PLMD::isdb::PRE Member List

This is the complete list of members for PLMD::isdb::PRE, including all inherited members.

Action(const ActionOptions &)PLMD::Actionexplicit
Action(const Action &a)=deletePLMD::Actionprivate
ActionAtomistic(const ActionOptions &ao)PLMD::ActionAtomisticexplicit
ActionWithArguments(const ActionOptions &)PLMD::ActionWithArgumentsexplicit
ActionWithValue(const ActionOptions &ao)PLMD::ActionWithValueexplicit
activate()PLMD::Actionvirtual
activePLMD::Actionprivate
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
afterPLMD::Actionprivate
allowToAccessGlobalForces()PLMD::ActionAtomisticinline
apply() overridePLMD::isdb::MetainferenceBaseinlinevirtual
applyForces()PLMD::ActionAtomistic
argumentsPLMD::ActionWithArgumentsprivate
atomsPLMD::ActionAtomisticprotected
average_weights_PLMD::isdb::MetainferenceBaseprivate
beforeUpdate()PLMD::Actioninlinevirtual
bringBackInPbc(int i, double d1) constPLMD::ActionWithArgumentsinline
calc_data_PLMD::isdb::MetainferenceBaseprivate
calculate() overridePLMD::isdb::PREvirtual
calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum)PLMD::ActionAtomistic
calculateFromPDB(const PDB &)PLMD::Action
calculateNumericalDerivatives(ActionWithValue *a) overridePLMD::isdb::MetainferenceBaseinlinevirtual
changeBox(const Tensor &newbox)PLMD::ActionAtomistic
chargesPLMD::ActionAtomisticprivate
chargesWereSetPLMD::ActionAtomisticprivate
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
clearOutputForces()PLMD::ActionAtomistic
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
constantPLMD::isdb::PREprivate
copyOutput(const std::string &name) constPLMD::ActionWithValue
copyOutput(const unsigned &n) constPLMD::ActionWithValue
deactivate()PLMD::Actioninlinevirtual
decay_w_PLMD::isdb::MetainferenceBaseprivate
Dependencies typedefPLMD::Action
Dftilde_PLMD::isdb::MetainferenceBaseprivate
difference(int, double, double) constPLMD::ActionWithArgumentsinline
do_optsigmamean_PLMD::isdb::MetainferenceBaseprivate
do_regression_zero(const std::vector< double > &mean)PLMD::isdb::MetainferenceBaseprivate
do_reweight_PLMD::isdb::MetainferenceBaseprivate
doCheckPointPLMD::Actionprivate
Doffset_PLMD::isdb::MetainferenceBaseprivate
doMonteCarlo(const std::vector< double > &mean)PLMD::isdb::MetainferenceBaseprivate
doNotCalculateDerivatives() constPLMD::ActionWithValueinlinevirtual
donotforcePLMD::ActionAtomisticprivate
doNotForce()PLMD::ActionAtomisticinline
donotretrievePLMD::ActionAtomisticprivate
doNotRetrieve()PLMD::ActionAtomisticinline
dooffset_PLMD::isdb::MetainferenceBaseprivate
doratioPLMD::isdb::PREprivate
doregres_zero_PLMD::isdb::MetainferenceBaseprivate
doscale_PLMD::isdb::MetainferenceBaseprivate
doscore_PLMD::isdb::MetainferenceBaseprivate
Dscale_PLMD::isdb::MetainferenceBaseprivate
Dsigma_PLMD::isdb::MetainferenceBaseprivate
energyPLMD::ActionAtomisticprivate
error(const std::string &msg) constPLMD::Action
exists(const std::string &name) constPLMD::ActionWithValue
exit(int c=0)PLMD::Action
expandArgKeywordInPDB(const PDB &pdb)PLMD::ActionWithArgumentsprotected
extraCVPLMD::ActionAtomisticprivate
fclose(FILE *fp)PLMD::Action
fflush()PLMD::Action
filesPLMD::Action
firstTimePLMD::isdb::MetainferenceBaseprivate
firstTimeWPLMD::isdb::MetainferenceBaseprivate
fopen(const char *path, const char *mode)PLMD::Action
forceOnEnergyPLMD::ActionAtomisticprivate
forceOnExtraCVPLMD::ActionAtomisticprivate
forcesPLMD::isdb::MetainferenceBaseprivate
forcesToApplyPLMD::isdb::MetainferenceBaseprivate
ftilde_PLMD::isdb::MetainferenceBaseprivate
GAUSS enum valuePLMD::isdb::MetainferenceBaseprivate
gen_likelihood_PLMD::isdb::MetainferenceBaseprivate
GENERIC enum valuePLMD::isdb::MetainferenceBaseprivate
get_sigma_mean(const double weight, const double norm, const double neff, const std::vector< double > &mean)PLMD::isdb::MetainferenceBaseprivate
get_weights(double &weight, double &norm, double &neff)PLMD::isdb::MetainferenceBaseprivate
getAbsoluteIndex(int i) constPLMD::ActionAtomisticinline
getAbsoluteIndexes() constPLMD::ActionAtomisticinlinevirtual
getArgument(const unsigned n) constPLMD::ActionWithArgumentsinline
getArguments() constPLMD::ActionWithArgumentsinlinevirtual
getBox() constPLMD::ActionAtomisticinline
getCalcData(const unsigned index)PLMD::isdb::MetainferenceBaseinlineprivate
getCharge(int i) constPLMD::ActionAtomisticinline
getComponent(const std::string &name) constPLMD::ActionWithValueprivate
getComponentsList() constPLMD::ActionWithValue
getComponentsVector() constPLMD::ActionWithValue
getCPT() constPLMD::Action
getDependencies() constPLMD::Actioninline
getDocumentation() constPLMD::Actionvirtual
getDoScore()PLMD::isdb::MetainferenceBaseinline
getEnergy() constPLMD::ActionAtomisticinline
getEnergyForceGJ(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
getEnergyForceGJE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
getEnergyForceMIGEN(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
getEnergyForceSP(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
getEnergyForceSPE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
getEnergyGJ(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)PLMD::isdb::MetainferenceBaseprivate
getEnergyGJE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)PLMD::isdb::MetainferenceBaseprivate
getEnergyMIGEN(const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset)PLMD::isdb::MetainferenceBaseprivate
getEnergySP(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)PLMD::isdb::MetainferenceBaseprivate
getEnergySPE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)PLMD::isdb::MetainferenceBaseprivate
getExchangeStep() constPLMD::Action
getGlobalPosition(AtomNumber) constPLMD::ActionAtomisticinline
getKeyword(const std::string &key)PLMD::Action
getLabel() constPLMD::Actioninline
getMass(int i) constPLMD::ActionAtomisticinline
getMetaDer(const unsigned index)PLMD::isdb::MetainferenceBaseinline
getName() constPLMD::Actioninline
getNarg()PLMD::isdb::MetainferenceBaseinline
getNumberOfArguments() constPLMD::ActionWithArgumentsinlinevirtual
getNumberOfAtoms() constPLMD::ActionAtomisticinline
getNumberOfComponents() constPLMD::ActionWithValueinline
getNumberOfDerivatives() overridePLMD::isdb::MetainferenceBaseinlinevirtual
getOutputQuantity(const unsigned j) constPLMD::ActionWithValueinline
getOutputQuantity(const std::string &name) constPLMD::ActionWithValueinline
getPbc() constPLMD::ActionAtomisticinline
getPntrToArgument(const unsigned n)PLMD::ActionWithArgumentsinline
getPntrToComponent(int i)PLMD::ActionWithValueprotected
getPntrToComponent(const std::string &name)PLMD::ActionWithValueprotected
getPntrToValue()PLMD::ActionWithValueprotected
getPosition(int) constPLMD::ActionAtomisticinline
getPositions() constPLMD::ActionAtomisticinline
getProjection(unsigned i, unsigned j) constPLMD::ActionWithArguments
getRestart() constPLMD::Actioninline
getScore()PLMD::isdb::MetainferenceBase
getStep() constPLMD::Action
getTime() constPLMD::Action
getTimeStep() constPLMD::Action
getTotAtoms() constPLMD::ActionAtomisticinline
getUnique() constPLMD::ActionAtomisticinline
getUniqueLocal() constPLMD::ActionAtomisticinline
getWstride()PLMD::isdb::MetainferenceBaseinline
indexesPLMD::ActionAtomisticprivate
ineptPLMD::isdb::PREprivate
Initialise(const unsigned input)PLMD::isdb::MetainferenceBase
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)PLMD::ActionWithArguments
interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
isActive() constPLMD::Actioninline
iselectPLMD::isdb::MetainferenceBaseprivate
isOptionOn(const std::string &s) constPLMD::Actioninline
kbt_PLMD::isdb::MetainferenceBaseprivate
keywordsPLMD::Action
labelPLMD::Actionprivate
LIKE_GAUSS enum valuePLMD::isdb::MetainferenceBaseprivate
LIKE_LOGN enum valuePLMD::isdb::MetainferenceBaseprivate
linePLMD::Actionprivate
lockRequestArgumentsPLMD::ActionWithArgumentsprivate
lockRequestAtomsPLMD::ActionAtomisticprivate
lockRequests() overridePLMD::isdb::MetainferenceBaseinlinevirtual
logPLMD::Action
makeWhole()PLMD::ActionAtomistic
massesPLMD::ActionAtomisticprivate
masterPLMD::isdb::MetainferenceBaseprivate
MCaccept_PLMD::isdb::MetainferenceBaseprivate
MCacceptFT_PLMD::isdb::MetainferenceBaseprivate
MCacceptScale_PLMD::isdb::MetainferenceBaseprivate
MCchunksize_PLMD::isdb::MetainferenceBaseprivate
MCsteps_PLMD::isdb::MetainferenceBaseprivate
MCtrial_PLMD::isdb::MetainferenceBaseprivate
metader_PLMD::isdb::MetainferenceBaseprivate
MetainferenceBase(const ActionOptions &)PLMD::isdb::MetainferenceBaseexplicit
MGAUSS enum valuePLMD::isdb::MetainferenceBaseprivate
modifyForceOnEnergy()PLMD::ActionAtomisticinline
modifyForceOnExtraCV()PLMD::ActionAtomisticinline
modifyForces()PLMD::ActionAtomisticinline
modifyGlobalForce(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalPbc()PLMD::ActionAtomisticinline
modifyGlobalPosition(AtomNumber)PLMD::ActionAtomisticinline
modifyGlobalVirial()PLMD::ActionAtomisticinline
modifyVirial()PLMD::ActionAtomisticinline
MOUTLIERS enum valuePLMD::isdb::MetainferenceBaseprivate
moveScaleOffset(const std::vector< double > &mean_, double &old_energy)PLMD::isdb::MetainferenceBaseprivate
moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow)PLMD::isdb::MetainferenceBaseprivate
moveTilde(const std::vector< double > &mean_, double &old_energy)PLMD::isdb::MetainferenceBaseprivate
multi_sim_commPLMD::Action
N_optimized_step_PLMD::isdb::MetainferenceBaseprivate
namePLMD::Actionprivate
nargPLMD::isdb::MetainferenceBaseprivate
ngaPLMD::isdb::PREprivate
nlPLMD::isdb::PREprivate
noAnalyticalDerivatives(Keywords &keys)PLMD::ActionWithValuestatic
noderivPLMD::ActionWithValueprivate
noise_type_PLMD::isdb::MetainferenceBaseprivate
nregres_zero_PLMD::isdb::MetainferenceBaseprivate
nrep_PLMD::isdb::MetainferenceBaseprivate
nsel_PLMD::isdb::MetainferenceBaseprivate
numericalDerivativesPLMD::ActionWithValueprivate
offset_PLMD::isdb::MetainferenceBaseprivate
offset_max_PLMD::isdb::MetainferenceBaseprivate
offset_min_PLMD::isdb::MetainferenceBaseprivate
offset_mu_PLMD::isdb::MetainferenceBaseprivate
offset_prior_PLMD::isdb::MetainferenceBaseprivate
operator=(const Action &a)=deletePLMD::Actionprivate
optimized_step_PLMD::isdb::MetainferenceBaseprivate
optionsPLMD::Actionprivate
optsigmamean_stride_PLMD::isdb::MetainferenceBaseprivate
OUTLIERS enum valuePLMD::isdb::MetainferenceBaseprivate
parametersPLMD::isdb::MetainferenceBaseprivate
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
parseAtomList(const std::string &key, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t)PLMD::ActionAtomistic
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
pbcPLMD::isdb::PREprivate
pbc_fwdPLMD::ActionAtomisticprivate
pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) constPLMD::ActionAtomistic
pbcDistance(const Vector &, const Vector &) constPLMD::ActionAtomistic
plumedPLMD::Action
positionsPLMD::ActionAtomisticprivate
PRE(const ActionOptions &)PLMD::isdb::PREexplicit
prepare()PLMD::Actionvirtual
randomPLMD::isdb::MetainferenceBaseprivate
readAtomsFromPDB(const PDB &pdb) overridePLMD::ActionAtomisticvirtual
registerKeywords(Keywords &keys)PLMD::isdb::PREstatic
replica_PLMD::isdb::MetainferenceBaseprivate
replica_averaging(const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b)PLMD::isdb::MetainferenceBaseprivate
replica_indexPLMD::Actionprivate
requestArguments(const std::vector< Value * > &arg)PLMD::ActionWithArguments
requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true)PLMD::ActionAtomistic
requestExtraDependencies(const std::vector< Value * > &extra)PLMD::ActionWithArguments
restartPLMD::Actionprivate
retrieveAtoms()PLMD::ActionAtomisticvirtual
rtwoPLMD::isdb::PREprivate
runFinalJobs()PLMD::Actioninlinevirtual
SC_FLAT enum valuePLMD::isdb::MetainferenceBaseprivate
SC_GAUSS enum valuePLMD::isdb::MetainferenceBaseprivate
scale_PLMD::isdb::MetainferenceBaseprivate
scale_max_PLMD::isdb::MetainferenceBaseprivate
scale_min_PLMD::isdb::MetainferenceBaseprivate
scale_mu_PLMD::isdb::MetainferenceBaseprivate
scale_prior_PLMD::isdb::MetainferenceBaseprivate
Selector()PLMD::isdb::MetainferenceBase
selector_PLMD::isdb::MetainferenceBaseprivate
setArgDerivatives(Value *v, const double &d)PLMD::isdb::MetainferenceBaseinline
setAtomsDerivatives(Value *v, const unsigned i, const Vector &d)PLMD::isdb::MetainferenceBaseinline
setBoxDerivatives(Value *v, const Tensor &d)PLMD::isdb::MetainferenceBaseinline
setCalcData(const unsigned index, const double datum)PLMD::isdb::MetainferenceBaseinline
setCalcData(const std::vector< double > &data)PLMD::isdb::MetainferenceBaseinline
setDerivatives()PLMD::isdb::MetainferenceBaseinline
setExtraCV(const std::string &name)PLMD::ActionAtomisticinlineprotected
setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0)PLMD::ActionAtomistic
setGradientsIfNeeded()PLMD::ActionWithValue
setMetaDer(const unsigned index, const double der)PLMD::isdb::MetainferenceBaseinlineprivate
setNarg(const unsigned input)PLMD::isdb::MetainferenceBaseinline
setNotPeriodic()PLMD::ActionWithValue
setOption(const std::string &s)PLMD::Actionvirtual
setParameter(const double input)PLMD::isdb::MetainferenceBaseinline
setParameters(const std::vector< double > &input)PLMD::isdb::MetainferenceBaseinline
setPeriodic(const std::string &min, const std::string &max)PLMD::ActionWithValue
setScore(const double score)PLMD::isdb::MetainferenceBaseinline
setValue(const double &d)PLMD::ActionWithValueinlineprotected
setValue(Value *, double)PLMD::ActionWithValue
sfile_PLMD::isdb::MetainferenceBaseprivate
sigma_PLMD::isdb::MetainferenceBaseprivate
sigma_max_PLMD::isdb::MetainferenceBaseprivate
sigma_max_est_PLMD::isdb::MetainferenceBaseprivate
sigma_mean2_PLMD::isdb::MetainferenceBaseprivate
sigma_mean2_last_PLMD::isdb::MetainferenceBaseprivate
sigma_min_PLMD::isdb::MetainferenceBaseprivate
sigmamax_opt_done_PLMD::isdb::MetainferenceBaseprivate
status_file_name_PLMD::isdb::MetainferenceBaseprivate
tot_sizePLMD::isdb::PREprivate
turnOnDerivatives() overridePLMD::isdb::MetainferenceBaseinlinevirtual
uniquePLMD::ActionAtomisticprivate
unique_localPLMD::ActionAtomisticprivate
unlockRequests() overridePLMD::isdb::MetainferenceBaseinlinevirtual
update() overridePLMD::isdb::PREvirtual
update_fromPLMD::Actionprivate
update_untilPLMD::Actionprivate
updateUniqueLocal()PLMD::ActionAtomistic
useCustomisableComponents(Keywords &keys)PLMD::ActionWithValuestatic
useNumericalDerivatives()PLMD::ActionWithValueinline
valueAcceptPLMD::isdb::MetainferenceBaseprivate
valueAcceptFTPLMD::isdb::MetainferenceBaseprivate
valueAcceptScalePLMD::isdb::MetainferenceBaseprivate
valueFtildePLMD::isdb::MetainferenceBaseprivate
valueOffsetPLMD::isdb::MetainferenceBaseprivate
valuesPLMD::ActionWithValueprivate
valueScalePLMD::isdb::MetainferenceBaseprivate
valueScorePLMD::isdb::MetainferenceBaseprivate
valueSigmaPLMD::isdb::MetainferenceBaseprivate
valueSigmaMeanPLMD::isdb::MetainferenceBaseprivate
virialPLMD::ActionAtomisticprivate
warning(const std::string &msg)PLMD::Action
write_stride_PLMD::isdb::MetainferenceBaseprivate
writeStatus()PLMD::isdb::MetainferenceBase
~Action()PLMD::Actionvirtual
~ActionAtomistic()PLMD::ActionAtomistic
~ActionWithArguments()PLMD::ActionWithArgumentsinlinevirtual
~ActionWithValue()PLMD::ActionWithValue
~MetainferenceBase()PLMD::isdb::MetainferenceBase