Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
PLMD::ves::Optimizer Class Referenceabstract

#include <Optimizer.h>

Inheritance diagram for PLMD::ves::Optimizer:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Optimizer (const ActionOptions &ao)
 
 ~Optimizer ()
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with a name like label.name. More...
 
virtual void addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
 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 addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with the name label. More...
 
virtual void addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
 Add a value with the name label that has derivatives. More...
 
void apply () override
 Apply an Action. More...
 
virtual void beforeUpdate ()
 Before Update. 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...
 
virtual bool calculateOnUpdate ()
 This is used to check if we run calculate during the update step. More...
 
virtual ActionAtomisticcastToActionAtomistic () noexcept
 
virtual ActionForInterfacecastToActionForInterface () noexcept
 
virtual ActionShortcutcastToActionShortcut () noexcept
 
virtual ActionToGetDatacastToActionToGetData () noexcept
 
virtual ActionToPutDatacastToActionToPutData () noexcept
 
virtual ActionWithArgumentscastToActionWithArguments () noexcept
 
virtual ActionWithValuecastToActionWithValue () noexcept
 Specialized casts, to make PlumedMain run faster. More...
 
ActionWithValuecastToActionWithValue () noexcept final
 Specialized casts, to make PlumedMain run faster. More...
 
virtual ActionWithVirtualAtomcastToActionWithVirtualAtom () noexcept
 
virtual DomainDecompositioncastToDomainDecomposition () noexcept
 
virtual PbcActioncastToPbcAction () noexcept
 
virtual void checkFieldsAllowed ()
 
bool checkForDependency (Action *)
 Check that this action does not depend on the action in the argument. More...
 
virtual bool checkNeedsGradients () const
 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 (const bool &force=false)
 Clear the derivatives of values wrt parameters. More...
 
virtual void clearInputForces (const bool &force=false)
 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...
 
bool diagonalHessian () const
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
bool dynamicStepSize () const
 
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...
 
bool fixedStepSize () const
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
std::vector< CoeffsVector * > getAuxCoeffsPntrs () const
 
unsigned int getBiasOutputStride () const
 
std::vector< VesBias * > getBiasPntrs () const
 
std::vector< CoeffsVector * > getCoeffsMaskPntrs () const
 
std::vector< CoeffsVector * > getCoeffsPntrs () const
 
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...
 
double getCurrentStepSize (const unsigned int coeffs_id=0) const
 
std::vector< double > getCurrentStepSizes () const
 
std::string getDefaultString () const
 Get the defaults. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
std::string getDescription () const
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
unsigned int getFesOutputStride () const
 
unsigned int getFesProjOutputStride () const
 
std::vector< CoeffsVector * > getGradientPntrs () const
 
std::vector< CoeffsMatrix * > getHessianPntrs () const
 
unsigned int getIterationCounter () const
 
double getIterationCounterDbl () const
 
std::string getIterationCounterStr (const int offset=0) const
 
double getkBT ()
 Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. 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...
 
virtual void getMatrixColumnTitles (std::vector< std::string > &argnames) const
 Get the titles to use for the columns of the matrix. More...
 
const std::string & getName () const
 Returns the name. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned int getNumberOfDerivatives () override
 
virtual std::string getOutputComponentDescription (const std::string &cname, const Keywords &keys) const
 Get the description of this component. 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...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long long int getStep () const
 Return the present timestep. More...
 
double getStepSize (const unsigned int coeffs_id=0) const
 
std::vector< double > getStepSizes () const
 
int getStride () const
 Get the stride. More...
 
std::vector< CoeffsVector * > getTargetDistAveragesPntrs () const
 
unsigned int getTargetDistOutputStride () const
 
unsigned int getTargetDistProjOutputStride () const
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
std::string getType () const
 
void increaseIterationCounter ()
 
bool isActive () const
 Check if action is active. More...
 
bool isBiasOutputActive () const
 
bool isFesOutputActive () const
 
bool isFesProjOutputActive () const
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
bool isTargetDistOutputActive () const
 
bool isTargetDistProjOutputActive () const
 
virtual void lockRequests ()
 
unsigned int numberOfBiases () const
 
unsigned int numberOfCoeffsSets () const
 
virtual bool onStep () const
 Check if the action is active on this step. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse one keyword as generic type. More...
 
void 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 resetStoredTimestep ()
 Set the timestep that is stored in the action to the correct value. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void setBiasOutputStride (unsigned int stride)
 
void setFesOutputStride (unsigned int stride)
 
void setFesProjOutputStride (unsigned int stride)
 
virtual void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setIterationCounter (const unsigned int)
 
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 setStepSize (const double, const unsigned int coeffs_id=0)
 
void setStepSizes (const std::vector< double > &)
 
void setStride (const int &n)
 Set the value of the stride. More...
 
void setTargetDistOutputStride (unsigned int stride)
 
void setTargetDistProjOutputStride (unsigned int stride)
 
void setupConstantValues (const bool &have_atoms)
 This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...
 
void setValue (Value *, double)
 Set the value. More...
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
virtual void unlockRequests ()
 
void update () override
 Update. More...
 
bool useHessian () const
 
bool useMultipleWalkers () const
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
void writeBiasOutputFiles () const
 
void writeFesOutputFiles () const
 
void writeFesProjOutputFiles () const
 
virtual std::string writeInGraph () const
 Get the info on what to calculate. More...
 
void writeTargetDistOutputFiles () const
 
void writeTargetDistProjOutputFiles () const
 

Static Public Member Functions

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 &)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 
static void useDynamicStepSizeKeywords (Keywords &)
 
static void useDynamicTargetDistributionKeywords (Keywords &)
 
static void useFixedStepSizeKeywords (Keywords &)
 
static void useHessianKeywords (Keywords &)
 
static void useMaskKeywords (Keywords &)
 
static void useMonitorAverageGradientKeywords (Keywords &)
 
static void useMultipleWalkersKeywords (Keywords &)
 
static void useRestartKeywords (Keywords &)
 
static void useReweightFactorKeywords (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 addCoeffsSetIDsToFilenames (std::vector< std::string > &, std::string &)
 
CoeffsVectorAuxCoeffs (const unsigned int coeffs_id=0) const
 
bool checkForForces ()
 Accumulate the forces from the Values. More...
 
CoeffsVectorCoeffs (const unsigned int coeffs_id=0) const
 
CoeffsVectorCoeffsMask (const unsigned int coeffs_id=0) const
 
virtual void coeffsUpdate (const unsigned int coeffs_id=0)=0
 
std::vector< CoeffsMatrix * > enableHessian (VesBias *, const bool diagonal_hessian=false)
 
const ValuegetConstPntrToComponent (int i) const
 Get a const pointer to the ith component. More...
 
const std::vector< double > & getForcesToApply () const
 Get the forces to apply. More...
 
double getKBoltzmann () const
 Get the value of Boltzmann's constant. 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...
 
const UnitsgetUnits () const
 Get the units that we are operating in. More...
 
CoeffsVectorGradient (const unsigned int coeffs_id=0) const
 
CoeffsMatrixHessian (const unsigned int coeffs_id=0) const
 
void parseFilenames (const std::string &, std::vector< std::string > &)
 
void parseFilenames (const std::string &, std::vector< std::string > &, const std::string &)
 
template<class T >
bool parseMultipleValues (const std::string &, std::vector< T > &)
 
template<class T >
bool parseMultipleValues (const std::string &, std::vector< T > &, const T &)
 
void setCurrentStepSize (const double, const unsigned int i=0)
 
void setCurrentStepSizes (const std::vector< double > &)
 
void setupOFiles (std::vector< std::string > &, std::vector< std::unique_ptr< OFile >> &, const bool multi_sim_single_files=false)
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
double StepSize (const unsigned int coeffs_id=0) const
 
CoeffsVectorTargetDistAverages (const unsigned int coeffs_id=0) const
 
void turnOffCoeffsOutputFiles ()
 
void turnOffHessian ()
 
void turnOnHessian ()
 
bool usingNaturalUnits () const
 Are we using natural units. More...
 

Private Member Functions

int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 
void readCoeffsFromFiles (const std::vector< std::string > &, const bool)
 
void setAllCoeffsSetIterationCounters ()
 
void updateOutputComponents ()
 
void writeOutputFiles (const unsigned int coeffs_id=0)
 

Private Attributes

bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
std::vector< std::unique_ptr< CoeffsVector > > aux_coeffs_pntrs_
 
std::vector< std::unique_ptr< CoeffsVector > > aver_gradient_pntrs_
 
bool bias_output_active_
 
unsigned int bias_output_stride_
 
std::vector< VesBias * > bias_pntrs_
 
std::vector< std::unique_ptr< CoeffsVector > > coeffs_mask_pntrs_
 
std::string coeffs_output_fmt_
 
std::vector< CoeffsVector * > coeffs_pntrs_
 
unsigned int coeffs_wstride_
 
std::vector< std::unique_ptr< OFile > > coeffsOFiles_
 
std::string coeffssetid_prefix_
 
std::vector< double > current_stepsizes
 
std::string defaults
 The set of default arguments that we are using. More...
 
const std::string description_
 
bool diagonal_hessian_
 
bool doCheckPoint
 
std::vector< bool > dynamic_targetdists_
 
bool fes_output_active_
 
unsigned int fes_output_stride_
 
bool fesproj_output_active_
 
unsigned int fesproj_output_stride_
 
bool firststep
 This finishes setup on first step to check if actions are calculated during update. More...
 
bool fixed_stepsize_
 
std::vector< double > forcesForApply
 A vector that is used to hold the forces that we will apply on the input quantities. More...
 
std::string gradient_output_fmt_
 
std::vector< CoeffsVector * > gradient_pntrs_
 
unsigned int gradient_wstride_
 
std::vector< std::unique_ptr< OFile > > gradientOFiles_
 
bool hessian_covariance_from_averages_
 
std::string hessian_output_fmt_
 
std::vector< CoeffsMatrix * > hessian_pntrs_
 
unsigned int hessian_wstride_
 
std::vector< std::unique_ptr< OFile > > hessianOFiles_
 
bool identical_coeffs_shape_
 
bool isFirstStep
 
unsigned int iter_counter
 
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 monitor_instantaneous_gradient_
 
bool mwalkers_mpi_single_files_
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
unsigned int nbiases_
 
unsigned int ncoeffssets_
 
bool never_activate
 
bool noderiv
 Are we skipping the calculation of the derivatives. More...
 
bool numericalDerivatives
 Are we using numerical derivatives to differentiate. More...
 
std::set< std::string > options
 Option that you might have enabled. More...
 
int replica_index
 
bool restart
 
std::vector< double > stepsizes_
 
int stride
 
std::string targetdist_averages_output_fmt_
 
std::vector< CoeffsVector * > targetdist_averages_pntrs_
 
unsigned int targetdist_averages_wstride_
 
std::vector< std::unique_ptr< OFile > > targetdist_averagesOFiles_
 
bool targetdist_output_active_
 
unsigned int targetdist_output_stride_
 
bool targetdist_proj_output_active_
 
unsigned int targetdist_proj_output_stride_
 
double timestep
 Save the timestep here. More...
 
const std::string type_
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
bool use_hessian_
 
bool use_mwalkers_mpi_
 
unsigned int ustride_reweightfactor_
 
unsigned int ustride_targetdist_
 
std::vector< unsigned > valsToForce
 
std::vector< std::unique_ptr< Value > > values
 An array containing the values for this action. More...
 

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Optimizer()

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

◆ ~Optimizer()

PLMD::ves::Optimizer::~Optimizer ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addCoeffsSetIDsToFilenames()

void PLMD::ves::Optimizer::addCoeffsSetIDsToFilenames ( std::vector< std::string > &  fnames,
std::string &  coeffssetid_prefix 
)
protected

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name,
const std::vector< unsigned > &  shape = std::vector<unsigned>() 
)
inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name,
const std::vector< unsigned > &  shape = std::vector<unsigned>() 
)
virtualinherited

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

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > &  shape = std::vector<unsigned>())
inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > &  shape = std::vector<unsigned>())
virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ apply()

void PLMD::ves::Optimizer::apply ( )
inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ AuxCoeffs()

CoeffsVector & PLMD::ves::Optimizer::AuxCoeffs ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ 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.

◆ calculate()

void PLMD::ves::Optimizer::calculate ( )
inlineoverridevirtual

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

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )
virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments()

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )
inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )
inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )
inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ checkFieldsAllowed()

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

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

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action action)
inherited

Check that this action does not depend on the action in the argument.

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )
protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

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

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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 ( const bool &  force = false)
virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionForInterface, PLMD::generic::Constant, and PLMD::mapping::PathDisplacements.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( const bool &  force = false)
virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ Coeffs()

CoeffsVector & PLMD::ves::Optimizer::Coeffs ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ CoeffsMask()

CoeffsVector & PLMD::ves::Optimizer::CoeffsMask ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ coeffsUpdate()

virtual void PLMD::ves::Optimizer::coeffsUpdate ( const unsigned int  coeffs_id = 0)
protectedpure virtual

◆ 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.

◆ 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.

◆ diagonalHessian()

bool PLMD::ves::Optimizer::diagonalHessian ( ) const
inline

◆ doNotCalculateDerivatives()

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

Are we not calculating derivatives.

◆ dynamicStepSize()

bool PLMD::ves::Optimizer::dynamicStepSize ( ) const
inline

◆ enableHessian()

std::vector< CoeffsMatrix * > PLMD::ves::Optimizer::enableHessian ( VesBias bias_pntr_in,
const bool  diagonal_hessian = false 
)
protected

◆ error()

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

Crash calculation and print documentation.

◆ exists()

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

Check if a value with a particular name is present.

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

◆ exit()

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

Exit with error code c.

◆ 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.

◆ fixedStepSize()

bool PLMD::ves::Optimizer::fixedStepSize ( ) const
inline

◆ 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)

◆ getAuxCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getAuxCoeffsPntrs ( ) const
inline

◆ getBiasOutputStride()

unsigned int PLMD::ves::Optimizer::getBiasOutputStride ( ) const
inline

◆ getBiasPntrs()

std::vector<VesBias*> PLMD::ves::Optimizer::getBiasPntrs ( ) const
inline

◆ getCoeffsMaskPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getCoeffsMaskPntrs ( ) const
inline

◆ getCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getCoeffsPntrs ( ) const
inline

◆ 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

◆ getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int  i) const
protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

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

Return true if we are doing at a checkpoint step.

◆ getCurrentStepSize()

double PLMD::ves::Optimizer::getCurrentStepSize ( const unsigned int  coeffs_id = 0) const
inline

◆ getCurrentStepSizes()

std::vector< double > PLMD::ves::Optimizer::getCurrentStepSizes ( ) const
inline

◆ getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const
inlineinherited

Get the defaults.

◆ getDependencies()

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

Return dependencies.

◆ getDescription()

std::string PLMD::ves::Optimizer::getDescription ( ) const
inline

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getFesOutputStride()

unsigned int PLMD::ves::Optimizer::getFesOutputStride ( ) const
inline

◆ getFesProjOutputStride()

unsigned int PLMD::ves::Optimizer::getFesProjOutputStride ( ) const
inline

◆ getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const
inlineprotectedinherited

Get the forces to apply.

◆ getGradientPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getGradientPntrs ( ) const
inline

◆ getHessianPntrs()

std::vector<CoeffsMatrix*> PLMD::ves::Optimizer::getHessianPntrs ( ) const
inline

◆ getIterationCounter()

unsigned int PLMD::ves::Optimizer::getIterationCounter ( ) const
inline

◆ getIterationCounterDbl()

double PLMD::ves::Optimizer::getIterationCounterDbl ( ) const
inline

◆ getIterationCounterStr()

std::string PLMD::ves::Optimizer::getIterationCounterStr ( const int  offset = 0) const

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const
protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )
inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

◆ 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.

◆ getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > &  argnames) const
virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

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

Returns the name.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned int PLMD::ves::Optimizer::getNumberOfDerivatives ( )
inlineoverridevirtual

Implements PLMD::ActionWithValue.

◆ getOutputComponentDescription()

std::string PLMD::ActionWithValue::getOutputComponentDescription ( const std::string &  cname,
const Keywords keys 
) const
virtualinherited

◆ 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.

◆ 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 ( )
inlineprotectedinherited

Get a pointer to the default value.

◆ getRestart()

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

Return true if we are doing a restart.

◆ getStep()

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

Return the present timestep.

◆ getStepSize()

double PLMD::ves::Optimizer::getStepSize ( const unsigned int  coeffs_id = 0) const
inline

◆ getStepSizes()

std::vector< double > PLMD::ves::Optimizer::getStepSizes ( ) const
inline

◆ getStride()

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

Get the stride.

◆ getTargetDistAveragesPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getTargetDistAveragesPntrs ( ) const
inline

◆ getTargetDistOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistOutputStride ( ) const
inline

◆ getTargetDistProjOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistProjOutputStride ( ) const
inline

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getType()

std::string PLMD::ves::Optimizer::getType ( ) const
inline

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const
protectedinherited

Get the units that we are operating in.

◆ Gradient()

CoeffsVector & PLMD::ves::Optimizer::Gradient ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ Hessian()

CoeffsMatrix & PLMD::ves::Optimizer::Hessian ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ increaseIterationCounter()

void PLMD::ves::Optimizer::increaseIterationCounter ( )
inline

◆ isActive()

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

Check if action is active.

◆ isBiasOutputActive()

bool PLMD::ves::Optimizer::isBiasOutputActive ( ) const
inline

◆ isFesOutputActive()

bool PLMD::ves::Optimizer::isFesOutputActive ( ) const
inline

◆ isFesProjOutputActive()

bool PLMD::ves::Optimizer::isFesProjOutputActive ( ) const
inline

◆ isOptionOn()

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

Check if an option is on.

◆ isTargetDistOutputActive()

bool PLMD::ves::Optimizer::isTargetDistOutputActive ( ) const
inline

◆ isTargetDistProjOutputActive()

bool PLMD::ves::Optimizer::isTargetDistProjOutputActive ( ) const
inline

◆ lockRequests()

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

◆ noAnalyticalDerivatives()

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

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

◆ numberOfBiases()

unsigned int PLMD::ves::Optimizer::numberOfBiases ( ) const
inline

◆ numberOfCoeffsSets()

unsigned int PLMD::ves::Optimizer::numberOfCoeffsSets ( ) const
inline

◆ onStep()

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

Check if the action is active on this step.

◆ parse()

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

Parse one keyword as generic type.

◆ parseFilenames() [1/2]

void PLMD::ves::Optimizer::parseFilenames ( const std::string &  keyword,
std::vector< std::string > &  fnames 
)
inlineprotected

◆ parseFilenames() [2/2]

void PLMD::ves::Optimizer::parseFilenames ( const std::string &  keyword,
std::vector< std::string > &  fnames,
const std::string &  default_fname 
)
inlineprotected

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseMultipleValues() [1/2]

template<class T >
bool PLMD::ves::Optimizer::parseMultipleValues ( const std::string &  keyword,
std::vector< T > &  values 
)
protected

◆ parseMultipleValues() [2/2]

template<class T >
bool PLMD::ves::Optimizer::parseMultipleValues ( const std::string &  keyword,
std::vector< T > &  values,
const T &  default_value 
)
protected

◆ 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

◆ 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.

◆ readCoeffsFromFiles()

void PLMD::ves::Optimizer::readCoeffsFromFiles ( const std::vector< std::string > &  fnames,
const bool  read_aux_coeffs 
)
private

◆ registerKeywords()

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

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )
inherited

Set the timestep that is stored in the action to the correct value.

◆ 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.

◆ setAllCoeffsSetIterationCounters()

void PLMD::ves::Optimizer::setAllCoeffsSetIterationCounters ( )
private

◆ setBiasOutputStride()

void PLMD::ves::Optimizer::setBiasOutputStride ( unsigned int  stride)
inline

◆ setCurrentStepSize()

void PLMD::ves::Optimizer::setCurrentStepSize ( const double  current_stepsize_in,
const unsigned int  i = 0 
)
inlineprotected

◆ setCurrentStepSizes()

void PLMD::ves::Optimizer::setCurrentStepSizes ( const std::vector< double > &  current_stepsizes_in)
inlineprotected

◆ setFesOutputStride()

void PLMD::ves::Optimizer::setFesOutputStride ( unsigned int  stride)
inline

◆ setFesProjOutputStride()

void PLMD::ves::Optimizer::setFesProjOutputStride ( unsigned int  stride)
inline

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
virtualinherited

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

Reimplemented in PLMD::ActionForInterface.

◆ setIterationCounter()

void PLMD::ves::Optimizer::setIterationCounter ( const unsigned int  iter_counter_in)
inline

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

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

◆ setPeriodic()

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

Set the value to be periodic with a particular domain.

◆ setStepSize()

void PLMD::ves::Optimizer::setStepSize ( const double  stepsize_in,
const unsigned int  coeffs_id = 0 
)
inline

◆ setStepSizes()

void PLMD::ves::Optimizer::setStepSizes ( const std::vector< double > &  stepsizes_in)
inline

◆ setStride()

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

Set the value of the stride.

◆ setTargetDistOutputStride()

void PLMD::ves::Optimizer::setTargetDistOutputStride ( unsigned int  stride)
inline

◆ setTargetDistProjOutputStride()

void PLMD::ves::Optimizer::setTargetDistProjOutputStride ( unsigned int  stride)
inline

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool &  have_atoms)
inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setupOFiles()

void PLMD::ves::Optimizer::setupOFiles ( std::vector< std::string > &  fnames,
std::vector< std::unique_ptr< OFile >> &  OFiles,
const bool  multi_sim_single_files = false 
)
protected

◆ 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.

◆ StepSize()

double PLMD::ves::Optimizer::StepSize ( const unsigned int  coeffs_id = 0) const
inlineprotected

◆ TargetDistAverages()

CoeffsVector& PLMD::ves::Optimizer::TargetDistAverages ( const unsigned int  coeffs_id = 0) const
protected

◆ turnOffCoeffsOutputFiles()

void PLMD::ves::Optimizer::turnOffCoeffsOutputFiles ( )
protected

◆ turnOffHessian()

void PLMD::ves::Optimizer::turnOffHessian ( )
protected

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ turnOnHessian()

void PLMD::ves::Optimizer::turnOnHessian ( )
protected

◆ unlockRequests()

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

◆ update()

void PLMD::ves::Optimizer::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.

◆ updateOutputComponents()

void PLMD::ves::Optimizer::updateOutputComponents ( )
private

◆ useCustomisableComponents()

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

The components in the action will depend on the user.

◆ useDynamicStepSizeKeywords()

void PLMD::ves::Optimizer::useDynamicStepSizeKeywords ( Keywords keys)
static

◆ useDynamicTargetDistributionKeywords()

void PLMD::ves::Optimizer::useDynamicTargetDistributionKeywords ( Keywords keys)
static

◆ useFixedStepSizeKeywords()

void PLMD::ves::Optimizer::useFixedStepSizeKeywords ( Keywords keys)
static

◆ useHessian()

bool PLMD::ves::Optimizer::useHessian ( ) const
inline

◆ useHessianKeywords()

void PLMD::ves::Optimizer::useHessianKeywords ( Keywords keys)
static

◆ useMaskKeywords()

void PLMD::ves::Optimizer::useMaskKeywords ( Keywords keys)
static

◆ useMonitorAverageGradientKeywords()

void PLMD::ves::Optimizer::useMonitorAverageGradientKeywords ( Keywords keys)
static

◆ useMultipleWalkers()

bool PLMD::ves::Optimizer::useMultipleWalkers ( ) const
inline

◆ useMultipleWalkersKeywords()

void PLMD::ves::Optimizer::useMultipleWalkersKeywords ( Keywords keys)
static

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ useRestartKeywords()

void PLMD::ves::Optimizer::useRestartKeywords ( Keywords keys)
static

◆ useReweightFactorKeywords()

void PLMD::ves::Optimizer::useReweightFactorKeywords ( Keywords keys)
static

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const
protectedinherited

Are we using natural units.

◆ warning()

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

Issue a warning.

◆ writeBiasOutputFiles()

void PLMD::ves::Optimizer::writeBiasOutputFiles ( ) const

◆ writeFesOutputFiles()

void PLMD::ves::Optimizer::writeFesOutputFiles ( ) const

◆ writeFesProjOutputFiles()

void PLMD::ves::Optimizer::writeFesProjOutputFiles ( ) const

◆ writeInGraph()

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

◆ writeOutputFiles()

void PLMD::ves::Optimizer::writeOutputFiles ( const unsigned int  coeffs_id = 0)
private

◆ writeTargetDistOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistOutputFiles ( ) const

◆ writeTargetDistProjOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistProjOutputFiles ( ) const

Member Data Documentation

◆ 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.

◆ aux_coeffs_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::aux_coeffs_pntrs_
private

◆ aver_gradient_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::aver_gradient_pntrs_
private

◆ bias_output_active_

bool PLMD::ves::Optimizer::bias_output_active_
private

◆ bias_output_stride_

unsigned int PLMD::ves::Optimizer::bias_output_stride_
private

◆ bias_pntrs_

std::vector<VesBias*> PLMD::ves::Optimizer::bias_pntrs_
private

◆ coeffs_mask_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::coeffs_mask_pntrs_
private

◆ coeffs_output_fmt_

std::string PLMD::ves::Optimizer::coeffs_output_fmt_
private

◆ coeffs_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::coeffs_pntrs_
private

◆ coeffs_wstride_

unsigned int PLMD::ves::Optimizer::coeffs_wstride_
private

◆ coeffsOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::coeffsOFiles_
private

◆ coeffssetid_prefix_

std::string PLMD::ves::Optimizer::coeffssetid_prefix_
private

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ current_stepsizes

std::vector<double> PLMD::ves::Optimizer::current_stepsizes
private

◆ defaults

std::string PLMD::Action::defaults
privateinherited

The set of default arguments that we are using.

◆ description_

const std::string PLMD::ves::Optimizer::description_
private

◆ diagonal_hessian_

bool PLMD::ves::Optimizer::diagonal_hessian_
private

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ dynamic_targetdists_

std::vector<bool> PLMD::ves::Optimizer::dynamic_targetdists_
private

◆ fes_output_active_

bool PLMD::ves::Optimizer::fes_output_active_
private

◆ fes_output_stride_

unsigned int PLMD::ves::Optimizer::fes_output_stride_
private

◆ fesproj_output_active_

bool PLMD::ves::Optimizer::fesproj_output_active_
private

◆ fesproj_output_stride_

unsigned int PLMD::ves::Optimizer::fesproj_output_stride_
private

◆ files

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

◆ firststep

bool PLMD::ActionWithValue::firststep
privateinherited

This finishes setup on first step to check if actions are calculated during update.

◆ fixed_stepsize_

bool PLMD::ves::Optimizer::fixed_stepsize_
private

◆ forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply
privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

◆ gradient_output_fmt_

std::string PLMD::ves::Optimizer::gradient_output_fmt_
private

◆ gradient_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::gradient_pntrs_
private

◆ gradient_wstride_

unsigned int PLMD::ves::Optimizer::gradient_wstride_
private

◆ gradientOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::gradientOFiles_
private

◆ hessian_covariance_from_averages_

bool PLMD::ves::Optimizer::hessian_covariance_from_averages_
private

◆ hessian_output_fmt_

std::string PLMD::ves::Optimizer::hessian_output_fmt_
private

◆ hessian_pntrs_

std::vector<CoeffsMatrix*> PLMD::ves::Optimizer::hessian_pntrs_
private

◆ hessian_wstride_

unsigned int PLMD::ves::Optimizer::hessian_wstride_
private

◆ hessianOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::hessianOFiles_
private

◆ identical_coeffs_shape_

bool PLMD::ves::Optimizer::identical_coeffs_shape_
private

◆ isFirstStep

bool PLMD::ves::Optimizer::isFirstStep
private

◆ iter_counter

unsigned int PLMD::ves::Optimizer::iter_counter
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.

◆ monitor_instantaneous_gradient_

bool PLMD::ves::Optimizer::monitor_instantaneous_gradient_
private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ mwalkers_mpi_single_files_

bool PLMD::ves::Optimizer::mwalkers_mpi_single_files_
private

◆ name

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

Name of the directive in the plumed.dat file.

◆ nbiases_

unsigned int PLMD::ves::Optimizer::nbiases_
private

◆ ncoeffssets_

unsigned int PLMD::ves::Optimizer::ncoeffssets_
private

◆ never_activate

bool PLMD::Action::never_activate
privateinherited

◆ noderiv

bool PLMD::ActionWithValue::noderiv
privateinherited

Are we skipping the calculation of the derivatives.

◆ 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.

◆ 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

◆ stepsizes_

std::vector<double> PLMD::ves::Optimizer::stepsizes_
private

◆ stride

int PLMD::ActionPilot::stride
privateinherited

◆ targetdist_averages_output_fmt_

std::string PLMD::ves::Optimizer::targetdist_averages_output_fmt_
private

◆ targetdist_averages_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::targetdist_averages_pntrs_
private

◆ targetdist_averages_wstride_

unsigned int PLMD::ves::Optimizer::targetdist_averages_wstride_
private

◆ targetdist_averagesOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::targetdist_averagesOFiles_
private

◆ targetdist_output_active_

bool PLMD::ves::Optimizer::targetdist_output_active_
private

◆ targetdist_output_stride_

unsigned int PLMD::ves::Optimizer::targetdist_output_stride_
private

◆ targetdist_proj_output_active_

bool PLMD::ves::Optimizer::targetdist_proj_output_active_
private

◆ targetdist_proj_output_stride_

unsigned int PLMD::ves::Optimizer::targetdist_proj_output_stride_
private

◆ timestep

double PLMD::Action::timestep
privateinherited

Save the timestep here.

◆ type_

const std::string PLMD::ves::Optimizer::type_
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.

◆ use_hessian_

bool PLMD::ves::Optimizer::use_hessian_
private

◆ use_mwalkers_mpi_

bool PLMD::ves::Optimizer::use_mwalkers_mpi_
private

◆ ustride_reweightfactor_

unsigned int PLMD::ves::Optimizer::ustride_reweightfactor_
private

◆ ustride_targetdist_

unsigned int PLMD::ves::Optimizer::ustride_targetdist_
private

◆ valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce
privateinherited

◆ values

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

An array containing the values for this action.


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