PLMD::bias::MetaD Member List

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

acc	PLMD::bias::MetaD	private
acceleration	PLMD::bias::MetaD	private
Action(const ActionOptions &)	PLMD::Action	explicit
ActionPilot(const ActionOptions &)	PLMD::ActionPilot	explicit
ActionWithArguments(const ActionOptions &)	PLMD::ActionWithArguments	explicit
ActionWithValue(const ActionOptions &ao)	PLMD::ActionWithValue	explicit
activate()	PLMD::Action	virtual
adaptive_	PLMD::bias::MetaD	private
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::MetaD	private
addValue()	PLMD::ActionWithValue
addValueWithDerivatives()	PLMD::ActionWithValue
apply()	PLMD::bias::Bias	virtual
Bias(const ActionOptions &ao)	PLMD::bias::Bias	explicit
biasf_	PLMD::bias::MetaD	private
BiasGrid_	PLMD::bias::MetaD	private
bringBackInPbc(int i, double d1) const	PLMD::ActionWithArguments	inline
calculate()	PLMD::bias::MetaD	virtual
calculateFromPDB(const PDB &)	PLMD::Action
PLMD::calculateNumericalDerivatives(ActionWithValue *a=NULL)	PLMD::Action	virtual
PLMD::ActionWithArguments::calculateNumericalDerivatives(ActionWithValue *a=NULL)	PLMD::ActionWithArguments	virtual
checkFieldsAllowed()	PLMD::ActionWithValue	inlinevirtual
checkNeedsGradients() const	PLMD::bias::MetaD	inlinevirtual
PLMD::checkNumericalDerivatives() const	PLMD::Action	inlinevirtual
PLMD::ActionWithValue::checkNumericalDerivatives() const	PLMD::ActionWithValue	inlinevirtual
checkRead()	PLMD::Action
checkUpdate() const	PLMD::Action
cite(const std::string &s)	PLMD::Action
clearDependencies()	PLMD::Action
clearDerivatives()	PLMD::ActionWithValue	virtual
clearInputForces()	PLMD::ActionWithValue
clearOptions()	PLMD::Action	virtual
comm	PLMD::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::ActionWithValue	static
computeReweightingFactor()	PLMD::bias::MetaD	private
copyOutput(const std::string &name) const	PLMD::ActionWithValue
copyOutput(const unsigned &n) const	PLMD::ActionWithValue
deactivate()	PLMD::Action	inlinevirtual
Dependencies typedef	PLMD::Action
difference(int, double, double) const	PLMD::ActionWithArguments	inline
doInt_	PLMD::bias::MetaD	private
doNotCalculateDerivatives() const	PLMD::ActionWithValue	inline
dp_	PLMD::bias::MetaD	private
error(const std::string &msg) const	PLMD::Action
evaluateGaussian(const vector< double > &, const Gaussian &, double *der=NULL)	PLMD::bias::MetaD	private
exists(const std::string &name) const	PLMD::ActionWithValue
exit(int c=0)	PLMD::Action
expandArgKeywordInPDB(PDB &pdb)	PLMD::ActionWithArguments	protected
ExtGrid_	PLMD::bias::MetaD	private
fclose(FILE *fp)	PLMD::Action
fflush()	PLMD::Action
files	PLMD::Action
files_iterator typedef	PLMD::Action
finiteDifferenceGaussian(const vector< double > &, const Gaussian &)	PLMD::bias::MetaD	private
flexbin	PLMD::bias::MetaD	private
fmt	PLMD::bias::MetaD	private
fopen(const char *path, const char *mode)	PLMD::Action
getArgument(const unsigned n) const	PLMD::ActionWithArguments	inline
getArguments() const	PLMD::ActionWithArguments	inline
getBiasAndDerivatives(const vector< double > &, double *der=NULL)	PLMD::bias::MetaD	private
getComponentsList() const	PLMD::ActionWithValue
getComponentsVector() const	PLMD::ActionWithValue
getDependencies() const	PLMD::Action	inline
getDocumentation() const	PLMD::Action	virtual
getExchangeStep() const	PLMD::Action
getGaussianNormalization(const Gaussian &)	PLMD::bias::MetaD	private
getGaussianSupport(const Gaussian &)	PLMD::bias::MetaD	private
getHeight(const vector< double > &)	PLMD::bias::MetaD	private
getLabel() const	PLMD::Action	inline
getName() const	PLMD::Action	inline
getNumberOfArguments() const	PLMD::ActionWithArguments	inline
getNumberOfComponents() const	PLMD::ActionWithValue	inline
getNumberOfDerivatives()	PLMD::bias::Bias	inlinevirtual
getOutputQuantity(const unsigned j) const	PLMD::ActionWithValue	inline
getOutputQuantity(const std::string &name) const	PLMD::ActionWithValue	inline
getPntrToArgument(const unsigned n)	PLMD::ActionWithArguments	inline
getPntrToComponent(int i)	PLMD::ActionWithValue	protected
getPntrToComponent(const std::string &name)	PLMD::ActionWithValue	protected
getPntrToValue()	PLMD::ActionWithValue	protected
getProjection(unsigned i, unsigned j) const	PLMD::ActionWithArguments
getRestart() const	PLMD::Action	inline
getStep() const	PLMD::Action
getStride() const	PLMD::ActionPilot	protected
getTime() const	PLMD::Action
getTimeStep() const	PLMD::Action
grid_	PLMD::bias::MetaD	private
gridfile_	PLMD::bias::MetaD	private
gridfilename_	PLMD::bias::MetaD	private
gridreadfilename_	PLMD::bias::MetaD	private
hasextgrid_	PLMD::bias::MetaD	private
height0_	PLMD::bias::MetaD	private
hills_	PLMD::bias::MetaD	private
hillsOfile_	PLMD::bias::MetaD	private
ifiles	PLMD::bias::MetaD	private
ifilesnames	PLMD::bias::MetaD	private
interpretArgumentList(const std::vector< std::string > &c, std::vector< Value * > &arg)	PLMD::ActionWithArguments
isActive() const	PLMD::Action	inline
isFirstStep	PLMD::bias::MetaD	private
isOptionOn(const std::string &s) const	PLMD::Action	inline
kbt_	PLMD::bias::MetaD	private
keywords	PLMD::Action
last_step_warn_grid	PLMD::bias::MetaD	private
PLMD::lockRequests()	PLMD::Action	inlinevirtual
PLMD::ActionWithArguments::lockRequests()	PLMD::ActionWithArguments	inlinevirtual
log	PLMD::Action
lowI_	PLMD::bias::MetaD	private
MetaD(const ActionOptions &)	PLMD::bias::MetaD	explicit
multi_sim_comm	PLMD::Action
mw_dir_	PLMD::bias::MetaD	private
mw_id_	PLMD::bias::MetaD	private
mw_n_	PLMD::bias::MetaD	private
mw_rstride_	PLMD::bias::MetaD	private
noAnalyticalDerivatives(Keywords &keys)	PLMD::ActionWithValue	static
onStep() const	PLMD::ActionPilot
parse(const std::string &key, T &t)	PLMD::Action
parseArgumentList(const std::string &key, 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
plumed	PLMD::Action
prepare()	PLMD::Action	virtual
readAtomsFromPDB(const PDB &)	PLMD::Action	inlinevirtual
readChunkOfGaussians(IFile *ifile, unsigned n)	PLMD::bias::MetaD	private
readGaussians(IFile *)	PLMD::bias::MetaD	private
registerKeywords(Keywords &keys)	PLMD::bias::MetaD	static
requestArguments(const std::vector< Value * > &arg)	PLMD::ActionWithArguments
resetOutputForces()	PLMD::bias::Bias	inlineprotected
reweight_factor	PLMD::bias::MetaD	private
rewf_grid_	PLMD::bias::MetaD	private
rewf_ustride_	PLMD::bias::MetaD	private
runFinalJobs()	PLMD::Action	inlinevirtual
scanOneHill(IFile *ifile, vector< Value > &v, vector< double > &center, vector< double > &sigma, double &height, bool &multivariate)	PLMD::bias::MetaD	private
setGradientsIfNeeded()	PLMD::ActionWithValue
setNotPeriodic()	PLMD::ActionWithValue
setOption(const std::string &s)	PLMD::Action	virtual
setOutputForce(int i, double g)	PLMD::bias::Bias	inlineprotected
setPeriodic(const std::string &min, const std::string &max)	PLMD::ActionWithValue
setValue(const double &d)	PLMD::ActionWithValue	inlineprotected
setValue(Value *, double)	PLMD::ActionWithValue
sigma0_	PLMD::bias::MetaD	private
sigma0max_	PLMD::bias::MetaD	private
sigma0min_	PLMD::bias::MetaD	private
storeOldGrids_	PLMD::bias::MetaD	private
stride_	PLMD::bias::MetaD	private
turnOnDerivatives()	PLMD::bias::Bias	virtual
PLMD::unlockRequests()	PLMD::Action	inlinevirtual
PLMD::ActionWithArguments::unlockRequests()	PLMD::ActionWithArguments	inlinevirtual
update()	PLMD::bias::MetaD	virtual
uppI_	PLMD::bias::MetaD	private
useCustomisableComponents(Keywords &keys)	PLMD::ActionWithValue	static
useNumericalDerivatives()	PLMD::ActionWithValue	inline
walkers_mpi	PLMD::bias::MetaD	private
warning(const std::string &msg)	PLMD::Action
welltemp_	PLMD::bias::MetaD	private
wgridstride_	PLMD::bias::MetaD	private
work_	PLMD::bias::MetaD	private
writeGaussian(const Gaussian &, OFile &)	PLMD::bias::MetaD	private
~Action()	PLMD::Action	virtual
~ActionWithArguments()	PLMD::ActionWithArguments	inlinevirtual
~ActionWithValue()	PLMD::ActionWithValue
~MetaD()	PLMD::bias::MetaD