Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
PLMD::isdb::Metainference Class Reference

Provides the keyword METAINFERENCE More...

Inheritance diagram for PLMD::isdb::Metainference:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Metainference (const ActionOptions &)
 
 ~Metainference ()
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name)
 Add a value with a name like label.name. More...
 
void addComponentWithDerivatives (const std::string &name)
 Add a value with a name like label.name that has derivatives. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) More...
 
void addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void apply ()
 Apply an Action. More...
 
virtual void beforeUpdate ()
 Before Update. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. More...
 
void calculate ()
 Calculate an Action. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Calculate the numerical derivatives N.B. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
virtual void checkFieldsAllowed ()
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void componentIsNotPeriodic (const std::string &name)
 Set your value component to have no periodicity. More...
 
void componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
virtual void deactivate ()
 Set action to inactive. More...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
virtual const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. More...
 
std::string getComponentsList () const
 get a string that contains all the available components More...
 
std::vector< std::string > getComponentsVector () const
 get a vector that contains the label for all the components More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual std::string getDocumentation () const
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned getNumberOfDerivatives ()
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
double getOutputQuantity (const std::string &name) const
 Get the value with a specific name (N.B. if there is no such value this returns zero) More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long int getStep () const
 Return the present timestep. More...
 
int getStride () const
 Get the stride. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
void interpretArgumentList (const std::vector< std::string > &c, std::vector< Value *> &arg)
 Convert a list of argument names into a list of pointers to the values. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
void lockRequests ()
 
virtual void lockRequests ()
 
virtual bool onStep () const
 Check if the action is active on this step. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
void parseArgumentList (const std::string &key, std::vector< Value *> &args)
 Parse a list of arguments. More...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
 Parse a numbered list of arguments. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
template<class T >
bool parseNumbered (const std::string &key, const int no, T &t)
 Parse one numbered keyword as generic type. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
virtual void prepare ()
 Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
 
virtual void readAtomsFromPDB (const PDB &)
 This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...
 
void requestArguments (const std::vector< Value *> &arg)
 Setup the dependencies. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
void setValue (Value *, double)
 Set the value. More...
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
void unlockRequests ()
 
virtual void unlockRequests ()
 
void update ()
 Update. More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 

Static Public Member Functions

static void componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &keys)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

Communicatorcomm
 
std::set< FILE * > files
 
const Keywordskeywords
 
Loglog
 Reference to the log stream. More...
 
Communicatormulti_sim_comm
 
PlumedMainplumed
 Reference to main plumed object. More...
 

Protected Member Functions

void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void setBias (double bias)
 set the value of the bias More...
 
void setOutputForce (int i, double f)
 set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 

Private Types

enum  {
  GAUSS, MGAUSS, OUTLIERS, MOUTLIERS,
  GENERIC
}
 
enum  { LIKE_GAUSS, LIKE_LOGN }
 
enum  { SC_GAUSS, SC_FLAT }
 

Private Member Functions

void do_regression_zero (const vector< double > &mean)
 
void doMonteCarlo (const vector< double > &mean)
 
void get_sigma_mean (const unsigned iselect, const double fact, const double var_fact, const vector< double > &mean)
 
void get_weights (const unsigned iselect, double &fact, double &var_fact)
 
double getEnergyForceGJ (const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)
 
double getEnergyForceGJE (const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)
 
double getEnergyForceMIGEN (const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)
 
double getEnergyForceSP (const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)
 
double getEnergyForceSPE (const vector< double > &mean, const vector< double > &dmean_x, const vector< double > &dmean_b)
 
double getEnergyGJ (const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)
 
double getEnergyGJE (const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)
 
double getEnergyMIGEN (const vector< double > &mean, const vector< double > &ftilde, const vector< double > &sigma, const double scale, const double offset)
 
double getEnergySP (const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)
 
double getEnergySPE (const vector< double > &mean, const vector< double > &sigma, const double scale, const double offset)
 
void replica_averaging (const double fact, std::vector< double > &mean, std::vector< double > &dmean_b)
 
void writeStatus ()
 

Private Attributes

vector< vector< double > > average_weights_
 
unsigned average_weights_stride_
 
double Dftilde_
 
unsigned do_optsigmamean_
 
bool do_reweight_
 
double Doffset_
 
bool dooffset_
 
bool doregres_zero_
 
bool doscale_
 
double Dscale_
 
vector< double > Dsigma_
 
bool firstTime
 
vector< bool > firstTimeW
 
vector< double > ftilde_
 
unsigned gen_likelihood_
 
double kbt_
 
bool master
 
long unsigned MCaccept_
 
long unsigned MCacceptFT_
 
long unsigned MCacceptScale_
 
unsigned MCchunksize_
 
unsigned MCsteps_
 
unsigned MCstride_
 
long unsigned MCtrial_
 
unsigned narg
 
unsigned noise_type_
 
int nregres_zero_
 
unsigned nrep_
 
double offset_
 
double offset_max_
 
double offset_min_
 
double offset_mu_
 
unsigned offset_prior_
 
unsigned optsigmamean_stride_
 
vector< double > parameters
 
vector< Randomrandom
 
unsigned replica_
 
double scale_
 
double scale_max_
 
double scale_min_
 
double scale_mu_
 
unsigned scale_prior_
 
string selector_
 
OFile sfile_
 
vector< double > sigma_
 
vector< double > sigma_max_
 
vector< double > sigma_mean2_
 
vector< vector< vector< double > > > sigma_mean2_last_
 
vector< double > sigma_min_
 
ValuevalueAccept
 
ValuevalueAcceptFT
 
ValuevalueAcceptScale
 
vector< Value * > valueFtilde
 
ValuevalueOffset
 
ValuevalueScale
 
vector< Value * > valueSigma
 
vector< Value * > valueSigmaMean
 
unsigned write_stride_
 

Detailed Description

Provides the keyword METAINFERENCE

Member Typedef Documentation

◆ Dependencies

typedef std::vector<Action*> PLMD::Action::Dependencies
inherited

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
private
Enumerator
GAUSS 
MGAUSS 
OUTLIERS 
MOUTLIERS 
GENERIC 

◆ anonymous enum

anonymous enum
private
Enumerator
LIKE_GAUSS 
LIKE_LOGN 

◆ anonymous enum

anonymous enum
private
Enumerator
SC_GAUSS 
SC_FLAT 

Constructor & Destructor Documentation

◆ Metainference()

PLMD::isdb::Metainference::Metainference ( const ActionOptions ao)
explicit

◆ ~Metainference()

PLMD::isdb::Metainference::~Metainference ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name)
inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name)
inherited

Add a value with a name like label.name that has derivatives.

◆ addDependency()

void PLMD::Action::addDependency ( Action action)
inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > &  forces)
inherited

Add forces to arguments (used in apply)

◆ addValue()

void PLMD::ActionWithValue::addValue ( )
inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )
inherited

Add a value with the name label that has derivatives.

◆ apply()

void PLMD::bias::Bias::apply ( )
virtualinherited

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

Reimplemented in PLMD::ves::VesBias.

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )
inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc ( int  i,
double  d1 
) const
inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ calculate()

void PLMD::isdb::Metainference::calculate ( )
virtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

Implements PLMD::Action.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB pdb)
inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives() [1/2]

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, and PLMD::mapping::Mapping.

◆ calculateNumericalDerivatives() [2/2]

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )
inlinevirtualinherited

Reimplemented in PLMD::piv::PIV, and PLMD::colvar::ContactMap.

◆ checkNeedsGradients()

virtual bool PLMD::Action::checkNeedsGradients ( ) const
inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const
inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const
inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )
inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const
inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string &  s)
inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name)
inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic ( const std::string &  name,
const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords keys)
staticinherited

Puts a message into the manual that the components always output.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string &  name) const
inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned &  n) const
inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ difference()

double PLMD::ActionWithArguments::difference ( int  i,
double  d1,
double  d2 
) const
inlineinherited

Takes the difference taking into account pbc for arg i.

◆ do_regression_zero()

void PLMD::isdb::Metainference::do_regression_zero ( const vector< double > &  mean)
private

◆ doMonteCarlo()

void PLMD::isdb::Metainference::doMonteCarlo ( const vector< double > &  mean)
private

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const
inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ error()

void PLMD::Action::error ( const std::string &  msg) const
inherited

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string &  name) const
inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

void PLMD::Action::exit ( int  c = 0)
inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( PDB pdb)
protectedinherited

This changes the arg keyword in the pdb file.

◆ fclose()

int PLMD::Action::fclose ( FILE *  fp)
inherited

Closes a file opened with Action::fclose().

◆ fflush()

void PLMD::Action::fflush ( )
inherited

Tell to the Action to flush open files.

◆ fopen()

FILE * PLMD::Action::fopen ( const char *  path,
const char *  mode 
)
inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

  • When opened for writing, processors other than the one with rank 0 just open /dev/null
  • PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

◆ get_sigma_mean()

void PLMD::isdb::Metainference::get_sigma_mean ( const unsigned  iselect,
const double  fact,
const double  var_fact,
const vector< double > &  mean 
)
private

◆ get_weights()

void PLMD::isdb::Metainference::get_weights ( const unsigned  iselect,
double &  fact,
double &  var_fact 
)
private

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned  n) const
inlineinherited

Returns the value of an argument.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const
inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const
inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const
inherited

get a vector that contains the label for all the components

◆ getCPT()

bool PLMD::Action::getCPT ( ) const
inherited

Return true if we are doing at a checkpoint step.

◆ getDependencies()

const Dependencies& PLMD::Action::getDependencies ( ) const
inlineinherited

Return dependencies.

◆ getDocumentation()

std::string PLMD::Action::getDocumentation ( ) const
virtualinherited

◆ getEnergyForceGJ()

double PLMD::isdb::Metainference::getEnergyForceGJ ( const vector< double > &  mean,
const vector< double > &  dmean_x,
const vector< double > &  dmean_b 
)
private

◆ getEnergyForceGJE()

double PLMD::isdb::Metainference::getEnergyForceGJE ( const vector< double > &  mean,
const vector< double > &  dmean_x,
const vector< double > &  dmean_b 
)
private

◆ getEnergyForceMIGEN()

double PLMD::isdb::Metainference::getEnergyForceMIGEN ( const vector< double > &  mean,
const vector< double > &  dmean_x,
const vector< double > &  dmean_b 
)
private

◆ getEnergyForceSP()

double PLMD::isdb::Metainference::getEnergyForceSP ( const vector< double > &  mean,
const vector< double > &  dmean_x,
const vector< double > &  dmean_b 
)
private

◆ getEnergyForceSPE()

double PLMD::isdb::Metainference::getEnergyForceSPE ( const vector< double > &  mean,
const vector< double > &  dmean_x,
const vector< double > &  dmean_b 
)
private

◆ getEnergyGJ()

double PLMD::isdb::Metainference::getEnergyGJ ( const vector< double > &  mean,
const vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergyGJE()

double PLMD::isdb::Metainference::getEnergyGJE ( const vector< double > &  mean,
const vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergyMIGEN()

double PLMD::isdb::Metainference::getEnergyMIGEN ( const vector< double > &  mean,
const vector< double > &  ftilde,
const vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergySP()

double PLMD::isdb::Metainference::getEnergySP ( const vector< double > &  mean,
const vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getEnergySPE()

double PLMD::isdb::Metainference::getEnergySPE ( const vector< double > &  mean,
const vector< double > &  sigma,
const double  scale,
const double  offset 
)
private

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const
inherited

Check if we are on an exchange step.

◆ getKeyword()

std::string PLMD::Action::getKeyword ( const std::string &  key)
inherited

Just read one of the keywords and return the whole thing as a string.

◆ getLabel()

const std::string & PLMD::Action::getLabel ( ) const
inlineinherited

Returns the label.

◆ getName()

const std::string & PLMD::Action::getName ( ) const
inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const
inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const
inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::bias::Bias::getNumberOfDerivatives ( )
inlinevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned  j) const
inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string &  name) const
inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned  n)
inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int  i)
protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string &  name)
protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )
protectedinherited

Get a pointer to the default value.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection ( unsigned  i,
unsigned  j 
) const
inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const
inlineinherited

Return true if we are doing a restart.

◆ getStep()

long int PLMD::Action::getStep ( ) const
inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const
inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const
inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const
inherited

Return the timestep.

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList ( const std::vector< std::string > &  c,
std::vector< Value *> &  arg 
)
inherited

Convert a list of argument names into a list of pointers to the values.

◆ isActive()

bool PLMD::Action::isActive ( ) const
inlineinherited

Check if action is active.

◆ isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string &  s) const
inlineinherited

Check if an option is on.

◆ lockRequests() [1/2]

void PLMD::ActionWithArguments::lockRequests ( )
inlinevirtualinherited

◆ lockRequests() [2/2]

virtual void PLMD::Action::lockRequests ( )
inlinevirtualinherited

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords keys)
staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const
virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

template<class T >
void PLMD::Action::parse ( const std::string &  key,
T &  t 
)
inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

void PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
std::vector< Value *> &  args 
)
inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

bool PLMD::ActionWithArguments::parseArgumentList ( const std::string &  key,
int  i,
std::vector< Value *> &  args 
)
inherited

Parse a numbered list of arguments.

◆ parseFlag()

void PLMD::Action::parseFlag ( const std::string &  key,
bool &  t 
)
inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >
bool PLMD::Action::parseNumbered ( const std::string &  key,
const int  no,
T &  t 
)
inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >
bool PLMD::Action::parseNumberedVector ( const std::string &  key,
const int  no,
std::vector< T > &  t 
)
inherited

Parse a vector with a number.

◆ parseVector()

template<class T >
void PLMD::Action::parseVector ( const std::string &  key,
std::vector< T > &  t 
)
inherited

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )
virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::function::FuncPathMSD, PLMD::isdb::EMMI, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::bias::ReweightTemperature, PLMD::colvar::Energy, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB )
inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

void PLMD::isdb::Metainference::registerKeywords ( Keywords keys)
static

◆ replica_averaging()

void PLMD::isdb::Metainference::replica_averaging ( const double  fact,
std::vector< double > &  mean,
std::vector< double > &  dmean_b 
)
private

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value *> &  arg)
inherited

Setup the dependencies.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )
inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

◆ setBias()

void PLMD::bias::Bias::setBias ( double  bias)
inlineprotectedinherited

set the value of the bias

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

Calculate the gradients and store them for all the values (need for projections)

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited

◆ setOutputForce()

void PLMD::bias::Bias::setOutputForce ( int  i,
double  f 
)
inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ setStride()

void PLMD::ActionPilot::setStride ( const int &  n)
inherited

Set the value of the stride.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double &  d)
inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue ( Value ,
double   
)
inherited

Set the value.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )
inlinevirtualinherited

◆ unlockRequests() [2/2]

virtual void PLMD::Action::unlockRequests ( )
inlinevirtualinherited

◆ update()

void PLMD::isdb::Metainference::update ( )
virtual

Update.

This method is called one time per step. The set of all Actions is updated in forward order.

Reimplemented from PLMD::Action.

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords keys)
staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ warning()

void PLMD::Action::warning ( const std::string &  msg)
inherited

Issue a warning.

◆ writeStatus()

void PLMD::isdb::Metainference::writeStatus ( )
private

Member Data Documentation

◆ average_weights_

vector< vector <double> > PLMD::isdb::Metainference::average_weights_
private

◆ average_weights_stride_

unsigned PLMD::isdb::Metainference::average_weights_stride_
private

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ Dftilde_

double PLMD::isdb::Metainference::Dftilde_
private

◆ do_optsigmamean_

unsigned PLMD::isdb::Metainference::do_optsigmamean_
private

◆ do_reweight_

bool PLMD::isdb::Metainference::do_reweight_
private

◆ Doffset_

double PLMD::isdb::Metainference::Doffset_
private

◆ dooffset_

bool PLMD::isdb::Metainference::dooffset_
private

◆ doregres_zero_

bool PLMD::isdb::Metainference::doregres_zero_
private

◆ doscale_

bool PLMD::isdb::Metainference::doscale_
private

◆ Dscale_

double PLMD::isdb::Metainference::Dscale_
private

◆ Dsigma_

vector<double> PLMD::isdb::Metainference::Dsigma_
private

◆ files

std::set<FILE*> PLMD::Action::files
inherited

◆ firstTime

bool PLMD::isdb::Metainference::firstTime
private

◆ firstTimeW

vector<bool> PLMD::isdb::Metainference::firstTimeW
private

◆ ftilde_

vector<double> PLMD::isdb::Metainference::ftilde_
private

◆ gen_likelihood_

unsigned PLMD::isdb::Metainference::gen_likelihood_
private

◆ kbt_

double PLMD::isdb::Metainference::kbt_
private

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ master

bool PLMD::isdb::Metainference::master
private

◆ MCaccept_

long unsigned PLMD::isdb::Metainference::MCaccept_
private

◆ MCacceptFT_

long unsigned PLMD::isdb::Metainference::MCacceptFT_
private

◆ MCacceptScale_

long unsigned PLMD::isdb::Metainference::MCacceptScale_
private

◆ MCchunksize_

unsigned PLMD::isdb::Metainference::MCchunksize_
private

◆ MCsteps_

unsigned PLMD::isdb::Metainference::MCsteps_
private

◆ MCstride_

unsigned PLMD::isdb::Metainference::MCstride_
private

◆ MCtrial_

long unsigned PLMD::isdb::Metainference::MCtrial_
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ narg

unsigned PLMD::isdb::Metainference::narg
private

◆ noise_type_

unsigned PLMD::isdb::Metainference::noise_type_
private

◆ nregres_zero_

int PLMD::isdb::Metainference::nregres_zero_
private

◆ nrep_

unsigned PLMD::isdb::Metainference::nrep_
private

◆ offset_

double PLMD::isdb::Metainference::offset_
private

◆ offset_max_

double PLMD::isdb::Metainference::offset_max_
private

◆ offset_min_

double PLMD::isdb::Metainference::offset_min_
private

◆ offset_mu_

double PLMD::isdb::Metainference::offset_mu_
private

◆ offset_prior_

unsigned PLMD::isdb::Metainference::offset_prior_
private

◆ optsigmamean_stride_

unsigned PLMD::isdb::Metainference::optsigmamean_stride_
private

◆ parameters

vector<double> PLMD::isdb::Metainference::parameters
private

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ random

vector<Random> PLMD::isdb::Metainference::random
private

◆ replica_

unsigned PLMD::isdb::Metainference::replica_
private

◆ scale_

double PLMD::isdb::Metainference::scale_
private

◆ scale_max_

double PLMD::isdb::Metainference::scale_max_
private

◆ scale_min_

double PLMD::isdb::Metainference::scale_min_
private

◆ scale_mu_

double PLMD::isdb::Metainference::scale_mu_
private

◆ scale_prior_

unsigned PLMD::isdb::Metainference::scale_prior_
private

◆ selector_

string PLMD::isdb::Metainference::selector_
private

◆ sfile_

OFile PLMD::isdb::Metainference::sfile_
private

◆ sigma_

vector<double> PLMD::isdb::Metainference::sigma_
private

◆ sigma_max_

vector<double> PLMD::isdb::Metainference::sigma_max_
private

◆ sigma_mean2_

vector<double> PLMD::isdb::Metainference::sigma_mean2_
private

◆ sigma_mean2_last_

vector< vector < vector <double> > > PLMD::isdb::Metainference::sigma_mean2_last_
private

◆ sigma_min_

vector<double> PLMD::isdb::Metainference::sigma_min_
private

◆ valueAccept

Value* PLMD::isdb::Metainference::valueAccept
private

◆ valueAcceptFT

Value* PLMD::isdb::Metainference::valueAcceptFT
private

◆ valueAcceptScale

Value* PLMD::isdb::Metainference::valueAcceptScale
private

◆ valueFtilde

vector<Value*> PLMD::isdb::Metainference::valueFtilde
private

◆ valueOffset

Value* PLMD::isdb::Metainference::valueOffset
private

◆ valueScale

Value* PLMD::isdb::Metainference::valueScale
private

◆ valueSigma

vector<Value*> PLMD::isdb::Metainference::valueSigma
private

◆ valueSigmaMean

vector<Value*> PLMD::isdb::Metainference::valueSigmaMean
private

◆ write_stride_

unsigned PLMD::isdb::Metainference::write_stride_
private

The documentation for this class was generated from the following file: