Inheritance diagram for PLMD::secondarystructure::AlphaRMSD:

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

typedef std::set< FILE * > ::iterator	files_iterator

Public Member Functions
	AlphaRMSD (const ActionOptions &)

unsigned	getNumberOfFunctionsInAction ()

unsigned	getNumberOfDerivatives ()

void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

void	calculate ()
	Calculate an Action. More...

void	performTask (const unsigned &j)
	Calculate one of the functions in the distribution. More...

void	clearDerivativesAfterTask (const unsigned &)

void	apply ()
	Apply an Action. More...

void	mergeDerivatives (const unsigned &, const double &)

bool	isPeriodic ()
	Are the base quantities periodic. More...

void	requestAtoms (const std::vector< AtomNumber > &a)
	Request an array of atoms. More...

const Vector &	getPosition (int) const
	Get position of i-th atom. More...

const Tensor &	getBox () const
	Get position of i-th atom. More...

const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...

const double &	getEnergy () const
	Get energy. More...

double	getMass (int i) const
	Get mass of i-th atom. More...

double	getCharge (int i) const
	Get charge of i-th atom. More...

std::vector< Vector > &	modifyForces ()
	Get a reference to forces array. More...

Tensor &	modifyVirial ()
	Get a reference to virial array. More...

double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...

unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...

Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...

const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...

AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...

void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. More...

void	parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
	Parse an list of atom with a numbred keyword. More...

const Pbc &	getPbc () const
	Get reference to Pbc. More...

void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
	Add the forces to the atoms. More...

void	clearOutputForces ()

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	N.B. More...

void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...

void	retrieveAtoms ()

void	applyForces ()

void	lockRequests ()

void	unlockRequests ()

const std::set< AtomNumber > &	getUnique () const

void	readAtomsFromPDB (const PDB &pdb)
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	clearDependencies ()
	Clear the dependence list for this Action. More...

long int	getStep () const
	Return the present timestep. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. 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 >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

void	error (const std::string &msg) const
	Crash calculation and print documentation. More...

void	warning (const std::string &msg)
	Issue a warning. More...

void	exit (int c=0)
	Exit with error code c. More...

void	checkRead ()
	Check if Action was properly read. More...

virtual void	update ()
	Update. More...

virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...

void	fflush ()
	Tell to the Action to flush open files. More...

virtual std::string	getDocumentation () const

const std::string &	getLabel () const
	Returns the label. More...

const std::string &	getName () const
	Returns the name. More...

virtual void	activate ()
	Set action to active. More...

virtual void	setOption (const std::string &s)

virtual void	clearOptions ()

virtual void	deactivate ()
	Set action to inactive. More...

bool	isActive () const
	Check if action is active. More...

bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...

const Dependencies &	getDependencies () const
	Return dependencies. More...

virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...

bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be used. More...

virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. 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	setNotPeriodic ()
	Set your default value to have no periodicity. More...

void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

void	setValue (Value *, double)
	Set the value. 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	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...

double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...

double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...

bool	exists (const std::string &name) const
	Check if a value with a particular name is present. More...

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. More...

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. 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...

int	getNumberOfComponents () const
	Returns the number of values defined. More...

void	clearInputForces ()
	Clear the forces on the values. More...

virtual void	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...

void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...

virtual void	checkFieldsAllowed ()

virtual void	mergeFieldDerivatives (const std::vector< double > &derivatives, Value *val_out)

virtual void	unlockContributors ()
	Used to make sure we are calculating everything during neighbor list update step. More...

virtual void	lockContributors ()

virtual void	deactivate_task ()
	Activate the jth colvar Deactivate the current task in future loops. More...

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *)
	Merge the derivatives. More...

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)

virtual void	retrieveDomain (std::string &min, std::string &max)
	What are the domains of the base quantities. More...

virtual void	doJobsRequiredBeforeTaskList ()
	Do any jobs that are required before the task list is undertaken. More...

Vessel *	getVessel (const std::string &name)
	Return a pointer to the field. More...

void	addElementDerivative (const unsigned &, const double &)
	Add some derivative of the quantity in the sum wrt to a numbered element. More...

void	setElementValue (const unsigned &, const double &)
	Set the value of the element. More...

double	getElementValue (const unsigned &ival) const
	Get the value of this element. More...

double	getElementDerivative (const unsigned &) const
	Retrieve the derivative of the quantity in the sum wrt to a numbered element. More...

virtual void	applyBridgeForces (const std::vector< double > &bb)
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

Public Attributes
PlumedMain &	plumed
	Reference to main plumed object. More...

Log &	log
	Reference to the log stream. More...

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
void	readBackboneAtoms (const std::vector< std::string > &backnames, std::vector< unsigned > &chain_lengths)
	Get the atoms in the backbone. More...

void	addColvar (const std::vector< unsigned > &newatoms)
	Add a set of atoms to calculat ethe rmsd from. More...

void	setSecondaryStructure (std::vector< Vector > &structure, double bondlength, double units)
	Set a reference configuration. More...

void	setAtomsFromStrands (const unsigned &atom1, const unsigned &atom2)
	Setup a pair of atoms to use for strands cutoff. More...

Value *	getPntrToValue ()
	Get a pointer to the default value. More...

void	setValue (const double &d)
	Set the default value (the one without name) More...

Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...

Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

void	addVessel (const std::string &name, const std::string &input, const int numlab=0, const std::string thislab="")
	Add a vessel to the list of vessels. More...

void	addVessel (Vessel *vv)

BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels. More...

void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...

double	getTolerance () const
	Return the value of the tolerance. More...

double	getNLTolerance () const
	Return the value for the neighbor list tolerance. More...

unsigned	getNumberOfVessels () const
	Get the number of vessels. More...

Vessel *	getPntrToVessel (const unsigned &i)
	Get a pointer to the ith vessel. More...

void	runAllTasks ()
	Calculate the values of all the vessels. More...

void	finishComputations ()
	Finish running all the calculations. More...

void	resizeFunctions ()
	Resize all the functions when the number of derivatives change. More...

void	setElementDerivative (const unsigned &, const double &)
	Set the derivative of the jth element wrt to a numbered element. More...

bool	calculateAllVessels ()
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

bool	getForcesFromVessels (std::vector< double > &forcesToApply)
	Retrieve the forces from all the vessels (used in apply) More...

void	accumulateDerivative (const unsigned &ider, const double &df)
	This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More...

void	clearAfterTask ()
	Clear tempory data that is calculated for each task. More...

Protected Attributes
Atoms &	atoms

bool	contributorsAreUnlocked
	The terms in the series are locked. More...

bool	weightHasDerivatives
	Does the weight have derivatives. More...

unsigned	current
	The numerical index of the task we are curently performing. More...

unsigned	bridgeVariable
	This is used for numerical derivatives of bridge variables. More...

DynamicList< unsigned >	taskList
	The list of tasks we have to perform. More...

Detailed Description

Provides the keyword ALPHARMSD

Definition at line 80 of file AlphaRMSD.cpp.

Member Typedef Documentation

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

inherited

Definition at line 75 of file Action.h.

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Definition at line 140 of file Action.h.

Constructor & Destructor Documentation

PLMD::secondarystructure::AlphaRMSD::AlphaRMSD ( const ActionOptions & ao )

Definition at line 92 of file AlphaRMSD.cpp.

Member Function Documentation

void PLMD::vesselbase::ActionWithVessel::accumulateDerivative	(	const unsigned &	ider,
		const double &	df
	)

inlineprotectedinherited

This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.

Definition at line 213 of file ActionWithVessel.h.

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

Definition at line 127 of file Action.cpp.

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

protectedinherited

Add a bridging vessel to the list of vessels.

Definition at line 85 of file ActionWithVessel.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::addColvar ( const std::vector< unsigned > & newatoms )

protectedinherited

Add a set of atoms to calculat ethe rmsd from.

Definition at line 133 of file SecondaryStructureRMSD.cpp.

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

inherited

Add a value with a name like label.name.

Definition at line 128 of file ActionWithValue.cpp.

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

inherited

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

Definition at line 144 of file ActionWithValue.cpp.

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

inherited

Specify that this Action depends on another one.

Definition at line 123 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::addElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inlineinherited

Add some derivative of the quantity in the sum wrt to a numbered element.

Definition at line 197 of file ActionWithVessel.h.

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

Definition at line 97 of file ActionWithValue.cpp.

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

Definition at line 102 of file ActionWithValue.cpp.

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

protectedinherited

Add a vessel to the list of vessels.

Definition at line 73 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel * vv )

protectedinherited

Definition at line 79 of file ActionWithVessel.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::apply ( )

virtualinherited

Apply an Action.

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

Implements PLMD::Action.

Definition at line 296 of file SecondaryStructureRMSD.cpp.

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > & bb )

inlinevirtualinherited

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

Reimplemented in PLMD::multicolvar::ActionVolume.

Definition at line 152 of file ActionWithVessel.h.

void ActionAtomistic::applyForces ( )

inherited

Definition at line 218 of file ActionAtomistic.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::calculate ( )

virtualinherited

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.

Definition at line 220 of file SecondaryStructureRMSD.cpp.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( )

protectedinherited

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

Definition at line 221 of file ActionWithVessel.cpp.

void ActionAtomistic::calculateAtomicNumericalDerivatives	(	ActionWithValue *	a,
		const unsigned &	startnum
	)

inherited

Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.

Definition at line 87 of file ActionAtomistic.cpp.

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

Definition at line 205 of file Action.cpp.

void ActionAtomistic::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

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::ActionVolume, and PLMD::multicolvar::MultiColvarFunction.

Definition at line 83 of file ActionAtomistic.cpp.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const double &	df,
		Vessel *	valout
	)

inherited

Merge the derivatives.

Definition at line 240 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const unsigned &	stride,
		const unsigned &	off,
		const double &	df,
		Vessel *	valout
	)

inherited

Definition at line 246 of file ActionWithVessel.cpp.

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

Definition at line 162 of file ActionWithValue.h.

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

inlinevirtualinherited

Check if the action needs gradient.

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

Definition at line 230 of file Action.h.

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

Definition at line 200 of file ActionWithValue.h.

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

Definition at line 227 of file Action.h.

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

Definition at line 161 of file Action.cpp.

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

Definition at line 221 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::clearAfterTask ( )

protectedinherited

Clear tempory data that is calculated for each task.

Definition at line 208 of file ActionWithVessel.cpp.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

Definition at line 153 of file Action.cpp.

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::ActionVolume.

Definition at line 69 of file ActionWithValue.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::clearDerivativesAfterTask ( const unsigned & )

inlinevirtualinherited

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Definition at line 94 of file SecondaryStructureRMSD.h.

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

Definition at line 66 of file ActionWithValue.cpp.

void PLMD::Action::clearOptions ( )

virtualinherited

Definition at line 147 of file Action.cpp.

void PLMD::ActionAtomistic::clearOutputForces ( )

inlineinherited

Definition at line 183 of file ActionAtomistic.h.

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

inherited

Set your value component to have no periodicity.

Definition at line 188 of file ActionWithValue.cpp.

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.

Definition at line 200 of file ActionWithValue.cpp.

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

staticinherited

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

Definition at line 42 of file ActionWithValue.cpp.

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.

Definition at line 82 of file ActionWithValue.cpp.

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.

Definition at line 90 of file ActionWithValue.cpp.

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

Definition at line 369 of file Action.h.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( )

virtualinherited

Activate the jth colvar Deactivate the current task in future loops.

Reimplemented in PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.

Definition at line 147 of file ActionWithVessel.cpp.

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )

virtualinherited

Do any jobs that are required before the task list is undertaken.

Reimplemented in PLMD::multicolvar::ActionVolume.

Definition at line 165 of file ActionWithVessel.cpp.

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

inherited

Crash calculation and print documentation.

Definition at line 195 of file Action.cpp.

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.

Definition at line 75 of file ActionWithValue.cpp.

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

inherited

Exit with error code c.

Definition at line 183 of file Action.cpp.

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

inherited

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

Definition at line 93 of file Action.cpp.

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

Definition at line 98 of file Action.cpp.

void PLMD::vesselbase::ActionWithVessel::finishComputations ( )

protectedinherited

Finish running all the calculations.

Definition at line 232 of file ActionWithVessel.cpp.

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)

Definition at line 83 of file Action.cpp.

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int i ) const

inlineinherited

Get the absolute index of an atom.

Definition at line 153 of file ActionAtomistic.h.

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getAbsoluteIndexes ( ) const

inlineinherited

Get the vector of absolute indexes.

Definition at line 148 of file ActionAtomistic.h.

const Tensor & PLMD::ActionAtomistic::getBox ( ) const

inlineinherited

Get position of i-th atom.

Definition at line 168 of file ActionAtomistic.h.

double PLMD::ActionAtomistic::getCharge ( int i ) const

inlineinherited

Get charge of i-th atom.

Definition at line 142 of file ActionAtomistic.h.

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

inherited

get a string that contains all the available components

Definition at line 170 of file ActionWithValue.cpp.

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

inherited

get a vector that contains the label for all the components

Definition at line 179 of file ActionWithValue.cpp.

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

inlineinherited

Return dependencies.

Definition at line 224 of file Action.h.

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

virtualinherited

Definition at line 157 of file Action.cpp.

double PLMD::vesselbase::ActionWithVessel::getElementDerivative ( const unsigned & ider ) const

inlineinherited

Retrieve the derivative of the quantity in the sum wrt to a numbered element.

Definition at line 191 of file ActionWithVessel.h.

double PLMD::vesselbase::ActionWithVessel::getElementValue ( const unsigned & ival ) const

inlineinherited

Get the value of this element.

Definition at line 177 of file ActionWithVessel.h.

const double & PLMD::ActionAtomistic::getEnergy ( ) const

inlineinherited

Get energy.

Definition at line 163 of file ActionAtomistic.h.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

Definition at line 217 of file Action.cpp.

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

protectedinherited

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

Definition at line 261 of file ActionWithVessel.cpp.

const std::string & PLMD::Action::getLabel ( ) const

inlineinherited

Returns the label.

Definition at line 263 of file Action.h.

double PLMD::ActionAtomistic::getMass ( int i ) const

inlineinherited

Get mass of i-th atom.

Definition at line 137 of file ActionAtomistic.h.

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

inlineinherited

Returns the name.

Definition at line 268 of file Action.h.

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

inlineprotectedinherited

Return the value for the neighbor list tolerance.

Definition at line 161 of file ActionWithVessel.h.

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

Definition at line 88 of file ActionAtomistic.h.

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

Definition at line 190 of file ActionWithValue.h.

unsigned PLMD::secondarystructure::SecondaryStructureRMSD::getNumberOfDerivatives ( )

inlinevirtualinherited

Reimplemented from PLMD::ActionWithValue.

Definition at line 106 of file SecondaryStructureRMSD.h.

unsigned PLMD::secondarystructure::SecondaryStructureRMSD::getNumberOfFunctionsInAction ( )

inlineinherited

Definition at line 101 of file SecondaryStructureRMSD.h.

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

inlineprotectedinherited

Get the number of vessels.

Definition at line 166 of file ActionWithVessel.h.

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

inlineinherited

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

Definition at line 168 of file ActionWithValue.h.

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)

Definition at line 174 of file ActionWithValue.h.

const Pbc & PLMD::ActionAtomistic::getPbc ( ) const

inlineinherited

Get reference to Pbc.

Definition at line 195 of file ActionAtomistic.h.

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

protectedinherited

Return a pointer to the component by index.

Definition at line 210 of file ActionWithValue.cpp.

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

protectedinherited

Return a pointer to the value by name.

Definition at line 205 of file ActionWithValue.cpp.

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

Definition at line 120 of file ActionWithValue.cpp.

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

inlineprotectedinherited

Get a pointer to the ith vessel.

Definition at line 171 of file ActionWithVessel.h.

const Vector & PLMD::ActionAtomistic::getPosition ( int i ) const

inlineinherited

Get position of i-th atom.

Definition at line 132 of file ActionAtomistic.h.

const std::vector< Vector > & PLMD::ActionAtomistic::getPositions ( ) const

inlineinherited

Get the array of all positions.

Definition at line 158 of file ActionAtomistic.h.

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

inherited

Return the present timestep.

Definition at line 169 of file Action.cpp.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

Definition at line 173 of file Action.cpp.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

Definition at line 177 of file Action.cpp.

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

inlineprotectedinherited

Return the value of the tolerance.

Definition at line 156 of file ActionWithVessel.h.

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const

inlineinherited

Definition at line 210 of file ActionAtomistic.h.

Vessel* PLMD::vesselbase::ActionWithVessel::getVessel ( const std::string & name )

inherited

Return a pointer to the field.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

Definition at line 375 of file Action.h.

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

inlineinherited

Check if an option is on.

Definition at line 380 of file Action.h.

bool PLMD::secondarystructure::SecondaryStructureRMSD::isPeriodic ( )

inlinevirtualinherited

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

Definition at line 97 of file SecondaryStructureRMSD.h.

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

inlinevirtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarFunction.

Definition at line 225 of file ActionWithVessel.h.

void PLMD::ActionAtomistic::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Definition at line 200 of file ActionAtomistic.h.

void PLMD::secondarystructure::SecondaryStructureRMSD::mergeDerivatives	(	const unsigned &	ider,
		const double &	df
	)

virtualinherited

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Definition at line 267 of file SecondaryStructureRMSD.cpp.

void PLMD::ActionWithValue::mergeFieldDerivatives	(	const std::vector< double > &	derivatives,
		Value *	val_out
	)

virtualinherited

Definition at line 215 of file ActionWithValue.cpp.

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

Definition at line 190 of file ActionAtomistic.h.

std::vector< Vector > & PLMD::ActionAtomistic::modifyForces ( )

inlineinherited

Get a reference to forces array.

Definition at line 173 of file ActionAtomistic.h.

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

Definition at line 178 of file ActionAtomistic.h.

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.

Definition at line 37 of file ActionWithValue.cpp.

template<class T >

void PLMD::Action::parse	(	const std::string &	key,
		T &	t
	)

inherited

Parse one keyword as generic type.

Definition at line 273 of file Action.h.

void ActionAtomistic::parseAtomList	(	const std::string &	key,
		std::vector< AtomNumber > &	t
	)

inherited

Parse a list of atoms without a numbered keyword.

Definition at line 141 of file ActionAtomistic.cpp.

void ActionAtomistic::parseAtomList	(	const std::string &	key,
		const int	num,
		std::vector< AtomNumber > &	t
	)

inherited

Parse an list of atom with a numbred keyword.

Definition at line 145 of file ActionAtomistic.cpp.

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

inherited

Parse one keyword as boolean flag.

Definition at line 104 of file Action.cpp.

template<class T >

bool PLMD::Action::parseNumbered	(	const std::string &	key,
		const int	no,
		T &	t
	)

inherited

Parse one numbered keyword as generic type.

Definition at line 300 of file Action.h.

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.

Definition at line 352 of file Action.h.

template<class T >

void PLMD::Action::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

inherited

Parse one keyword as std::vector.

Definition at line 311 of file Action.h.

Vector ActionAtomistic::pbcDistance	(	const Vector &	v1,
		const Vector &	v2
	)		const

inherited

Compute the pbc distance between two positions.

Definition at line 79 of file ActionAtomistic.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::performTask ( const unsigned & j )

virtualinherited

Calculate one of the functions in the distribution.

Implements PLMD::vesselbase::ActionWithVessel.

Definition at line 224 of file SecondaryStructureRMSD.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::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 from PLMD::Action.

Definition at line 198 of file SecondaryStructureRMSD.cpp.

void ActionAtomistic::readAtomsFromPDB ( const PDB & pdb )

virtualinherited

Read in an input file containing atom positions and calculate the action for the atomic configuration therin.

Reimplemented from PLMD::Action.

Definition at line 226 of file ActionAtomistic.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::readBackboneAtoms	(	const std::vector< std::string > &	backnames,
		std::vector< unsigned > &	chain_lengths
	)

protectedinherited

Get the atoms in the backbone.

Definition at line 109 of file SecondaryStructureRMSD.cpp.

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

protectedinherited

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

Definition at line 94 of file ActionWithVessel.cpp.

void PLMD::secondarystructure::AlphaRMSD::registerKeywords ( Keywords & keys )

static

Definition at line 88 of file AlphaRMSD.cpp.

void ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > & a )

inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

Definition at line 59 of file ActionAtomistic.cpp.

