double &fact, double &var_fact)PLMD::isdb::Metainferenceprivate
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getEnergyForceGJ(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
getEnergyForceGJE(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
getEnergyForceMIGEN(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
getEnergyForceSP(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
getEnergyForceSPE(const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
getEnergyGJ(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)PLMD::isdb::Metainferenceprivate
getEnergyGJE(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)PLMD::isdb::Metainferenceprivate
getEnergyMIGEN(const vector< double > &mean, const vector< double > &ftilde, const vector< double > &sigma, const double scale, const double offset)PLMD::isdb::Metainferenceprivate
getEnergySP(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)PLMD::isdb::Metainferenceprivate
getEnergySPE(const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)PLMD::isdb::Metainferenceprivate
getExchangeStep() constPLMD::Action
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
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg)PLMD::ActionWithArguments
isActive() constPLMD::Actioninline
isOptionOn(const std::string &s) constPLMD::Actioninline
kbt_PLMD::isdb::Metainferenceprivate
keywordsPLMD::Action
LIKE_GAUSS enum valuePLMD::isdb::Metainferenceprivate
LIKE_LOGN enum valuePLMD::isdb::Metainferenceprivate
PLMD::lockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::lockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
logPLMD::Action
masterPLMD::isdb::Metainferenceprivate
MCaccept_PLMD::isdb::Metainferenceprivate
MCacceptFT_PLMD::isdb::Metainferenceprivate
MCacceptScale_PLMD::isdb::Metainferenceprivate
MCchunksize_PLMD::isdb::Metainferenceprivate
MCsteps_PLMD::isdb::Metainferenceprivate
MCtrial_PLMD::isdb::Metainferenceprivate
Metainference(const ActionOptions &)PLMD::isdb::Metainferenceexplicit
MGAUSS enum valuePLMD::isdb::Metainferenceprivate
MOUTLIERS enum valuePLMD::isdb::Metainferenceprivate
moveScaleOffset(const std::vector< double > &mean_, double &old_energy)PLMD::isdb::Metainferenceprivate
moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow)PLMD::isdb::Metainferenceprivate
moveTilde(const std::vector< double > &mean_, double &old_energy)PLMD::isdb::Metainferenceprivate
multi_sim_commPLMD::Action
nargPLMD::isdb::Metainferenceprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noise_type_PLMD::isdb::Metainferenceprivate
nregres_zero_PLMD::isdb::Metainferenceprivate
nrep_PLMD::isdb::Metainferenceprivate
offset_PLMD::isdb::Metainferenceprivate
offset_max_PLMD::isdb::Metainferenceprivate
offset_min_PLMD::isdb::Metainferenceprivate
offset_mu_PLMD::isdb::Metainferenceprivate
offset_prior_PLMD::isdb::Metainferenceprivate
onStep() constPLMD::ActionPilotvirtual
optsigmamean_stride_PLMD::isdb::Metainferenceprivate
OUTLIERS enum valuePLMD::isdb::Metainferenceprivate
parametersPLMD::isdb::Metainferenceprivate
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
randomPLMD::isdb::Metainferenceprivate
readAtomsFromPDB(const PDB &)PLMD::Actioninlinevirtual
registerKeywords(Keywords &keys)PLMD::isdb::Metainferencestatic
replica_PLMD::isdb::Metainferenceprivate
replica_averaging(const double fact, std::vector< double > &mean, std::vector< double > &dmean_b)PLMD::isdb::Metainferenceprivate
requestArguments(const std::vector< Value *> &arg)PLMD::ActionWithArguments
runFinalJobs()PLMD::Actioninlinevirtual
SC_FLAT enum valuePLMD::isdb::Metainferenceprivate
SC_GAUSS enum valuePLMD::isdb::Metainferenceprivate
scale_PLMD::isdb::Metainferenceprivate
scale_max_PLMD::isdb::Metainferenceprivate
scale_min_PLMD::isdb::Metainferenceprivate
scale_mu_PLMD::isdb::Metainferenceprivate
scale_prior_PLMD::isdb::Metainferenceprivate
selector_PLMD::isdb::Metainferenceprivate
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
sfile_PLMD::isdb::Metainferenceprivate
sigma_PLMD::isdb::Metainferenceprivate
sigma_max_PLMD::isdb::Metainferenceprivate
sigma_mean2_PLMD::isdb::Metainferenceprivate
sigma_mean2_last_PLMD::isdb::Metainferenceprivate
sigma_min_PLMD::isdb::Metainferenceprivate
turnOnDerivatives()PLMD::ActionWithValuevirtual
PLMD::unlockRequests()PLMD::Actioninlinevirtual
PLMD::ActionWithArguments::unlockRequests() overridePLMD::ActionWithArgumentsinlinevirtual
update() overridePLMD::isdb::Metainferencevirtual
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
valueAcceptPLMD::isdb::Metainferenceprivate
valueAcceptFTPLMD::isdb::Metainferenceprivate
valueAcceptScalePLMD::isdb::Metainferenceprivate
valueFtildePLMD::isdb::Metainferenceprivate
valueOffsetPLMD::isdb::Metainferenceprivate
valueScalePLMD::isdb::Metainferenceprivate
valueSigmaPLMD::isdb::Metainferenceprivate
valueSigmaMeanPLMD::isdb::Metainferenceprivate
warning(const std::string &msg)PLMD::Action
write_stride_PLMD::isdb::Metainferenceprivate
writeStatus()PLMD::isdb::Metainferenceprivate
~Action()PLMD::Actionvirtual
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
~Metainference()PLMD::isdb::Metainference