#include <ManyRestraintsBase.h>

Inheritance diagram for PLMD::manyrestraints::ManyRestraintsBase:

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	ManyRestraintsBase (const ActionOptions &)
virtual void	activate ()
	Set action to active.
virtual void	addBridgeForces (const std::vector< double > &bb)
	Apply forces from the bridge.
void	addComponent (const std::string &name)
	Add a value with a name like label.name.
void	addComponentWithDerivatives (const std::string &name)
	Add a value with a name like label.name that has derivatives.
void	addDependency (Action *)
	Specify that this Action depends on another one.
void	addValue ()
	Add a value with the name label.
void	addValueWithDerivatives ()
	Add a value with the name label that has derivatives.
void	apply () override
	Deactivate task now does nothing.
void	applyBridgeForces (const std::vector< double > &bb) override
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.
virtual void	beforeUpdate ()
	Before Update.
StoreDataVessel *	buildDataStashes (ActionWithVessel *actionThatUses)
	Ensure that data required in other vessels is stored.
virtual double	calcPotential (const double &val, double &df) const =0
	Calculate the potential.
void	calculate () override
	Calculate an Action.
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input.
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Calculate the numerical derivatives N.B.
virtual void	checkFieldsAllowed ()
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient.
bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used.
void	checkRead ()
	Check if Action was properly read.
bool	checkUpdate () const
	Check if action should be updated.
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite.
void	clearDependencies ()
	Clear the dependence list for this Action.
void	clearDerivatives () override
	Don't actually clear the derivatives when this is called from plumed main.
void	clearInputForces ()
	Clear the forces on the values.
virtual void	clearOptions ()
void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity.
void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain.
Value *	copyOutput (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.
Value *	copyOutput (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.
virtual void	deactivate ()
	Set action to inactive.
void	deactivate_task (const unsigned &task_index)
	Routines that have to be defined so as not to have problems with virtual methods.
bool	derivativesAreRequired () const
	Are derivatives required for this quantity.
void	doJobsRequiredBeforeTaskList () override
	Do jobs required before tasks are undertaken.
virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives.
void	error (const std::string &msg) const
	Crash calculation and print documentation.
bool	exists (const std::string &name) const
	Check if a value with a particular name is present.
void	exit (int c=0)
	Exit with error code c.
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose().
void	fflush ()
	Tell to the Action to flush open files.
virtual void	finishComputations (const std::vector< double > &buffer)
	Finish running all the calculations.
FILE *	fopen (const char path, const char mode)
	Opens a file.
unsigned	getActiveTask (const unsigned &ii) const
	Get the ith of the currently active tasks.
std::string	getComponentsList () const
	get a string that contains all the available components
std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components
bool	getCPT () const
	Return true if we are doing at a checkpoint step.
unsigned	getCurrentNumberOfActiveTasks () const
	Get the number of tasks that are currently active.
std::string	getDefaultString () const
	Get the defaults.
const Dependencies &	getDependencies () const
	Return dependencies.
bool	getExchangeStep () const
	Check if we are on an exchange step.
unsigned	getFullNumberOfTasks () const
	Get the full size of the taskList dynamic list.
std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string.
const std::string &	getLabel () const
	Returns the label.
const std::string &	getName () const
	Returns the name.
int	getNumberOfComponents () const
	Returns the number of values defined.
unsigned	getNumberOfDerivatives () override
virtual unsigned	getNumberOfQuantities () const
	Get the number of quantities that are calculated during each task.
unsigned	getNumberOfVessels () const
	Get the number of vessels.
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).
double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action.
Vessel *	getPntrToVessel (const unsigned &i)
	Get a pointer to the ith vessel.
unsigned	getPositionInCurrentTaskList (const unsigned &myind) const
	Return the position in the current task list.
unsigned	getPositionInFullTaskList (const unsigned &ii) const
	Get the position of the ith active task in the full list.
bool	getRestart () const
	Return true if we are doing a restart.
long long int	getStep () const
	Return the present timestep.
int	getStride () const
	Get the stride.
unsigned	getTaskCode (const unsigned &ii) const
	Get the code for the ii th task in the list.
double	getTime () const
	Return the present time.
double	getTimeStep () const
	Return the timestep.
Vessel *	getVesselWithName (const std::string &mynam)
	These are overwritten in MultiColvarFunction.
bool	isActive () const
	Check if action is active.
bool	isOptionOn (const std::string &s) const
	Check if an option is on.
bool	isPeriodic () override
	Are the base quantities periodic.
void	lockContributors ()
virtual void	lockRequests ()
virtual void	normalizeVector (std::vector< double > &vals) const
	These normalizes vectors and is used in StoreDataVessel.
virtual void	normalizeVectorDerivatives (MultiValue &myvals) const
virtual bool	onStep () const
	Check if the action is active on this step.
template<class T>
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type.
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag.
template<class T>
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type.
template<class T>
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number.
template<class T>
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector.
void	performTask (const unsigned &, const unsigned &, MultiValue &) const override
	This should never be called.
virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
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.
virtual void	retrieveDomain (std::string &min, std::string &max)
	What are the domains of the base quantities.
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation.
void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections).
void	setNotPeriodic ()
	Set your default value to have no periodicity.
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.
void	setStride (const int &n)
	Set the value of the stride.
void	setValue (Value *, double)
	Set the value.
bool	taskIsCurrentlyActive (const unsigned &index) const
	Check whether or not a particular task is currently active.
virtual bool	threadSafe () const
	Is this action thread safe.
void	transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const override
	This actually does the calculation.
virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives.
virtual void	unlockRequests ()
virtual void	update ()
	Update.
void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives.
void	warning (const std::string &msg)
	Issue a warning.
bool	weightWithDerivatives () const
	Does the weight have derivatives.

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

Public Attributes
Communicator &	comm
std::set< FILE * >	files
const Keywords &	keywords
Log &	log
	Reference to the log stream.
Communicator &	multi_sim_comm
PlumedMain &	plumed
	Reference to main plumed object.

Protected Member Functions
BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels.
void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply).
void	addTaskToList (const unsigned &taskCode)
	Add a task to the full list.
void	addVessel (const std::string &name, const std::string &input, const int numlab=0)
	Add a vessel to the list of vessels.
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.
void	deactivateAllTasks ()
	Deactivate all the tasks in the task list.
bool	getForcesFromVessels (std::vector< double > &forcesToApply)
	Retrieve the forces from all the vessels (used in apply).
double	getNLTolerance () const
	Return the value for the neighbor list tolerance.
Vessel *	getPntrToArgument ()
	Return a pointer to specific argument.
Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name.
Value *	getPntrToComponent (int i)
	Return a pointer to the component by index.
Value *	getPntrToValue ()
	Get a pointer to the default value.
unsigned	getSizeOfBuffer (unsigned &bufsize)
	Get the size of the buffer.
double	getTolerance () const
	Return the value of the tolerance.
void	needsDerivatives ()
	Turn on the derivatives in the vessel.
void	readArgument (const std::string &type)
	What type of arguments are we reading in.
void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue).
void	resizeFunctions ()
	Resize all the functions when the number of derivatives change.
void	runAllTasks ()
	Calculate the values of all the vessels.
bool	serialCalculation () const
	Is the calculation being done in serial.
void	setLowMemOption (const bool &)
	Set that we are using low memory.
void	setValue (const double &d)
	Set the default value (the one without name).
bool	usingLowMem () const
	Are we using low memory.

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

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

Private Attributes
bool	actionIsBridged
	This tells plumed that this is used in a bridge.
Vessel *	arguments
vesselbase::ActionWithVessel *	aves
	Pointer to underlying action with vessel.
std::vector< double >	buffer
	The buffer that we use (we keep a copy here to avoid resizing).
std::vector< unsigned >	der_list
	The list of atoms involved in derivatives (we keep a copy here to avoid resizing).
bool	dertime_can_be_off
	These are used to minmise computational expense in complex functions.
std::vector< unsigned >	fullTaskList
	Ths full list of tasks we have to perform.
std::vector< std::unique_ptr< Vessel > >	functions
	Pointers to the functions we are using on each value.
std::vector< unsigned >	indexOfTaskInFullList
	The indices of the tasks in the full list of tasks.
bool	lowmem
	Lower memory requirements.
unsigned	maxderivatives
	The maximum number of derivatives we can use before we need to invoke lowmem.
BridgeVessel *	myBridgeVessel
unsigned	nactive_tasks
	The current number of active tasks.
double	nl_tolerance
	Tolerance for quantities being put in neighbor lists.
bool	noderiv
	Are we skipping the calculation of the derivatives.
bool	numericalDerivatives
	Are we using numerical derivatives to differentiate.
std::vector< unsigned >	partialTaskList
	The list of currently active tasks.
bool	serial
	Do all calculations in serial.
Stopwatch &	stopwatch =*stopwatch_fwd
	The stopwatch that times the different parts of the calculation.
ForwardDecl< Stopwatch >	stopwatch_fwd
int	stride
bool	timers
	Do we want to output information on the timings of different parts of the calculation.
std::vector< double >	tmpforces
	Tempory storage for forces.
double	tolerance
	The tolerance on the accumulators.
std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ManyRestraintsBase()

PLMD::manyrestraints::ManyRestraintsBase::ManyRestraintsBase ( 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 ( )

overridevirtual

Deactivate task now does nothing.

Implements PLMD::Action.

◆ applyBridgeForces()

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

inlineoverridevirtual

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()

virtual double PLMD::manyrestraints::ManyRestraintsBase::calcPotential	(	const double &	val,
		double &	df ) const

pure virtual

Calculate the potential.

Implemented in PLMD::manyrestraints::LWalls, and PLMD::manyrestraints::UWalls.

◆ calculate()

void PLMD::manyrestraints::ManyRestraintsBase::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.

◆ 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()

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.

◆ 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 ( )

inlineoverridevirtual

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 )

inline

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 ( )

overridevirtual

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.

◆ getDefaultString()

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

inlineinherited

Get the defaults.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ 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 ( )

inlineoverridevirtual

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 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 ( )

inlineoverridevirtual

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

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

inherited

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::analysis::AnalysisBase, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::mapping::PCAVars, and PLMD::vesselbase::ActionWithAveraging.

◆ 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

These normalizes vectors and is used in StoreDataVessel.

Reimplemented in PLMD::crystallization::MoleculeOrientation, PLMD::crystallization::VectorMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::multicolvar::LocalAverage.

◆ normalizeVectorDerivatives()

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

inlinevirtualinherited

Reimplemented in PLMD::crystallization::MoleculeOrientation, PLMD::crystallization::VectorMultiColvar, and PLMD::multicolvar::BridgedMultiColvarFunction.

◆ 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

inlineoverridevirtual

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::colvar::CoordinationBase, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::function::FuncPathGeneral, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::Plumed, PLMD::generic::Print, PLMD::generic::Read, PLMD::generic::UpdateIf, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::isdb::EMMI, PLMD::maze::Optimizer, PLMD::multicolvar::MultiColvarBase, 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::ManyRestraintsBase::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::crystallization::InterMolecularTorsions, PLMD::multicolvar::Torsions, and PLMD::multicolvar::XYTorsion.

◆ 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::analysis::AnalysisBase, PLMD::analysis::ReadDissimilarityMatrix, PLMD::gridtools::ConvertToFES, PLMD::gridtools::GridPrintingBase, and PLMD::vesselbase::ActionWithAveraging.

◆ 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

overridevirtual

This actually does the calculation.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::adjmat::ClusterAnalysisBase, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusteringBase, PLMD::adjmat::ClusterSize, PLMD::analysis::Histogram, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::generic::Read, PLMD::gridtools::ActionWithGrid, PLMD::gridtools::ActionWithIntegral, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::multicolvar::MultiColvarBase, and PLMD::secondarystructure::SecondaryStructureRMSD.

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::analysis::AnalysisBase, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::mapping::Mapping, PLMD::mapping::PCAVars, and PLMD::vesselbase::ActionWithAveraging.

◆ update()

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

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

Reimplemented in PLMD::adjmat::DumpGraph, PLMD::adjmat::OutputCluster, PLMD::analysis::AnalysisBase, PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::ReadDissimilarityMatrix, PLMD::bias::ExtendedLagrangian, PLMD::bias::MaxEnt, PLMD::bias::MetaD, PLMD::bias::PBMetaD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::generic::DumpAtoms, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpMassCharge, PLMD::generic::DumpProjections, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::Flush, PLMD::generic::Plumed, PLMD::generic::Print, PLMD::generic::Read, PLMD::gridtools::GridPrintingBase, PLMD::isdb::CS2Backbone, PLMD::isdb::JCoupling, PLMD::isdb::Metainference, PLMD::isdb::NOE, PLMD::isdb::PRE, PLMD::isdb::RDC, PLMD::isdb::SAXS, PLMD::logmfd::LogMFD, PLMD::mapping::AdaptivePath, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::VolumeCavity, PLMD::multicolvar::VolumeTetrapore, PLMD::opes::OPESexpanded, PLMD::opes::OPESmetad< mode >, PLMD::opes::OPESmetad< convergence >, PLMD::opes::OPESmetad< exploration >, PLMD::ves::Optimizer, PLMD::ves::OutputFesBias, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::ves::VesLinearExpansion, and PLMD::vesselbase::ActionWithAveraging.

◆ 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.

◆ arguments

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

privateinherited

◆ aves

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

private

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.

◆ 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.

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ 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.

◆ 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.

◆ 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.

◆ 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.

◆ 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 files:

manyrestraints/ManyRestraintsBase.h
manyrestraints/ManyRestraintsBase.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ ManyRestraintsBase()

Member Function Documentation

◆ activate()

◆ addBridgeForces()

◆ addBridgingVessel()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addTaskToList()

◆ addValue()

◆ addValueWithDerivatives()

◆ addVessel() [1/2]

◆ addVessel() [2/2]

◆ apply()

◆ applyBridgeForces()

◆ beforeUpdate()

◆ buildDataStashes()

◆ calcPotential()

◆ calculate()

◆ calculateAllVessels()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ deactivate_task()

◆ deactivateAllTasks()

◆ derivativesAreRequired()

◆ doJobsRequiredBeforeTaskList()

◆ doNotCalculateDerivatives()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ finishComputations()

◆ fopen()

◆ getActiveTask()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getCurrentNumberOfActiveTasks()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getForcesFromVessels()

◆ getFullNumberOfTasks()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNLTolerance()

◆ getNumberOfComponents()

◆ getNumberOfDerivatives()

◆ getNumberOfQuantities()