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

protectedinherited

Resize all the functions when the number of derivatives change.

Definition at line 130 of file ActionWithVessel.cpp.

void ActionAtomistic::retrieveAtoms ( )

inherited

Definition at line 186 of file ActionAtomistic.cpp.

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

virtualinherited

What are the domains of the base quantities.

Definition at line 274 of file ActionWithVessel.cpp.

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

protectedinherited

Calculate the values of all the vessels.

Definition at line 172 of file ActionWithVessel.cpp.

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::Analysis.

Definition at line 193 of file Action.h.

void PLMD::secondarystructure::SecondaryStructureRMSD::setAtomsFromStrands	(	const unsigned &	atom1,
		const unsigned &	atom2
	)

protectedinherited

Setup a pair of atoms to use for strands cutoff.

Definition at line 105 of file SecondaryStructureRMSD.cpp.

void PLMD::vesselbase::ActionWithVessel::setElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inlineprotectedinherited

Set the derivative of the jth element wrt to a numbered element.

Definition at line 207 of file ActionWithVessel.h.

void PLMD::vesselbase::ActionWithVessel::setElementValue	(	const unsigned &	ival,
		const double &	val
	)

inlineinherited

Set the value of the element.

Definition at line 182 of file ActionWithVessel.h.

void ActionAtomistic::setForcesOnAtoms	(	const std::vector< double > &	forcesToApply,
		unsigned	ind = `0`
	)

inherited

Add the forces to the atoms.

Definition at line 200 of file ActionAtomistic.cpp.

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

Definition at line 194 of file ActionWithValue.cpp.

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

Definition at line 107 of file ActionWithValue.cpp.

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

virtualinherited

Definition at line 141 of file Action.cpp.

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

inherited

Set the value to be periodic with a particular domain.

Definition at line 114 of file ActionWithValue.cpp.

void PLMD::secondarystructure::SecondaryStructureRMSD::setSecondaryStructure	(	std::vector< Vector > &	structure,
		double	bondlength,
		double	units
	)

protectedinherited

Set a reference configuration.

Definition at line 144 of file SecondaryStructureRMSD.cpp.

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

inlineprotectedinherited

Set the default value (the one without name)

Definition at line 183 of file ActionWithValue.h.

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

inherited

Set the value.

void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )

inlinevirtualinherited

Used to make sure we are calculating everything during neighbor list update step.

Reimplemented in PLMD::multicolvar::MultiColvarFunction.

Definition at line 219 of file ActionWithVessel.h.

void PLMD::ActionAtomistic::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Definition at line 205 of file ActionAtomistic.h.

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::bias::MetaD, PLMD::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.

Definition at line 188 of file Action.h.

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

staticinherited

The components in the action will depend on the user.

Definition at line 48 of file ActionWithValue.cpp.

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

Definition at line 195 of file ActionWithValue.h.

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

inherited

Issue a warning.

Definition at line 201 of file Action.cpp.

Member Data Documentation

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

Definition at line 59 of file ActionAtomistic.h.

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

Definition at line 81 of file ActionWithVessel.h.

Communicator& PLMD::Action::comm

inherited

Definition at line 158 of file Action.h.

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

Definition at line 75 of file ActionWithVessel.h.

unsigned PLMD::vesselbase::ActionWithVessel::current

protectedinherited

The numerical index of the task we are curently performing.

Definition at line 79 of file ActionWithVessel.h.

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

inherited

Definition at line 139 of file Action.h.

const Keywords& PLMD::Action::keywords

inherited

Definition at line 161 of file Action.h.

Log& PLMD::Action::log

inherited

Reference to the log stream.

Definition at line 93 of file Action.h.

Communicator& PLMD::Action::multi_sim_comm

inherited

Definition at line 159 of file Action.h.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

Definition at line 90 of file Action.h.

DynamicList<unsigned> PLMD::vesselbase::ActionWithVessel::taskList

protectedinherited

The list of tasks we have to perform.

Definition at line 83 of file ActionWithVessel.h.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

Definition at line 77 of file ActionWithVessel.h.

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

secondarystructure/AlphaRMSD.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation