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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 &)
 
 ~MetaD ()
 
void calculate ()
 Calculate an Action. More...
 
void update ()
 Update. More...
 
bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
void apply ()
 Apply an Action. More...
 
unsigned getNumberOfDerivatives ()
 
virtual bool onStep () const
 Check if the action is active on this step. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
int getStride () const
 Get the stride. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
long int getStep () const
 Return the present timestep. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. 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 >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
template<class T >
bool parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
 Parse a vector with a number. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
void checkRead ()
 Check if Action was properly read. 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 lockRequests ()
 
void lockRequests ()
 
virtual void unlockRequests ()
 
void unlockRequests ()
 
virtual void beforeUpdate ()
 Before Update. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
virtual std::string getDocumentation () const
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
virtual void activate ()
 Set action to active. More...
 
virtual void setOption (const std::string &s)
 
virtual void clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Perform calculation using numerical derivatives N.B. More...
 
virtual void calculateNumericalDerivatives (ActionWithValue *a=NULL)
 Calculate the numerical derivatives N.B. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void calculateFromPDB (const PDB &)
 Calculate the action given a pdb file as input. 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...
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. 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 setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setValue (Value *, double)
 Set the value. 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 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...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
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...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. 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...
 
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...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
virtual void checkFieldsAllowed ()
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
double getProjection (unsigned i, unsigned j) const
 Get the scalar product between the gradients of two variables. More...
 
double getArgument (const unsigned n) const
 Returns the value of an argument. More...
 
ValuegetPntrToArgument (const unsigned n)
 Return a pointer to specific argument. More...
 
virtual unsigned getNumberOfArguments () const
 Returns the number of arguments. More...
 
double difference (int, double, double) const
 Takes the difference taking into account pbc for arg i. More...
 
double bringBackInPbc (int i, double d1) const
 Takes one value and brings it back into the pbc of argument i. 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 requestArguments (const std::vector< Value *> &arg)
 Setup the dependencies. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) More...
 
const std::vector< Value * > & getArguments () const
 Returns an array of pointers to the arguments. 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...
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 
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 componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

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

Protected Member Functions

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 setBias (double bias)
 set the value of the bias More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void setValue (const double &d)
 Set the default value (the one without name) 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...
 
void expandArgKeywordInPDB (PDB &pdb)
 This changes the arg keyword in the pdb file. More...
 

Private Member Functions

void readTemperingSpecs (TemperingSpecs &t_specs)
 
void logTemperingSpecs (const TemperingSpecs &t_specs)
 
void readGaussians (IFile *)
 
bool readChunkOfGaussians (IFile *ifile, unsigned n)
 
void writeGaussian (const Gaussian &, OFile &)
 
void addGaussian (const Gaussian &)
 
double getHeight (const vector< double > &)
 
void temperHeight (double &height, const TemperingSpecs &t_specs, const double tempering_bias)
 
double getBiasAndDerivatives (const vector< double > &, double *der=NULL)
 
double evaluateGaussian (const vector< double > &, const Gaussian &, double *der=NULL)
 
double getGaussianNormalization (const Gaussian &)
 
vector< unsigned > getGaussianSupport (const Gaussian &)
 
bool scanOneHill (IFile *ifile, vector< Value > &v, vector< double > &center, vector< double > &sigma, double &height, bool &multivariate)
 takes a pointer to the file and a template string with values v and gives back the next center, sigma and height More...
 
void computeReweightingFactor ()
 
double getTransitionBarrierBias ()
 

Static Private Member Functions

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

Private Attributes

vector< double > sigma0_
 
vector< double > sigma0min_
 
vector< double > sigma0max_
 
vector< Gaussianhills_
 
OFile hillsOfile_
 
OFile gridfile_
 
GridBiasGrid_
 
bool storeOldGrids_
 
int wgridstride_
 
bool grid_
 
double height0_
 
double biasf_
 
double dampfactor_
 
struct TemperingSpecs tt_specs_
 
std::string targetfilename_
 
GridTargetGrid_
 
double kbt_
 
int stride_
 
bool welltemp_
 
double * dp_
 
int adaptive_
 
FlexibleBinflexbin
 
int mw_n_
 
string mw_dir_
 
int mw_id_
 
int mw_rstride_
 
bool walkers_mpi
 
unsigned mpi_nw_
 
unsigned mpi_mw_
 
bool acceleration
 
double acc
 
double acc_restart_mean_
 
bool calc_max_bias_
 
double max_bias_
 
bool calc_transition_bias_
 
double transition_bias_
 
vector< vector< double > > transitionwells_
 
vector< IFile * > ifiles
 
vector< string > ifilesnames
 
double uppI_
 
double lowI_
 
bool doInt_
 
bool isFirstStep
 
double reweight_factor
 
vector< unsigned > rewf_grid_
 
unsigned rewf_ustride_
 
double work_
 
long int last_step_warn_grid
 
string fmt
 

Static Private Attributes

static const size_t n_tempering_options_ = 1
 
static const 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

◆ ~MetaD()

PLMD::bias::MetaD::~MetaD ( )

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 ( )
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::bias::MetaD::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::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::colvar::ContactMap.

◆ checkNeedsGradients()

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

Check if the action needs gradient.

Reimplemented from PLMD::Action.

◆ 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.

◆ 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 vector< double > &  cv,
const Gaussian hill,
double *  der = NULL 
)
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 ( 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
inlineinherited

Returns an array of pointers to the arguments.

◆ getBiasAndDerivatives()

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

◆ 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()

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

◆ getHeight()

double PLMD::bias::MetaD::getHeight ( const 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 ( )
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.

◆ 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]

void PLMD::ActionWithArguments::lockRequests ( )
inlinevirtualinherited

◆ lockRequests() [2/2]

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

◆ 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.

◆ 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::isdb::EMMI, PLMD::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, 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.

◆ readChunkOfGaussians()

bool PLMD::bias::MetaD::readChunkOfGaussians ( IFile ifile,
unsigned  n 
)
private

◆ 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.

◆ 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::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

◆ scanOneHill()

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

takes a pointer to the file and a template 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]

void PLMD::ActionWithArguments::unlockRequests ( )
inlinevirtualinherited

◆ unlockRequests() [2/2]

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

◆ update()

void PLMD::bias::MetaD::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.

◆ 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

◆ adaptive_

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

◆ biasf_

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

◆ BiasGrid_

Grid* PLMD::bias::MetaD::BiasGrid_
private

◆ calc_max_bias_

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

◆ calc_transition_bias_

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

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ dampfactor_

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

◆ doInt_

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

◆ dp_

double* PLMD::bias::MetaD::dp_
private

◆ files

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

◆ flexbin

FlexibleBin* PLMD::bias::MetaD::flexbin
private

◆ fmt

string PLMD::bias::MetaD::fmt
private

◆ grid_

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

◆ gridfile_

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

◆ height0_

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

◆ hills_

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

◆ hillsOfile_

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

◆ ifiles

vector<IFile*> PLMD::bias::MetaD::ifiles
private

◆ ifilesnames

vector<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

◆ last_step_warn_grid

long int PLMD::bias::MetaD::last_step_warn_grid
private

◆ 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_mw_

unsigned PLMD::bias::MetaD::mpi_mw_
private

◆ mpi_nw_

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

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ mw_dir_

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

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ reweight_factor

double PLMD::bias::MetaD::reweight_factor
private

◆ rewf_grid_

vector<unsigned> PLMD::bias::MetaD::rewf_grid_
private

◆ rewf_ustride_

unsigned PLMD::bias::MetaD::rewf_ustride_
private

◆ sigma0_

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

◆ sigma0max_

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

◆ sigma0min_

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

◆ storeOldGrids_

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

◆ stride_

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

◆ targetfilename_

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

◆ TargetGrid_

Grid* 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_

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

◆ tt_specs_

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

◆ uppI_

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

◆ 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: