Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | List of all members
PLMD::ves::Opt_Dummy Class Reference

Provides the keyword OPT_DUMMY More...

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

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Opt_Dummy (const ActionOptions &)
 
virtual void activate ()
 Set action to active. More...
 
void addComponent (const std::string &name)
 Add a value with a name like label.name. More...
 
void addComponentWithDerivatives (const std::string &name)
 Add a value with a name like label.name that has derivatives. More...
 
void addDependency (Action *)
 Specify that this Action depends on another one. More...
 
void addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void apply () override
 Apply an Action. More...
 
virtual void beforeUpdate ()
 Before Update. More...
 
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 void checkFieldsAllowed ()
 
virtual bool checkNeedsGradients () const
 Check if the action needs gradient. More...
 
bool checkNumericalDerivatives () const override
 Check if numerical derivatives should be used. More...
 
virtual bool checkNumericalDerivatives () const
 Check if numerical derivatives should be performed. More...
 
void checkRead ()
 Check if Action was properly read. More...
 
bool checkUpdate () const
 Check if action should be updated. More...
 
std::string cite (const std::string &s)
 Cite a paper see PlumedMain::cite. More...
 
void clearDependencies ()
 Clear the dependence list for this Action. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void coeffsUpdate (const unsigned int c_id=0) override
 
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
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
std::string getDescription () const
 
virtual std::string getDocumentation () 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
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned int getNumberOfDerivatives () override
 
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 getRestart () const
 Return true if we are doing a restart. More...
 
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...
 
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)
 
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 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
 
void writeTargetDistOutputFiles () const
 
void writeTargetDistProjOutputFiles () const
 

Static Public Member Functions

static void componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &)
 
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
 
CoeffsVectorCoeffs (const unsigned int coeffs_id=0) const
 
CoeffsVectorCoeffsMask (const unsigned int coeffs_id=0) const
 
std::vector< CoeffsMatrix * > enableHessian (VesBias *, const bool diagonal_hessian=false)
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
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 > &, const std::string &)
 
void parseFilenames (const std::string &, std::vector< 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< 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 ()
 

Detailed Description

Provides the keyword OPT_DUMMY

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Opt_Dummy()

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

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 
)
protectedinherited

◆ 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.

◆ 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::ves::Optimizer::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.

◆ AuxCoeffs()

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

◆ 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 ( )
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

◆ checkFieldsAllowed()

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

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

◆ checkNeedsGradients()

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

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

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

◆ Coeffs()

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

◆ CoeffsMask()

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

◆ coeffsUpdate()

void PLMD::ves::Opt_Dummy::coeffsUpdate ( const unsigned int  c_id = 0)
overridevirtual

Implements PLMD::ves::Optimizer.

◆ componentIsNotPeriodic()

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

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

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

◆ copyOutput() [1/2]

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

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

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

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ diagonalHessian()

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

◆ doNotCalculateDerivatives()

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

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ dynamicStepSize()

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

◆ enableHessian()

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

◆ 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
inlineinherited

◆ 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
inlineinherited

◆ getBiasOutputStride()

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

◆ getBiasPntrs()

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

◆ getCoeffsMaskPntrs()

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

◆ getCoeffsPntrs()

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

◆ 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.

◆ getCurrentStepSize()

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

◆ getCurrentStepSizes()

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

◆ getDependencies()

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

Return dependencies.

◆ getDescription()

std::string PLMD::ves::Optimizer::getDescription ( ) 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.

◆ getFesOutputStride()

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

◆ getFesProjOutputStride()

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

◆ getGradientPntrs()

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

◆ getHessianPntrs()

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

◆ getIterationCounter()

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

◆ getIterationCounterDbl()

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

◆ getIterationCounterStr()

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

◆ 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.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

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

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)

◆ 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.

◆ 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.

◆ getStepSize()

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

◆ getStepSizes()

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

◆ getStride()

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

Get the stride.

◆ getTargetDistAveragesPntrs()

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

◆ getTargetDistOutputStride()

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

◆ getTargetDistProjOutputStride()

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

◆ 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
inlineinherited

◆ Gradient()

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

◆ Hessian()

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

◆ increaseIterationCounter()

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

◆ isActive()

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

Check if action is active.

◆ isBiasOutputActive()

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

◆ isFesOutputActive()

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

◆ isFesProjOutputActive()

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

◆ isOptionOn()

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

Check if an option is on.

◆ isTargetDistOutputActive()

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

◆ isTargetDistProjOutputActive()

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

◆ 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
inlineinherited

◆ numberOfCoeffsSets()

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

◆ 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.

◆ parseFilenames() [1/2]

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

◆ parseFilenames() [2/2]

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

◆ 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 
)
protectedinherited

◆ parseMultipleValues() [2/2]

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

◆ 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::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::colvar::Energy, PLMD::SetupMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

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

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

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

void PLMD::ves::Opt_Dummy::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.

◆ setBiasOutputStride()

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

◆ setCurrentStepSize()

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

◆ setCurrentStepSizes()

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

◆ setFesOutputStride()

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

◆ setFesProjOutputStride()

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

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

◆ setIterationCounter()

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

◆ 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 
)
inlineinherited

◆ setStepSizes()

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

◆ setStride()

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

Set the value of the stride.

◆ setTargetDistOutputStride()

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

◆ setTargetDistProjOutputStride()

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

◆ setupOFiles()

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

◆ 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
inlineprotectedinherited

◆ TargetDistAverages()

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

◆ turnOffCoeffsOutputFiles()

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

◆ turnOffHessian()

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

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ turnOnHessian()

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

◆ unlockRequests()

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

◆ update()

void PLMD::ves::Optimizer::update ( )
overridevirtualinherited

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.

◆ useDynamicStepSizeKeywords()

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

◆ useDynamicTargetDistributionKeywords()

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

◆ useFixedStepSizeKeywords()

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

◆ useHessian()

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

◆ useHessianKeywords()

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

◆ useMaskKeywords()

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

◆ useMonitorAverageGradientKeywords()

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

◆ useMultipleWalkers()

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

◆ useMultipleWalkersKeywords()

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

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ useRestartKeywords()

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

◆ useReweightFactorKeywords()

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

◆ warning()

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

Issue a warning.

◆ writeBiasOutputFiles()

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

◆ writeFesOutputFiles()

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

◆ writeFesProjOutputFiles()

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

◆ writeTargetDistOutputFiles()

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

◆ writeTargetDistProjOutputFiles()

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

Member Data Documentation

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ files

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

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.


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