A class for holding the value of a function together with its derivatives. More...

#include <Value.h>

Public Member Functions
	Value ()
	A constructor that can be used to make Vectors of values. More...

	Value (ActionWithValue *av, const std::string &name, const bool withderiv)
	A constructor that is used throughout the code to setup the value poiters. More...

void	set (double)
	Set the value of the function. More...

void	add (double)
	Add something to the value of the function. More...

double	get () const
	Get the value of the function. More...

bool	valueHasBeenSet () const
	Find out if the value has been set. More...

bool	isPeriodic () const
	Check if the value is periodic. More...

void	setNotPeriodic ()
	Set the function not periodic. More...

void	setDomain (const std::string &, const std::string &)
	Set the domain of the function. More...

void	getDomain (std::string &, std::string &) const
	Get the domain of the quantity. More...

void	getDomain (double &, double &) const
	Get the domain of the quantity. More...

const std::string &	getName () const
	Get the name of the quantity. More...

bool	hasDerivatives () const
	Check whether or not this particular quantity has derivatives. More...

unsigned	getNumberOfDerivatives () const
	Get the number of derivatives that this particular value has. More...

void	resizeDerivatives (int n)
	Set the number of derivatives. More...

void	clearDerivatives ()
	Set all the derivatives to zero. More...

void	addDerivative (unsigned i, double d)
	Add some derivative to the ith component of the derivatives array. More...

void	setDerivative (unsigned i, double d)
	Set the value of the ith component of the derivatives array. More...

void	chainRule (double df)
	Apply the chain rule to the derivatives. More...

double	getDerivative (const unsigned n) const
	Get the derivative with respect to component n. More...

void	clearInputForce ()
	Clear the input force on the variable. More...

void	addForce (double f)
	Add some force on this value. More...

double	getForce () const
	Get the value of the force on this colvar. More...

bool	applyForce (std::vector< double > &forces) const
	Apply the forces to the derivatives using the chain rule (if there are no forces this routine returns false. More...

double	difference (double) const
	Calculate the difference between the instantaneous value of the function and some other point: other_point-inst_val. More...

double	difference (double d1, double d2) const
	Calculate the difference between two values of this function: d2 -d1. More...

ActionWithValue *	getPntrToAction ()
	This returns the pointer to the action where this value is calculated. More...

double	bringBackInPbc (double d1) const
	Bring back one value into the correct pbc if needed, else give back the value. More...

void	setGradients ()
	This sets up the gradients. More...

Static Public Member Functions
static double	projection (const Value &, const Value &)

Private Types
enum	{ unset, periodic, notperiodic }
	Is this quantity periodic. More...

Private Member Functions
void	setupPeriodicity ()
	Complete the setup of the periodicity. More...

void	applyPeriodicity ()

Private Attributes
ActionWithValue *	action
	The action in which this quantity is calculated. More...

bool	value_set
	Had the value been set. More...

double	value
	The value of the quantity. More...

double	inputForce
	The force acting on this quantity. More...

bool	hasForce
	A flag telling us we have a force acting on this quantity. More...

std::vector< double >	derivatives
	The derivatives of the quantity stored in value. More...

std::map< AtomNumber, Vector >	gradients

std::string	name
	The name of this quantiy. More...

bool	hasDeriv
	Does this quanity have derivatives. More...

enum PLMD::Value:: { ... }	periodicity
	Is this quantity periodic. More...

std::string	str_min
	Various quantities that describe the domain of this value. More...

std::string	str_max

double	min

double	max

double	max_minus_min

double	inv_max_minus_min

Friends
class	ActionWithValue

void	copy (const Value &val1, Value &val2)
	This copies the contents of a value into a second value (just the derivatives and value) More...

void	copy (const Value &val, Value *val2)
	This copies the contents of a value into a second value (but second value is a pointer) More...

void	add (const Value &val1, Value *valout)
	This adds some derivatives onto the value. More...

void	product (const Value &val1, const Value &val2, Value &valout)
	This calculates val1*val2 and sorts out the derivatives. More...

void	quotient (const Value &val1, const Value &val2, Value *valout)
	This calculates va1/val2 and sorts out the derivatives. More...

Detailed Description

A class for holding the value of a function together with its derivatives.

Typically, an object of type PLMD::ActionWithValue will contain one object of type PLUMD::Value that will be named after the label. If the PLMD::ActionWithValue is part of a class that calculates multiple components then the class will contain multiple that will be called label.component-name This class is used to pass information between different PLMD::Action objects. However, if you find a use for a tempory PLMD::Value in some method you are implementing please feel free to use it.

Member Enumeration Documentation

anonymous enum

private

Is this quantity periodic.

Enumerator
unset
periodic
notperiodic

Constructor & Destructor Documentation

PLMD::Value::Value ( )

A constructor that can be used to make Vectors of values.

PLMD::Value::Value	(	ActionWithValue *	av,
		const std::string &	name,
		const bool	withderiv
	)

A constructor that is used throughout the code to setup the value poiters.

Member Function Documentation

void PLMD::Value::add ( double v )

inline

Add something to the value of the function.

void PLMD::Value::addDerivative	(	unsigned	i,
		double	d
	)

inline

Add some derivative to the ith component of the derivatives array.

void PLMD::Value::addForce ( double f )

inline

Add some force on this value.

bool PLMD::Value::applyForce ( std::vector< double > & forces ) const

Apply the forces to the derivatives using the chain rule (if there are no forces this routine returns false.

void PLMD::Value::applyPeriodicity ( )

inlineprivate

double PLMD::Value::bringBackInPbc ( double d1 ) const

inline

Bring back one value into the correct pbc if needed, else give back the value.

void PLMD::Value::chainRule ( double df )

inline

Apply the chain rule to the derivatives.

void PLMD::Value::clearDerivatives ( )

inline

Set all the derivatives to zero.

void PLMD::Value::clearInputForce ( )

inline

Clear the input force on the variable.

double PLMD::Value::difference ( double d ) const

inline

Calculate the difference between the instantaneous value of the function and some other point: other_point-inst_val.

double PLMD::Value::difference	(	double	d1,
		double	d2
	)		const

inline

Calculate the difference between two values of this function: d2 -d1.

d2-d1

double PLMD::Value::get ( ) const

inline

Get the value of the function.

double PLMD::Value::getDerivative ( const unsigned n ) const

inline

Get the derivative with respect to component n.

void PLMD::Value::getDomain	(	std::string &	minout,
		std::string &	maxout
	)		const

Get the domain of the quantity.

void PLMD::Value::getDomain	(	double &	minout,
		double &	maxout
	)		const

Get the domain of the quantity.

double PLMD::Value::getForce ( ) const

inline

Get the value of the force on this colvar.

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

inline

Get the name of the quantity.

unsigned PLMD::Value::getNumberOfDerivatives ( ) const

inline

Get the number of derivatives that this particular value has.

ActionWithValue * PLMD::Value::getPntrToAction ( )

This returns the pointer to the action where this value is calculated.

bool PLMD::Value::hasDerivatives ( ) const

inline

Check whether or not this particular quantity has derivatives.

bool PLMD::Value::isPeriodic ( ) const

Check if the value is periodic.

double PLMD::Value::projection	(	const Value &	v1,
		const Value &	v2
	)

static

void PLMD::Value::resizeDerivatives ( int n )

inline

Set the number of derivatives.

void PLMD::Value::set ( double v )

inline

Set the value of the function.

void PLMD::Value::setDerivative	(	unsigned	i,
		double	d
	)

inline

Set the value of the ith component of the derivatives array.

void PLMD::Value::setDomain	(	const std::string &	pmin,
		const std::string &	pmax
	)

Set the domain of the function.

void PLMD::Value::setGradients ( )

This sets up the gradients.

void PLMD::Value::setNotPeriodic ( )

Set the function not periodic.

void PLMD::Value::setupPeriodicity ( )

private

Complete the setup of the periodicity.

bool PLMD::Value::valueHasBeenSet ( ) const

inline

Find out if the value has been set.

Friends And Related Function Documentation

friend class ActionWithValue

friend

void add	(	const Value &	val1,
		Value *	valout
	)

friend

This adds some derivatives onto the value.

void copy	(	const Value &	val1,
		Value &	val2
	)

friend

This copies the contents of a value into a second value (just the derivatives and value)

void copy	(	const Value &	val,
		Value *	val2
	)

friend

This copies the contents of a value into a second value (but second value is a pointer)

void product	(	const Value &	val1,
		const Value &	val2,
		Value &	valout
	)

friend

This calculates val1*val2 and sorts out the derivatives.

void quotient	(	const Value &	val1,
		const Value &	val2,
		Value *	valout
	)

friend

This calculates va1/val2 and sorts out the derivatives.

Member Data Documentation

ActionWithValue* PLMD::Value::action

private

The action in which this quantity is calculated.

std::vector<double> PLMD::Value::derivatives

private

The derivatives of the quantity stored in value.

std::map<AtomNumber,Vector> PLMD::Value::gradients

private

bool PLMD::Value::hasDeriv

private

Does this quanity have derivatives.

bool PLMD::Value::hasForce

private

A flag telling us we have a force acting on this quantity.

double PLMD::Value::inputForce

private

The force acting on this quantity.

double PLMD::Value::inv_max_minus_min

private

double PLMD::Value::max

private

double PLMD::Value::max_minus_min

private

double PLMD::Value::min

private

std::string PLMD::Value::name

private

The name of this quantiy.

enum { ... } PLMD::Value::periodicity

Is this quantity periodic.

std::string PLMD::Value::str_max

private

std::string PLMD::Value::str_min

private

Various quantities that describe the domain of this value.

double PLMD::Value::value

private

The value of the quantity.

bool PLMD::Value::value_set

private

Had the value been set.

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

core/Value.h
core/Value.cpp

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation