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::ves::TD_Chi Class Reference

Provides the keyword TD_CHI More...

Inheritance diagram for PLMD::ves::TD_Chi:
Inheritance graph
[legend]

Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 TD_Chi (const ActionOptions &ao)
 
virtual void activate ()
 Set action to active. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void allowBiasCutoff ()
 
void apply () override
 Apply an Action. More...
 
virtual void beforeUpdate ()
 Before Update. More...
 
bool biasCutoffActive () const
 
bool biasGridNeeded () const
 
bool biasWithoutCutoffGridNeeded () const
 
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...
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. 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...
 
void clearLogTargetDistGrid ()
 
virtual void clearOptions ()
 
virtual void deactivate ()
 Set action to inactive. More...
 
void doNotAllowBiasCutoff ()
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
bool fesGridNeeded () const
 
void fflush ()
 Tell to the Action to flush open files. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
bool forcedNormalization () const
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
unsigned getDimension () const
 
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...
 
GridgetLogTargetDistGridPntr () const
 
Grid getMarginal (const std::vector< std::string > &)
 
const std::string & getName () const
 Returns the name. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long int getStep () const
 Return the present timestep. More...
 
GridgetTargetDistGridPntr () const
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
double getValue (const std::vector< double > &) const override
 
bool isActive () const
 Check if action is active. More...
 
bool isBiasCutoffAllowed () const
 
bool isDynamic () const
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
bool isStatic () const
 
bool isTargetDistGridShiftedToZero () const
 
virtual void linkAction (Action *)
 
virtual void linkBiasGrid (Grid *)
 
virtual void linkBiasWithoutCutoffGrid (Grid *)
 
virtual void linkFesGrid (Grid *)
 
virtual void linkVesBias (VesBias *)
 
virtual void lockRequests ()
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. 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 readInRestartTargetDistGrid (const std::string &)
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void setDimension (const unsigned int dimension)
 
virtual void setOption (const std::string &s)
 
void setupBiasCutoff ()
 
void setupGrids (const std::vector< Value * > &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &)
 
virtual void unlockRequests ()
 
void update () override
 Update. More...
 
void updateTargetDist ()
 
void warning (const std::string &msg)
 Issue a warning. More...
 

Static Public Member Functions

static Grid getMarginalDistributionGrid (Grid *, const std::vector< std::string > &)
 
static double integrateGrid (const Grid *)
 
static double normalizeGrid (Grid *)
 
static void registerKeywords (Keywords &)
 

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 applyTargetDistModiferToGrid (TargetDistModifer *modifer_pntr)
 
double getBeta () const
 
GridgetBiasGridPntr () const
 
GridgetBiasWithoutCutoffGridPntr () const
 
GridgetFesGridPntr () const
 
ActiongetPntrToAction () const
 
VesBiasgetPntrToVesBias () const
 
GridlogTargetDistGrid () const
 
void normalizeTargetDistGrid ()
 
void setBiasGridNeeded ()
 
void setBiasWithoutCutoffGridNeeded ()
 
void setDynamic ()
 
void setFesGridNeeded ()
 
void setForcedNormalization ()
 
void setMinimumOfTargetDistGridToZero ()
 
void setStatic ()
 
virtual void setupAdditionalGrids (const std::vector< Value * > &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &)
 
GridtargetDistGrid () const
 
void unsetForcedNormalization ()
 
virtual void updateGrid ()
 
void updateLogTargetDistGrid ()
 

Private Types

enum  TargetDistType { static_targetdist, dynamic_targetdist }
 

Private Member Functions

void calculateStaticDistributionGrid ()
 
void checkNanAndInf ()
 
void updateBiasCutoffForTargetDistGrid ()
 

Private Attributes

Actionaction_pntr_
 
bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
bool allow_bias_cutoff_
 
bool bias_cutoff_active_
 
Gridbias_grid_pntr_
 
Gridbias_withoutcutoff_grid_pntr_
 
bool check_nan_inf_
 
bool check_nonnegative_
 
bool check_normalization_
 
unsigned int dimension_
 
bool doCheckPoint
 
Gridfes_grid_pntr_
 
bool force_normalization_
 
std::vector< Value * > grid_args_
 
std::vector< double > kappa_
 
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...
 
std::unique_ptr< Gridlog_targetdist_grid_pntr_
 
std::vector< double > minima_
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
bool needs_bias_grid_
 
bool needs_bias_withoutcutoff_grid_
 
bool needs_fes_grid_
 
std::vector< double > normalization_
 
std::set< std::string > options
 Option that you might have enabled. More...
 
int replica_index
 
bool restart
 
bool shift_targetdist_to_zero_
 
std::vector< double > sigma_
 
bool static_grid_calculated
 
std::unique_ptr< Gridtargetdist_grid_pntr_
 
std::vector< std::unique_ptr< TargetDistModifer > > targetdist_modifer_pntrs_
 
enum PLMD::ves::TargetDistribution::TargetDistType type_
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
VesBiasvesbias_pntr_
 

Detailed Description

Provides the keyword TD_CHI

Member Typedef Documentation

◆ Dependencies

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

Member Enumeration Documentation

◆ TargetDistType

Enumerator
static_targetdist 
dynamic_targetdist 

Constructor & Destructor Documentation

◆ TD_Chi()

PLMD::ves::TD_Chi::TD_Chi ( const ActionOptions ao)
explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ allowBiasCutoff()

void PLMD::ves::TargetDistribution::allowBiasCutoff ( )
inlineinherited

◆ apply()

void PLMD::ves::TargetDistribution::apply ( )
inlineoverridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ applyTargetDistModiferToGrid()

void PLMD::ves::TargetDistribution::applyTargetDistModiferToGrid ( TargetDistModifer modifer_pntr)
protectedinherited

◆ 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.

◆ biasCutoffActive()

bool PLMD::ves::TargetDistribution::biasCutoffActive ( ) const
inlineinherited

◆ biasGridNeeded()

bool PLMD::ves::TargetDistribution::biasGridNeeded ( ) const
inlineinherited

◆ biasWithoutCutoffGridNeeded()

bool PLMD::ves::TargetDistribution::biasWithoutCutoffGridNeeded ( ) const
inlineinherited

◆ calculate()

void PLMD::ves::TargetDistribution::calculate ( )
inlineoverridevirtualinherited

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()

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

◆ calculateStaticDistributionGrid()

void PLMD::ves::TargetDistribution::calculateStaticDistributionGrid ( )
privateinherited

◆ checkNanAndInf()

void PLMD::ves::TargetDistribution::checkNanAndInf ( )
privateinherited

◆ 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()

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.

◆ clearLogTargetDistGrid()

void PLMD::ves::TargetDistribution::clearLogTargetDistGrid ( )
inherited

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ doNotAllowBiasCutoff()

void PLMD::ves::TargetDistribution::doNotAllowBiasCutoff ( )
inlineinherited

◆ error()

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

Crash calculation and print documentation.

◆ exit()

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

Exit with error code c.

◆ fclose()

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

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

◆ fesGridNeeded()

bool PLMD::ves::TargetDistribution::fesGridNeeded ( ) const
inlineinherited

◆ 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)

◆ forcedNormalization()

bool PLMD::ves::TargetDistribution::forcedNormalization ( ) const
inlineinherited

◆ getBeta()

double PLMD::ves::TargetDistribution::getBeta ( ) const
protectedinherited

◆ getBiasGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasGridPntr ( ) const
inlineprotectedinherited

◆ getBiasWithoutCutoffGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasWithoutCutoffGridPntr ( ) const
inlineprotectedinherited

◆ 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.

◆ getDimension()

unsigned PLMD::ves::TargetDistribution::getDimension ( ) const
inlineinherited

◆ getDocumentation()

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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getFesGridPntr()

Grid* PLMD::ves::TargetDistribution::getFesGridPntr ( ) const
inlineprotectedinherited

◆ 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.

◆ getLogTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getLogTargetDistGridPntr ( ) const
inlineinherited

◆ getMarginal()

Grid PLMD::ves::TargetDistribution::getMarginal ( const std::vector< std::string > &  args)
inherited

◆ getMarginalDistributionGrid()

Grid PLMD::ves::TargetDistribution::getMarginalDistributionGrid ( Grid grid_pntr,
const std::vector< std::string > &  args 
)
staticinherited

◆ getName()

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

Returns the name.

◆ getPntrToAction()

Action * PLMD::ves::TargetDistribution::getPntrToAction ( ) const
inlineprotectedinherited

◆ getPntrToVesBias()

VesBias * PLMD::ves::TargetDistribution::getPntrToVesBias ( ) const
inlineprotectedinherited

◆ 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.

◆ getTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getTargetDistGridPntr ( ) const
inlineinherited

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getValue()

double PLMD::ves::TD_Chi::getValue ( const std::vector< double > &  argument) const
overridevirtual

◆ integrateGrid()

double PLMD::ves::TargetDistribution::integrateGrid ( const Grid grid_pntr)
staticinherited

◆ isActive()

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

Check if action is active.

◆ isBiasCutoffAllowed()

bool PLMD::ves::TargetDistribution::isBiasCutoffAllowed ( ) const
inlineinherited

◆ isDynamic()

bool PLMD::ves::TargetDistribution::isDynamic ( ) const
inlineinherited

◆ isOptionOn()

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

Check if an option is on.

◆ isStatic()

bool PLMD::ves::TargetDistribution::isStatic ( ) const
inlineinherited

◆ isTargetDistGridShiftedToZero()

bool PLMD::ves::TargetDistribution::isTargetDistGridShiftedToZero ( ) const
inlineinherited

◆ linkAction()

void PLMD::ves::TargetDistribution::linkAction ( Action action_pntr_in)
virtualinherited

◆ linkBiasGrid()

void PLMD::ves::TargetDistribution::linkBiasGrid ( Grid bias_grid_pntr_in)
virtualinherited

◆ linkBiasWithoutCutoffGrid()

void PLMD::ves::TargetDistribution::linkBiasWithoutCutoffGrid ( Grid bias_withoutcutoff_grid_pntr_in)
virtualinherited

◆ linkFesGrid()

void PLMD::ves::TargetDistribution::linkFesGrid ( Grid fes_grid_pntr_in)
virtualinherited

◆ linkVesBias()

void PLMD::ves::TargetDistribution::linkVesBias ( VesBias vesbias_pntr_in)
virtualinherited

◆ lockRequests()

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

◆ logTargetDistGrid()

Grid& PLMD::ves::TargetDistribution::logTargetDistGrid ( ) const
inlineprotectedinherited

◆ normalizeGrid()

double PLMD::ves::TargetDistribution::normalizeGrid ( Grid grid_pntr)
staticinherited

◆ normalizeTargetDistGrid()

void PLMD::ves::TargetDistribution::normalizeTargetDistGrid ( )
inlineprotectedinherited

◆ parse()

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

Parse one keyword as generic type.

◆ 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.

◆ readInRestartTargetDistGrid()

void PLMD::ves::TargetDistribution::readInRestartTargetDistGrid ( const std::string &  grid_fname)
inherited

◆ registerKeywords()

void PLMD::ves::TD_Chi::registerKeywords ( Keywords keys)
static

◆ 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.

◆ setBiasGridNeeded()

void PLMD::ves::TargetDistribution::setBiasGridNeeded ( )
inlineprotectedinherited

◆ setBiasWithoutCutoffGridNeeded()

void PLMD::ves::TargetDistribution::setBiasWithoutCutoffGridNeeded ( )
inlineprotectedinherited

◆ setDimension()

void PLMD::ves::TargetDistribution::setDimension ( const unsigned int  dimension)
inherited

◆ setDynamic()

void PLMD::ves::TargetDistribution::setDynamic ( )
inlineprotectedinherited

◆ setFesGridNeeded()

void PLMD::ves::TargetDistribution::setFesGridNeeded ( )
inlineprotectedinherited

◆ setForcedNormalization()

void PLMD::ves::TargetDistribution::setForcedNormalization ( )
inlineprotectedinherited

◆ setMinimumOfTargetDistGridToZero()

void PLMD::ves::TargetDistribution::setMinimumOfTargetDistGridToZero ( )
protectedinherited

◆ setOption()

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

◆ setStatic()

void PLMD::ves::TargetDistribution::setStatic ( )
inlineprotectedinherited

◆ setupAdditionalGrids()

virtual void PLMD::ves::TargetDistribution::setupAdditionalGrids ( const std::vector< Value * > &  ,
const std::vector< std::string > &  ,
const std::vector< std::string > &  ,
const std::vector< unsigned int > &   
)
inlineprotectedvirtualinherited

◆ setupBiasCutoff()

void PLMD::ves::TargetDistribution::setupBiasCutoff ( )
inherited

◆ setupGrids()

void PLMD::ves::TargetDistribution::setupGrids ( const std::vector< Value * > &  arguments,
const std::vector< std::string > &  min,
const std::vector< std::string > &  max,
const std::vector< unsigned int > &  nbins 
)
inherited

◆ targetDistGrid()

Grid& PLMD::ves::TargetDistribution::targetDistGrid ( ) const
inlineprotectedinherited

◆ unlockRequests()

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

◆ unsetForcedNormalization()

void PLMD::ves::TargetDistribution::unsetForcedNormalization ( )
inlineprotectedinherited

◆ update()

void PLMD::ves::TargetDistribution::update ( )
inlineoverridevirtualinherited

Update.

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

Reimplemented from PLMD::Action.

◆ updateBiasCutoffForTargetDistGrid()

void PLMD::ves::TargetDistribution::updateBiasCutoffForTargetDistGrid ( )
privateinherited

◆ updateGrid()

virtual void PLMD::ves::TargetDistribution::updateGrid ( )
inlineprotectedvirtualinherited

◆ updateLogTargetDistGrid()

void PLMD::ves::TargetDistribution::updateLogTargetDistGrid ( )
protectedinherited

◆ updateTargetDist()

void PLMD::ves::TargetDistribution::updateTargetDist ( )
inherited

◆ warning()

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

Issue a warning.

Member Data Documentation

◆ action_pntr_

Action* PLMD::ves::TargetDistribution::action_pntr_
privateinherited

◆ active

bool PLMD::Action::active
privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after
privateinherited

Actions on which this Action depends.

◆ allow_bias_cutoff_

bool PLMD::ves::TargetDistribution::allow_bias_cutoff_
privateinherited

◆ bias_cutoff_active_

bool PLMD::ves::TargetDistribution::bias_cutoff_active_
privateinherited

◆ bias_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_grid_pntr_
privateinherited

◆ bias_withoutcutoff_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_withoutcutoff_grid_pntr_
privateinherited

◆ check_nan_inf_

bool PLMD::ves::TargetDistribution::check_nan_inf_
privateinherited

◆ check_nonnegative_

bool PLMD::ves::TargetDistribution::check_nonnegative_
privateinherited

◆ check_normalization_

bool PLMD::ves::TargetDistribution::check_normalization_
privateinherited

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ dimension_

unsigned int PLMD::ves::TargetDistribution::dimension_
privateinherited

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ fes_grid_pntr_

Grid* PLMD::ves::TargetDistribution::fes_grid_pntr_
privateinherited

◆ files

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

◆ force_normalization_

bool PLMD::ves::TargetDistribution::force_normalization_
privateinherited

◆ grid_args_

std::vector<Value*> PLMD::ves::TargetDistribution::grid_args_
privateinherited

◆ kappa_

std::vector<double> PLMD::ves::TD_Chi::kappa_
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.

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ log_targetdist_grid_pntr_

std::unique_ptr<Grid> PLMD::ves::TargetDistribution::log_targetdist_grid_pntr_
privateinherited

◆ minima_

std::vector<double> PLMD::ves::TD_Chi::minima_
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ name

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

Name of the directive in the plumed.dat file.

◆ needs_bias_grid_

bool PLMD::ves::TargetDistribution::needs_bias_grid_
privateinherited

◆ needs_bias_withoutcutoff_grid_

bool PLMD::ves::TargetDistribution::needs_bias_withoutcutoff_grid_
privateinherited

◆ needs_fes_grid_

bool PLMD::ves::TargetDistribution::needs_fes_grid_
privateinherited

◆ normalization_

std::vector<double> PLMD::ves::TD_Chi::normalization_
private

◆ options

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

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index
privateinherited

◆ restart

bool PLMD::Action::restart
privateinherited

◆ shift_targetdist_to_zero_

bool PLMD::ves::TargetDistribution::shift_targetdist_to_zero_
privateinherited

◆ sigma_

std::vector<double> PLMD::ves::TD_Chi::sigma_
private

◆ static_grid_calculated

bool PLMD::ves::TargetDistribution::static_grid_calculated
privateinherited

◆ targetdist_grid_pntr_

std::unique_ptr<Grid> PLMD::ves::TargetDistribution::targetdist_grid_pntr_
privateinherited

◆ targetdist_modifer_pntrs_

std::vector<std::unique_ptr<TargetDistModifer> > PLMD::ves::TargetDistribution::targetdist_modifer_pntrs_
privateinherited

◆ type_

enum PLMD::ves::TargetDistribution::TargetDistType PLMD::ves::TargetDistribution::type_
privateinherited

◆ 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.

◆ vesbias_pntr_

VesBias* PLMD::ves::TargetDistribution::vesbias_pntr_
privateinherited

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