Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
PLMD::manyrestraints::UWalls Class Reference

Provides the keyword UWALLS More...

Inheritance diagram for PLMD::manyrestraints::UWalls:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 UWalls (const ActionOptions &)
 
virtual void activate ()
 Set action to active. More...
 
virtual void addBridgeForces (const std::vector< double > &bb)
 Apply forces from the bridge. 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
 Deactivate task now does nothing. More...
 
void applyBridgeForces (const std::vector< double > &bb) override
 Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...
 
virtual void beforeUpdate ()
 Before Update. More...
 
StoreDataVesselbuildDataStashes (ActionWithVessel *actionThatUses)
 Ensure that data required in other vessels is stored. More...
 
double calcPotential (const double &val, double &df) const override
 Calculate the potential. 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)
 Calculate the numerical derivatives N.B. 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...
 
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 clearDerivatives () override
 Don't actually clear the derivatives when this is called from plumed main. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearOptions ()
 
void componentIsNotPeriodic (const std::string &name)
 Set your value component to have no periodicity. More...
 
void componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
virtual void deactivate ()
 Set action to inactive. More...
 
void deactivate_task (const unsigned &task_index)
 Routines that have to be defined so as not to have problems with virtual methods. More...
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
void doJobsRequiredBeforeTaskList () override
 Do jobs required before tasks are undertaken. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
void error (const std::string &msg) const
 Crash calculation and print documentation. More...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. More...
 
void exit (int c=0)
 Exit with error code c. More...
 
int fclose (FILE *fp)
 Closes a file opened with Action::fclose(). More...
 
void fflush ()
 Tell to the Action to flush open files. More...
 
virtual void finishComputations (const std::vector< double > &buffer)
 Finish running all the calculations. More...
 
FILE * fopen (const char *path, const char *mode)
 Opens a file. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
std::string getComponentsList () const
 get a string that contains all the available components More...
 
std::vector< std::string > getComponentsVector () const
 get a vector that contains the label for all the components More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
unsigned getCurrentNumberOfActiveTasks () const
 Get the number of tasks that are currently active. More...
 
const DependenciesgetDependencies () const
 Return dependencies. More...
 
virtual std::string getDocumentation () const
 
bool getExchangeStep () const
 Check if we are on an exchange step. More...
 
unsigned getFullNumberOfTasks () const
 Get the full size of the taskList dynamic list. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. More...
 
const std::string & getLabel () const
 Returns the label. More...
 
const std::string & getName () const
 Returns the name. More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
unsigned getNumberOfDerivatives () override
 
virtual unsigned getNumberOfQuantities () const
 Get the number of quantities that are calculated during each task. More...
 
unsigned getNumberOfVessels () const
 Get the number of vessels. 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...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
unsigned getPositionInCurrentTaskList (const unsigned &myind) const
 Return the position in the current task list. More...
 
unsigned getPositionInFullTaskList (const unsigned &ii) const
 Get the position of the ith active task in the full list. More...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
long int getStep () const
 Return the present timestep. More...
 
int getStride () const
 Get the stride. More...
 
unsigned getTaskCode (const unsigned &ii) const
 Get the code for the ii th task in the list. More...
 
double getTime () const
 Return the present time. More...
 
double getTimeStep () const
 Return the timestep. More...
 
VesselgetVesselWithName (const std::string &mynam)
 These are overwritten in MultiColvarFunction. More...
 
bool isActive () const
 Check if action is active. More...
 
bool isOptionOn (const std::string &s) const
 Check if an option is on. More...
 
bool isPeriodic () override
 Are the base quantities periodic. More...
 
void lockContributors ()
 
virtual void lockRequests ()
 
virtual void normalizeVector (std::vector< double > &vals) const
 These normalizes vectors and is used in StoreDataVessel. More...
 
virtual void normalizeVectorDerivatives (MultiValue &myvals) 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...
 
void performTask (const unsigned &, const unsigned &, MultiValue &) const override
 This should never be called. 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 retrieveDomain (std::string &min, std::string &max)
 What are the domains of the base quantities. More...
 
virtual void runFinalJobs ()
 RunFinalJobs This method is called once at the very end of the calculation. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
virtual void setOption (const std::string &s)
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setStride (const int &n)
 Set the value of the stride. More...
 
void setValue (Value *, double)
 Set the value. More...
 
bool taskIsCurrentlyActive (const unsigned &index) const
 Check whether or not a particular task is currently active. More...
 
virtual bool threadSafe () const
 Is this action thread safe. More...
 
void transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const override
 This actually does the calculation. More...
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 
virtual void unlockRequests ()
 
virtual void update ()
 Update. More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
void warning (const std::string &msg)
 Issue a warning. More...
 
bool weightWithDerivatives () const
 Does the weight have derivatives. More...
 

Static Public Member Functions

static void componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void registerKeywords (Keywords &keys)
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

Public Attributes

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

Protected Member Functions

BridgeVesseladdBridgingVessel (ActionWithVessel *tome)
 Add a bridging vessel to the list of vessels. More...
 
void addForcesOnArguments (const std::vector< double > &forces)
 Add forces to arguments (used in apply) More...
 
void addTaskToList (const unsigned &taskCode)
 Add a task to the full list. More...
 
void addVessel (const std::string &name, const std::string &input, const int numlab=0)
 Add a vessel to the list of vessels. More...
 
void addVessel (std::unique_ptr< Vessel > vv)
 
void calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)
 This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...
 
void deactivateAllTasks ()
 Deactivate all the tasks in the task list. More...
 
bool getForcesFromVessels (std::vector< double > &forcesToApply)
 Retrieve the forces from all the vessels (used in apply) More...
 
double getNLTolerance () const
 Return the value for the neighbor list tolerance. More...
 
VesselgetPntrToArgument ()
 Return a pointer to specific argument. 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...
 
unsigned getSizeOfBuffer (unsigned &bufsize)
 Get the size of the buffer. More...
 
double getTolerance () const
 Return the value of the tolerance. More...
 
void needsDerivatives ()
 Turn on the derivatives in the vessel. More...
 
void readArgument (const std::string &type)
 What type of arguments are we reading in. More...
 
void readVesselKeywords ()
 Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...
 
void resizeFunctions ()
 Resize all the functions when the number of derivatives change. More...
 
void runAllTasks ()
 Calculate the values of all the vessels. More...
 
bool serialCalculation () const
 Is the calculation being done in serial. More...
 
void setLowMemOption (const bool &)
 Set that we are using low memory. More...
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
bool usingLowMem () const
 Are we using low memory. More...
 

Protected Attributes

unsigned bridgeVariable
 This is used for numerical derivatives of bridge variables. More...
 
bool contributorsAreUnlocked
 The terms in the series are locked. More...
 
bool dertime
 This is also used to minimise computational expense in complex functions. More...
 
StoreDataVesselmydata
 A pointer to the object that stores data. More...
 
std::vector< unsigned > taskFlags
 This list is used to update the neighbor list. More...
 
bool weightHasDerivatives
 Does the weight have derivatives. More...
 

Private Member Functions

int getComponent (const std::string &name) const
 Return the index for the component named name. More...
 

Private Attributes

bool actionIsBridged
 This tells plumed that this is used in a bridge. More...
 
bool active
 Switch to activate Action on this step. More...
 
Dependencies after
 Actions on which this Action depends. More...
 
Vesselarguments
 
double at
 
vesselbase::ActionWithVesselaves
 Pointer to underlying action with vessel. More...
 
std::vector< double > buffer
 The buffer that we use (we keep a copy here to avoid resizing) More...
 
std::vector< unsigned > der_list
 The list of atoms involved in derivatives (we keep a copy here to avoid resizing) More...
 
bool dertime_can_be_off
 These are used to minmise computational expense in complex functions. More...
 
bool doCheckPoint
 
double eps
 
double exp
 
std::vector< unsigned > fullTaskList
 Ths full list of tasks we have to perform. More...
 
std::vector< std::unique_ptr< Vessel > > functions
 Pointers to the functions we are using on each value. More...
 
std::vector< unsigned > indexOfTaskInFullList
 The indices of the tasks in the full list of tasks. More...
 
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...
 
bool lowmem
 Lower memory requirements. More...
 
unsigned maxderivatives
 The maximum number of derivatives we can use before we need to invoke lowmem. More...
 
BridgeVesselmyBridgeVessel
 
unsigned nactive_tasks
 The current number of active tasks. More...
 
const std::string name
 Name of the directive in the plumed.dat file. More...
 
double nl_tolerance
 Tolerance for quantities being put in neighbor lists. More...
 
bool noderiv
 Are we skipping the calculation of the derivatives. More...
 
bool numericalDerivatives
 Are we using numerical derivatives to differentiate. More...
 
double offset
 
std::set< std::string > options
 Option that you might have enabled. More...
 
std::vector< unsigned > partialTaskList
 The list of currently active tasks. More...
 
int replica_index
 
bool restart
 
bool serial
 Do all calculations in serial. More...
 
Stopwatchstopwatch =*stopwatch_fwd
 The stopwatch that times the different parts of the calculation. More...
 
ForwardDecl< Stopwatchstopwatch_fwd
 
int stride
 
bool timers
 Do we want to output information on the timings of different parts of the calculation. More...
 
std::vector< double > tmpforces
 Tempory storage for forces. More...
 
double tolerance
 The tolerance on the accumulators. More...
 
double update_from
 Update only after this time. More...
 
double update_until
 Update only until this time. More...
 
std::vector< std::unique_ptr< Value > > values
 An array containing the values for this action. More...
 

Detailed Description

Provides the keyword UWALLS

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ UWalls()

PLMD::manyrestraints::UWalls::UWalls ( const ActionOptions ao)
explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addBridgeForces()

virtual void PLMD::vesselbase::ActionWithInputVessel::addBridgeForces ( const std::vector< double > &  bb)
inlinevirtualinherited

Apply forces from the bridge.

◆ addBridgingVessel()

BridgeVessel * PLMD::vesselbase::ActionWithVessel::addBridgingVessel ( ActionWithVessel tome)
protectedinherited

Add a bridging vessel to the list of vessels.

◆ addComponent()

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

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

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

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

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::vesselbase::ActionWithInputVessel::addForcesOnArguments ( const std::vector< double > &  forces)
protectedinherited

Add forces to arguments (used in apply)

◆ addTaskToList()

void PLMD::vesselbase::ActionWithVessel::addTaskToList ( const unsigned &  taskCode)
protectedinherited

Add a task to the full list.

◆ 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.

◆ addVessel() [1/2]

void PLMD::vesselbase::ActionWithVessel::addVessel ( const std::string &  name,
const std::string &  input,
const int  numlab = 0 
)
protectedinherited

Add a vessel to the list of vessels.

◆ addVessel() [2/2]

void PLMD::vesselbase::ActionWithVessel::addVessel ( std::unique_ptr< Vessel vv)
protectedinherited

◆ apply()

void PLMD::manyrestraints::ManyRestraintsBase::apply ( )
overridevirtualinherited

Deactivate task now does nothing.

Implements PLMD::Action.

◆ applyBridgeForces()

void PLMD::manyrestraints::ManyRestraintsBase::applyBridgeForces ( const std::vector< double > &  bb)
inlineoverridevirtualinherited

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ 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.

◆ buildDataStashes()

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( ActionWithVessel actionThatUses)
inherited

Ensure that data required in other vessels is stored.

◆ calcPotential()

double PLMD::manyrestraints::UWalls::calcPotential ( const double &  val,
double &  df 
) const
overridevirtual

Calculate the potential.

Implements PLMD::manyrestraints::ManyRestraintsBase.

◆ calculate()

void PLMD::manyrestraints::ManyRestraintsBase::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.

◆ calculateAllVessels()

void PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( const unsigned &  taskCode,
MultiValue myvals,
MultiValue bvals,
std::vector< double > &  buffer,
std::vector< unsigned > &  der_list 
)
protectedinherited

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB pdb)
inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives() [1/2]

void PLMD::vesselbase::ActionWithInputVessel::calculateNumericalDerivatives ( ActionWithValue a = NULL)
virtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::multicolvar::DumpMultiColvar.

◆ calculateNumericalDerivatives() [2/2]

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

◆ checkFieldsAllowed()

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

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

◆ 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()

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::manyrestraints::ManyRestraintsBase::clearDerivatives ( )
inlineoverridevirtualinherited

Don't actually clear the derivatives when this is called from plumed main.

They are calculated inside another action and clearing them would be bad

Reimplemented from PLMD::ActionWithValue.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ componentIsNotPeriodic()

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

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

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

◆ 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.

◆ deactivate_task()

void PLMD::manyrestraints::ManyRestraintsBase::deactivate_task ( const unsigned &  task_index)
inlineinherited

Routines that have to be defined so as not to have problems with virtual methods.

◆ deactivateAllTasks()

void PLMD::vesselbase::ActionWithVessel::deactivateAllTasks ( )
protectedinherited

Deactivate all the tasks in the task list.

◆ derivativesAreRequired()

bool PLMD::vesselbase::ActionWithVessel::derivativesAreRequired ( ) const
inlineinherited

Are derivatives required for this quantity.

◆ doJobsRequiredBeforeTaskList()

void PLMD::manyrestraints::ManyRestraintsBase::doJobsRequiredBeforeTaskList ( )
overridevirtualinherited

Do jobs required before tasks are undertaken.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ doNotCalculateDerivatives()

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

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ error()

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

Crash calculation and print documentation.

◆ 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.

◆ finishComputations()

void PLMD::vesselbase::ActionWithVessel::finishComputations ( const std::vector< double > &  buffer)
virtualinherited

Finish running all the calculations.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ 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)

◆ getActiveTask()

unsigned PLMD::vesselbase::ActionWithVessel::getActiveTask ( const unsigned &  ii) const
inlineinherited

Get the ith of the currently active tasks.

◆ getComponent()

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

Return the index for the component named name.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const
inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const
inherited

get a vector that contains the label for all the components

◆ getCPT()

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

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentNumberOfActiveTasks ( ) const
inlineinherited

Get the number of tasks that are currently active.

◆ getDependencies()

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

Return dependencies.

◆ getDocumentation()

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

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getForcesFromVessels()

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > &  forcesToApply)
protectedinherited

Retrieve the forces from all the vessels (used in apply)

◆ getFullNumberOfTasks()

unsigned PLMD::vesselbase::ActionWithVessel::getFullNumberOfTasks ( ) const
inlineinherited

Get the full size of the taskList dynamic list.

◆ 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.

◆ getNLTolerance()

double PLMD::vesselbase::ActionWithVessel::getNLTolerance ( ) const
inlineprotectedinherited

Return the value for the neighbor list tolerance.

◆ getNumberOfComponents()

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

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::manyrestraints::ManyRestraintsBase::getNumberOfDerivatives ( )
inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getNumberOfQuantities()

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfQuantities ( ) const
inlinevirtualinherited

◆ getNumberOfVessels()

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const
inlineinherited

Get the number of vessels.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string &  name) const
inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

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

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

◆ getPntrToArgument()

Vessel * PLMD::vesselbase::ActionWithInputVessel::getPntrToArgument ( )
inlineprotectedinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )
protectedinherited

Get a pointer to the default value.

◆ getPntrToVessel()

Vessel * PLMD::vesselbase::ActionWithVessel::getPntrToVessel ( const unsigned &  i)
inlineinherited

Get a pointer to the ith vessel.

◆ getPositionInCurrentTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInCurrentTaskList ( const unsigned &  myind) const
inlineinherited

Return the position in the current task list.

◆ getPositionInFullTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInFullTaskList ( const unsigned &  ii) const
inlineinherited

Get the position of the ith active task in the full list.

◆ getRestart()

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

Return true if we are doing a restart.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::ActionWithVessel::getSizeOfBuffer ( unsigned &  bufsize)
protectedinherited

Get the size of the buffer.

◆ getStep()

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

Return the present timestep.

◆ getStride()

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

Get the stride.

◆ getTaskCode()

unsigned PLMD::vesselbase::ActionWithVessel::getTaskCode ( const unsigned &  ii) const
inlineinherited

Get the code for the ii th task in the list.

◆ getTime()

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

Return the present time.

◆ getTimeStep()

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

Return the timestep.

◆ getTolerance()

double PLMD::vesselbase::ActionWithVessel::getTolerance ( ) const
inlineprotectedinherited

Return the value of the tolerance.

◆ getVesselWithName()

Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string &  mynam)
inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ isActive()

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

Check if action is active.

◆ isOptionOn()

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

Check if an option is on.

◆ isPeriodic()

bool PLMD::manyrestraints::ManyRestraintsBase::isPeriodic ( )
inlineoverridevirtualinherited

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )
inherited

◆ lockRequests()

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

◆ needsDerivatives()

void PLMD::vesselbase::ActionWithVessel::needsDerivatives ( )
protectedinherited

Turn on the derivatives in the vessel.

◆ 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.

◆ normalizeVector()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVector ( std::vector< double > &  vals) const
inlinevirtualinherited

◆ normalizeVectorDerivatives()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVectorDerivatives ( MultiValue myvals) const
inlinevirtualinherited

◆ 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.

◆ 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.

◆ performTask()

void PLMD::manyrestraints::ManyRestraintsBase::performTask ( const unsigned &  ,
const unsigned &  ,
MultiValue  
) const
inlineoverridevirtualinherited

This should never be called.

Implements PLMD::vesselbase::ActionWithVessel.

◆ 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.

◆ readArgument()

void PLMD::vesselbase::ActionWithInputVessel::readArgument ( const std::string &  type)
protectedinherited

What type of arguments are we reading in.

◆ 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.

◆ readVesselKeywords()

void PLMD::vesselbase::ActionWithVessel::readVesselKeywords ( )
protectedinherited

Complete the setup of this object (this routine must be called after construction of ActionWithValue)

◆ registerKeywords()

void PLMD::manyrestraints::UWalls::registerKeywords ( Keywords keys)
static

◆ resizeFunctions()

void PLMD::vesselbase::ActionWithVessel::resizeFunctions ( )
protectedinherited

Resize all the functions when the number of derivatives change.

◆ retrieveDomain()

void PLMD::vesselbase::ActionWithVessel::retrieveDomain ( std::string &  min,
std::string &  max 
)
virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::multicolvar::Torsions, and PLMD::crystallization::InterMolecularTorsions.

◆ runAllTasks()

void PLMD::vesselbase::ActionWithVessel::runAllTasks ( )
protectedinherited

Calculate the values of all the vessels.

◆ 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.

◆ serialCalculation()

bool PLMD::vesselbase::ActionWithVessel::serialCalculation ( ) const
inlineprotectedinherited

Is the calculation being done in serial.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

◆ setLowMemOption()

void PLMD::vesselbase::ActionWithVessel::setLowMemOption ( const bool &  l)
inlineprotectedinherited

Set that we are using low memory.

◆ 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.

◆ setStride()

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

Set the value of the stride.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double &  d)
inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue ( Value ,
double   
)
inherited

Set the value.

◆ taskIsCurrentlyActive()

bool PLMD::vesselbase::ActionWithVessel::taskIsCurrentlyActive ( const unsigned &  index) const
inherited

Check whether or not a particular task is currently active.

◆ threadSafe()

virtual bool PLMD::vesselbase::ActionWithVessel::threadSafe ( ) const
inlinevirtualinherited

Is this action thread safe.

Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.

◆ transformBridgedDerivatives()

void PLMD::manyrestraints::ManyRestraintsBase::transformBridgedDerivatives ( const unsigned &  current,
MultiValue invals,
MultiValue outvals 
) const
overridevirtualinherited

This actually does the calculation.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests()

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

◆ update()

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

◆ useCustomisableComponents()

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

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ usingLowMem()

bool PLMD::vesselbase::ActionWithVessel::usingLowMem ( ) const
inlineprotectedinherited

Are we using low memory.

◆ warning()

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

Issue a warning.

◆ weightWithDerivatives()

bool PLMD::vesselbase::ActionWithVessel::weightWithDerivatives ( ) const
inlineinherited

Does the weight have derivatives.

Member Data Documentation

◆ actionIsBridged

bool PLMD::vesselbase::ActionWithVessel::actionIsBridged
privateinherited

This tells plumed that this is used in a bridge.

◆ 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.

◆ arguments

Vessel* PLMD::vesselbase::ActionWithInputVessel::arguments
privateinherited

◆ at

double PLMD::manyrestraints::UWalls::at
private

◆ aves

vesselbase::ActionWithVessel* PLMD::manyrestraints::ManyRestraintsBase::aves
privateinherited

Pointer to underlying action with vessel.

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable
protectedinherited

This is used for numerical derivatives of bridge variables.

◆ buffer

std::vector<double> PLMD::vesselbase::ActionWithVessel::buffer
privateinherited

The buffer that we use (we keep a copy here to avoid resizing)

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

◆ der_list

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::der_list
privateinherited

The list of atoms involved in derivatives (we keep a copy here to avoid resizing)

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime
protectedinherited

This is also used to minimise computational expense in complex functions.

◆ dertime_can_be_off

bool PLMD::vesselbase::ActionWithVessel::dertime_can_be_off
privateinherited

These are used to minmise computational expense in complex functions.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint
privateinherited

◆ eps

double PLMD::manyrestraints::UWalls::eps
private

◆ exp

double PLMD::manyrestraints::UWalls::exp
private

◆ files

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

◆ fullTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::fullTaskList
privateinherited

Ths full list of tasks we have to perform.

◆ functions

std::vector<std::unique_ptr<Vessel> > PLMD::vesselbase::ActionWithVessel::functions
privateinherited

Pointers to the functions we are using on each value.

◆ indexOfTaskInFullList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::indexOfTaskInFullList
privateinherited

The indices of the tasks in the full list of tasks.

◆ kappa

double PLMD::manyrestraints::UWalls::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.

◆ lowmem

bool PLMD::vesselbase::ActionWithVessel::lowmem
privateinherited

Lower memory requirements.

◆ maxderivatives

unsigned PLMD::vesselbase::ActionWithVessel::maxderivatives
privateinherited

The maximum number of derivatives we can use before we need to invoke lowmem.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ myBridgeVessel

BridgeVessel* PLMD::vesselbase::ActionWithInputVessel::myBridgeVessel
privateinherited

◆ mydata

StoreDataVessel* PLMD::vesselbase::ActionWithVessel::mydata
protectedinherited

A pointer to the object that stores data.

◆ nactive_tasks

unsigned PLMD::vesselbase::ActionWithVessel::nactive_tasks
privateinherited

The current number of active tasks.

◆ name

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

Name of the directive in the plumed.dat file.

◆ nl_tolerance

double PLMD::vesselbase::ActionWithVessel::nl_tolerance
privateinherited

Tolerance for quantities being put in neighbor lists.

◆ 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.

◆ offset

double PLMD::manyrestraints::UWalls::offset
private

◆ options

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

Option that you might have enabled.

◆ partialTaskList

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::partialTaskList
privateinherited

The list of currently active tasks.

◆ 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

◆ serial

bool PLMD::vesselbase::ActionWithVessel::serial
privateinherited

Do all calculations in serial.

◆ stopwatch

Stopwatch& PLMD::vesselbase::ActionWithVessel::stopwatch =*stopwatch_fwd
privateinherited

The stopwatch that times the different parts of the calculation.

◆ stopwatch_fwd

ForwardDecl<Stopwatch> PLMD::vesselbase::ActionWithVessel::stopwatch_fwd
privateinherited

◆ stride

int PLMD::ActionPilot::stride
privateinherited

◆ taskFlags

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::taskFlags
protectedinherited

This list is used to update the neighbor list.

◆ timers

bool PLMD::vesselbase::ActionWithVessel::timers
privateinherited

Do we want to output information on the timings of different parts of the calculation.

◆ tmpforces

std::vector<double> PLMD::vesselbase::ActionWithVessel::tmpforces
privateinherited

Tempory storage for forces.

◆ tolerance

double PLMD::vesselbase::ActionWithVessel::tolerance
privateinherited

The tolerance on the accumulators.

◆ 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.

◆ values

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

An array containing the values for this action.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives
protectedinherited

Does the weight have derivatives.


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