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PLMD::bias::MetaD Class Reference

Provides the keyword METAD More...

Inheritance diagram for PLMD::bias::MetaD:
Inheritance graph
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Classes

struct  Gaussian
 
struct  TemperingSpecs
 

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 MetaD (const ActionOptions &)
 
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 () override
 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 () override
 Calculate an Action. More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
void calculateNumericalDerivatives (ActionWithValue *a=NULL) override
 Calculate the numerical derivatives N.B. More...
 
virtual void checkFieldsAllowed ()
 
bool checkNeedsGradients () const override
 Check if the action needs gradient. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. 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 () override
 
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...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. 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...
 
virtual void lockRequests ()
 
void lockRequests () override
 
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...
 
bool parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
 Parse a numbered list of arguments. More...
 
void parseArgumentList (const std::string &key, std::vector< Value * > &args)
 Parse a 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...
 
void requestExtraDependencies (const std::vector< Value * > &extra)
 
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...
 
virtual void unlockRequests ()
 
void unlockRequests () override
 
void update () override
 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 (const PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. 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 Member Functions

void addGaussian (const Gaussian &)
 
void computeReweightingFactor ()
 
double evaluateGaussian (const std::vector< double > &, const Gaussian &)
 
double evaluateGaussianAndDerivatives (const std::vector< double > &, const Gaussian &, std::vector< double > &, std::vector< double > &)
 
double getBias (const std::vector< double > &)
 
double getBiasAndDerivatives (const std::vector< double > &, std::vector< double > &)
 
int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 
double getGaussianNormalization (const Gaussian &)
 
std::vector< unsigned > getGaussianSupport (const Gaussian &)
 
double getHeight (const std::vector< double > &)
 
double getTransitionBarrierBias ()
 
void logTemperingSpecs (const TemperingSpecs &t_specs)
 
void noStretchWarning ()
 
void readGaussians (IFile *)
 
void readTemperingSpecs (TemperingSpecs &t_specs)
 
bool scanOneHill (IFile *ifile, std::vector< Value > &v, std::vector< double > &center, std::vector< double > &sigma, double &height, bool &multivariate)
 takes a pointer to the file and a template std::string with values v and gives back the next center, sigma and height More...
 
void temperHeight (double &height, const TemperingSpecs &t_specs, const double tempering_bias)
 
void updateFrequencyAdaptiveStride ()
 
void updateNlist ()
 
void writeGaussian (const Gaussian &, OFile &)
 

Static Private Member Functions

static void registerTemperingKeywords (const std::string &name_stem, const std::string &name, Keywords &keys)
 

Private Attributes

double acc_
 
double acc_restart_mean_
 
bool acceleration_
 
bool active
 Switch to activate Action on this step. More...
 
int adaptive_
 
Dependencies after
 Actions on which this Action depends. More...
 
std::vector< Value * > arguments
 
double biasf_
 
std::unique_ptr< GridBaseBiasGrid_
 
bool calc_max_bias_
 
bool calc_rct_
 
bool calc_transition_bias_
 
bool calc_work_
 
int current_stride_
 
double dampfactor_
 
bool doCheckPoint
 
bool doInt_
 
int fa_max_stride_
 
double fa_min_acceleration_
 
int fa_update_frequency_
 
std::unique_ptr< FlexibleBinflexbin_
 
bool flying_
 
std::string fmt_
 
bool freq_adaptive_
 
bool grid_
 
OFile gridfile_
 
double height0_
 
std::vector< Gaussianhills_
 
OFile hillsOfile_
 
std::vector< std::unique_ptr< IFile > > ifiles_
 
std::vector< std::string > ifilesnames_
 
bool isFirstStep_
 
double kbt_
 
std::string label
 Label of the Action, as set with LABEL= in the plumed.dat file. More...
 
std::vector< std::string > line
 Directive line. More...
 
bool lockRequestArguments
 
double lowI_
 
double max_bias_
 
unsigned mpi_nw_
 
std::string mw_dir_
 
int mw_id_
 
int mw_n_
 
int mw_rstride_
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
bool nlist_
 
std::vector< double > nlist_center_
 
std::vector< double > nlist_dev2_
 
std::vector< Gaussiannlist_hills_
 
std::array< double, 2 > nlist_param_
 
unsigned nlist_steps_
 
bool nlist_update_
 
bool noderiv
 Are we skipping the calculation of the derivatives. More...
 
bool noStretchWarningDone =false
 
bool numericalDerivatives
 Are we using numerical derivatives to differentiate. More...
 
std::set< std::string > options
 Option that you might have enabled. More...
 
std::vector< double > outputForces
 the vector of the forces More...
 
unsigned rct_ustride_
 
int replica_index
 
bool restart
 
double reweight_factor_
 
std::vector< double > sigma0_
 
std::vector< double > sigma0max_
 
std::vector< double > sigma0min_
 
bool storeOldGrids_
 
double stretchA =1.0
 
double stretchB =0.0
 
int stride
 
int stride_
 
std::string targetfilename_
 
std::unique_ptr< GridBaseTargetGrid_
 
double transition_bias_
 
std::vector< std::vector< double > > transitionwells_
 
struct TemperingSpecs tt_specs_
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
double uppI_
 
ValuevalueBias
 the pointer to the bias component More...
 
std::vector< std::unique_ptr< Value > > values
 An array containing the values for this action. More...
 
bool walkers_mpi_
 
bool welltemp_
 
int wgridstride_
 
double work_
 

Static Private Attributes

static const size_t n_tempering_options_ = 1
 
static const std::string tempering_names_ [1][2] = {{"TT", "transition tempered"}}
 

Detailed Description

Provides the keyword METAD

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ MetaD()

PLMD::bias::MetaD::MetaD ( const ActionOptions ao)
explicit

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)

◆ addGaussian()

void PLMD::bias::MetaD::addGaussian ( const Gaussian hill)
private

◆ 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 ( )
overridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ 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::bias::MetaD::calculate ( )
overridevirtual

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

◆ calculateNumericalDerivatives() [2/2]

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

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::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.

◆ checkFieldsAllowed()

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

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

◆ checkNeedsGradients()

bool PLMD::bias::MetaD::checkNeedsGradients ( ) const
overridevirtual

Check if the action needs gradient.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [1/2]

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

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ 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.

◆ computeReweightingFactor()

void PLMD::bias::MetaD::computeReweightingFactor ( )
private

◆ 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.

◆ 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.

◆ evaluateGaussian()

double PLMD::bias::MetaD::evaluateGaussian ( const std::vector< double > &  cv,
const Gaussian hill 
)
private

◆ evaluateGaussianAndDerivatives()

double PLMD::bias::MetaD::evaluateGaussianAndDerivatives ( const std::vector< double > &  cv,
const Gaussian hill,
std::vector< double > &  der,
std::vector< double > &  dp_ 
)
private

◆ 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 ( const 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)

◆ 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.

◆ getBias()

double PLMD::bias::MetaD::getBias ( const std::vector< double > &  cv)
private

◆ getBiasAndDerivatives()

double PLMD::bias::MetaD::getBiasAndDerivatives ( const std::vector< double > &  cv,
std::vector< double > &  der 
)
private

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string &  name) const
privateinherited

Return the index for the component named name.

◆ 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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getGaussianNormalization()

double PLMD::bias::MetaD::getGaussianNormalization ( const Gaussian hill)
private

◆ getGaussianSupport()

std::vector< unsigned > PLMD::bias::MetaD::getGaussianSupport ( const Gaussian hill)
private

◆ getHeight()

double PLMD::bias::MetaD::getHeight ( const std::vector< double > &  cv)
private

◆ 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 ( )
inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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)

◆ getOutputQuantity() [2/2]

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

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

◆ getPntrToArgument()

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

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the component by index.

◆ 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.

◆ getTransitionBarrierBias()

double PLMD::bias::MetaD::getTransitionBarrierBias ( )
private

◆ 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]

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

◆ lockRequests() [2/2]

void PLMD::ActionWithArguments::lockRequests ( )
inlineoverridevirtualinherited

◆ logTemperingSpecs()

void PLMD::bias::MetaD::logTemperingSpecs ( const TemperingSpecs t_specs)
private

◆ 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.

◆ noStretchWarning()

void PLMD::bias::MetaD::noStretchWarning ( )
inlineprivate

◆ 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]

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

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

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

Parse a 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::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ 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.

◆ readGaussians()

void PLMD::bias::MetaD::readGaussians ( IFile ifile)
private

◆ readTemperingSpecs()

void PLMD::bias::MetaD::readTemperingSpecs ( TemperingSpecs t_specs)
private

◆ registerKeywords()

void PLMD::bias::MetaD::registerKeywords ( Keywords keys)
static

◆ registerTemperingKeywords()

void PLMD::bias::MetaD::registerTemperingKeywords ( const std::string &  name_stem,
const std::string &  name,
Keywords keys 
)
staticprivate

◆ requestArguments()

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

Setup the dependencies.

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > &  extra)
inherited

◆ 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.

◆ scanOneHill()

bool PLMD::bias::MetaD::scanOneHill ( IFile ifile,
std::vector< Value > &  v,
std::vector< double > &  center,
std::vector< double > &  sigma,
double &  height,
bool &  multivariate 
)
private

takes a pointer to the file and a template std::string with values v and gives back the next center, sigma and height

◆ 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.

◆ temperHeight()

void PLMD::bias::MetaD::temperHeight ( double &  height,
const TemperingSpecs t_specs,
const double  tempering_bias 
)
private

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests() [1/2]

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

◆ unlockRequests() [2/2]

void PLMD::ActionWithArguments::unlockRequests ( )
inlineoverridevirtualinherited

◆ update()

void PLMD::bias::MetaD::update ( )
overridevirtual

Update.

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

Reimplemented from PLMD::Action.

◆ updateFrequencyAdaptiveStride()

void PLMD::bias::MetaD::updateFrequencyAdaptiveStride ( )
private

◆ updateNlist()

void PLMD::bias::MetaD::updateNlist ( )
private

◆ 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.

◆ writeGaussian()

void PLMD::bias::MetaD::writeGaussian ( const Gaussian hill,
OFile file 
)
private

Member Data Documentation

◆ acc_

double PLMD::bias::MetaD::acc_
private

◆ acc_restart_mean_

double PLMD::bias::MetaD::acc_restart_mean_
private

◆ acceleration_

bool PLMD::bias::MetaD::acceleration_
private

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ adaptive_

int PLMD::bias::MetaD::adaptive_
private

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments
privateinherited

◆ biasf_

double PLMD::bias::MetaD::biasf_
private

◆ BiasGrid_

std::unique_ptr<GridBase> PLMD::bias::MetaD::BiasGrid_
private

◆ calc_max_bias_

bool PLMD::bias::MetaD::calc_max_bias_
private

◆ calc_rct_

bool PLMD::bias::MetaD::calc_rct_
private

◆ calc_transition_bias_

bool PLMD::bias::MetaD::calc_transition_bias_
private

◆ calc_work_

bool PLMD::bias::MetaD::calc_work_
private

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ current_stride_

int PLMD::bias::MetaD::current_stride_
private

◆ dampfactor_

double PLMD::bias::MetaD::dampfactor_
private

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ doInt_

bool PLMD::bias::MetaD::doInt_
private

◆ fa_max_stride_

int PLMD::bias::MetaD::fa_max_stride_
private

◆ fa_min_acceleration_

double PLMD::bias::MetaD::fa_min_acceleration_
private

◆ fa_update_frequency_

int PLMD::bias::MetaD::fa_update_frequency_
private

◆ files

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

◆ flexbin_

std::unique_ptr<FlexibleBin> PLMD::bias::MetaD::flexbin_
private

◆ flying_

bool PLMD::bias::MetaD::flying_
private

◆ fmt_

std::string PLMD::bias::MetaD::fmt_
private

◆ freq_adaptive_

bool PLMD::bias::MetaD::freq_adaptive_
private

◆ grid_

bool PLMD::bias::MetaD::grid_
private

◆ gridfile_

OFile PLMD::bias::MetaD::gridfile_
private

◆ height0_

double PLMD::bias::MetaD::height0_
private

◆ hills_

std::vector<Gaussian> PLMD::bias::MetaD::hills_
private

◆ hillsOfile_

OFile PLMD::bias::MetaD::hillsOfile_
private

◆ ifiles_

std::vector<std::unique_ptr<IFile> > PLMD::bias::MetaD::ifiles_
private

◆ ifilesnames_

std::vector<std::string> PLMD::bias::MetaD::ifilesnames_
private

◆ isFirstStep_

bool PLMD::bias::MetaD::isFirstStep_
private

◆ kbt_

double PLMD::bias::MetaD::kbt_
private

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ label

std::string PLMD::Action::label
privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line
privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments
privateinherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ lowI_

double PLMD::bias::MetaD::lowI_
private

◆ max_bias_

double PLMD::bias::MetaD::max_bias_
private

◆ mpi_nw_

unsigned PLMD::bias::MetaD::mpi_nw_
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ mw_dir_

std::string PLMD::bias::MetaD::mw_dir_
private

◆ mw_id_

int PLMD::bias::MetaD::mw_id_
private

◆ mw_n_

int PLMD::bias::MetaD::mw_n_
private

◆ mw_rstride_

int PLMD::bias::MetaD::mw_rstride_
private

◆ n_tempering_options_

const size_t PLMD::bias::MetaD::n_tempering_options_ = 1
staticprivate

◆ name

const std::string PLMD::Action::name
privateinherited

Name of the directive in the plumed.dat file.

◆ nlist_

bool PLMD::bias::MetaD::nlist_
private

◆ nlist_center_

std::vector<double> PLMD::bias::MetaD::nlist_center_
private

◆ nlist_dev2_

std::vector<double> PLMD::bias::MetaD::nlist_dev2_
private

◆ nlist_hills_

std::vector<Gaussian> PLMD::bias::MetaD::nlist_hills_
private

◆ nlist_param_

std::array<double,2> PLMD::bias::MetaD::nlist_param_
private

◆ nlist_steps_

unsigned PLMD::bias::MetaD::nlist_steps_
private

◆ nlist_update_

bool PLMD::bias::MetaD::nlist_update_
private

◆ noderiv

bool PLMD::ActionWithValue::noderiv
privateinherited

Are we skipping the calculation of the derivatives.

◆ noStretchWarningDone

bool PLMD::bias::MetaD::noStretchWarningDone =false
private

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives
privateinherited

Are we using numerical derivatives to differentiate.

◆ options

std::set<std::string> PLMD::Action::options
privateinherited

Option that you might have enabled.

◆ outputForces

std::vector<double> PLMD::bias::Bias::outputForces
privateinherited

the vector of the forces

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ rct_ustride_

unsigned PLMD::bias::MetaD::rct_ustride_
private

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ reweight_factor_

double PLMD::bias::MetaD::reweight_factor_
private

◆ sigma0_

std::vector<double> PLMD::bias::MetaD::sigma0_
private

◆ sigma0max_

std::vector<double> PLMD::bias::MetaD::sigma0max_
private

◆ sigma0min_

std::vector<double> PLMD::bias::MetaD::sigma0min_
private

◆ storeOldGrids_

bool PLMD::bias::MetaD::storeOldGrids_
private

◆ stretchA

double PLMD::bias::MetaD::stretchA =1.0
private

◆ stretchB

double PLMD::bias::MetaD::stretchB =0.0
private

◆ stride

int PLMD::ActionPilot::stride
privateinherited

◆ stride_

int PLMD::bias::MetaD::stride_
private

◆ targetfilename_

std::string PLMD::bias::MetaD::targetfilename_
private

◆ TargetGrid_

std::unique_ptr<GridBase> PLMD::bias::MetaD::TargetGrid_
private

◆ tempering_names_

const std::string PLMD::bias::MetaD::tempering_names_ = {{"TT", "transition tempered"}}
staticprivate

◆ transition_bias_

double PLMD::bias::MetaD::transition_bias_
private

◆ transitionwells_

std::vector<std::vector<double> > PLMD::bias::MetaD::transitionwells_
private

◆ tt_specs_

struct TemperingSpecs PLMD::bias::MetaD::tt_specs_
private

◆ update_from

double PLMD::Action::update_from
privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until
privateinherited

Update only until this time.

◆ uppI_

double PLMD::bias::MetaD::uppI_
private

◆ valueBias

Value* PLMD::bias::Bias::valueBias
privateinherited

the pointer to the bias component

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values
privateinherited

An array containing the values for this action.

◆ walkers_mpi_

bool PLMD::bias::MetaD::walkers_mpi_
private

◆ welltemp_

bool PLMD::bias::MetaD::welltemp_
private

◆ wgridstride_

int PLMD::bias::MetaD::wgridstride_
private

◆ work_

double PLMD::bias::MetaD::work_
private

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