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	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...

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.

Definition at line 46 of file Value.h.

Constructor & Destructor Documentation

PLMD::Value::Value ( )

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

Definition at line 33 of file Value.cpp.

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.

Definition at line 48 of file Value.cpp.

Member Function Documentation

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

inline

Add something to the value of the function.

Definition at line 180 of file Value.h.

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

inline

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

Definition at line 224 of file Value.h.

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

inline

Add some force on this value.

Definition at line 247 of file Value.h.

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.

Definition at line 80 of file Value.cpp.

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

inline

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

Definition at line 271 of file Value.h.

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

inline

Apply the chain rule to the derivatives.

Definition at line 230 of file Value.h.

void PLMD::Value::clearDerivatives ( )

inline

Set all the derivatives to zero.

Definition at line 241 of file Value.h.

void PLMD::Value::clearInputForce ( )

inline

Clear the input force on the variable.

Definition at line 235 of file Value.h.

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.

Definition at line 276 of file Value.h.

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

inline

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

d2-d1

Definition at line 259 of file Value.h.

double PLMD::Value::get ( ) const

inline

Get the value of the function.

Definition at line 186 of file Value.h.

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

inline

Get the derivative with respect to component n.

Definition at line 207 of file Value.h.

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

Get the domain of the quantity.

Definition at line 99 of file Value.cpp.

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

Get the domain of the quantity.

Definition at line 105 of file Value.cpp.

double PLMD::Value::getForce ( ) const

inline

Get the value of the force on this colvar.

Definition at line 254 of file Value.h.

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

inline

Get the name of the quantity.

Definition at line 196 of file Value.h.

unsigned PLMD::Value::getNumberOfDerivatives ( ) const

inline

Get the number of derivatives that this particular value has.

Definition at line 201 of file Value.h.

ActionWithValue * PLMD::Value::getPntrToAction ( )

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

Definition at line 154 of file Value.cpp.

bool PLMD::Value::hasDerivatives ( ) const

inline

Check whether or not this particular quantity has derivatives.

Definition at line 213 of file Value.h.

bool PLMD::Value::isPeriodic ( ) const

Check if the value is periodic.

Definition at line 75 of file Value.cpp.

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

static

Definition at line 140 of file Value.cpp.

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

inline

Set the number of derivatives.

Definition at line 218 of file Value.h.

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

inline

Set the value of the function.

Definition at line 174 of file Value.h.

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

Set the domain of the function.

Definition at line 91 of file Value.cpp.

void PLMD::Value::setGradients ( )

This sets up the gradients.

Definition at line 111 of file Value.cpp.

void PLMD::Value::setNotPeriodic ( )

Set the function not periodic.

Definition at line 87 of file Value.cpp.

void PLMD::Value::setupPeriodicity ( )

private

Complete the setup of the periodicity.

Definition at line 64 of file Value.cpp.

bool PLMD::Value::valueHasBeenSet ( ) const

inline

Find out if the value has been set.

Definition at line 191 of file Value.h.

Friends And Related Function Documentation

friend class ActionWithValue

friend

Definition at line 47 of file Value.h.

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

friend

This adds some derivatives onto the value.

Definition at line 175 of file Value.cpp.

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

friend

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

Definition at line 159 of file Value.cpp.

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)

Definition at line 167 of file Value.cpp.

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

friend

This calculates val1*val2 and sorts out the derivatives.

Definition at line 150 of file Value.h.

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

friend

This calculates va1/val2 and sorts out the derivatives.

Definition at line 162 of file Value.h.

Member Data Documentation

ActionWithValue* PLMD::Value::action

private

The action in which this quantity is calculated.

Definition at line 60 of file Value.h.

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

private

The derivatives of the quantity stored in value.

Definition at line 70 of file Value.h.

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

private

Definition at line 71 of file Value.h.

bool PLMD::Value::hasDeriv

private

Does this quanity have derivatives.

Definition at line 75 of file Value.h.

bool PLMD::Value::hasForce

private

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

Definition at line 68 of file Value.h.

double PLMD::Value::inputForce

private

The force acting on this quantity.

Definition at line 66 of file Value.h.

double PLMD::Value::inv_max_minus_min

private

Definition at line 82 of file Value.h.

double PLMD::Value::max

private

Definition at line 80 of file Value.h.

double PLMD::Value::max_minus_min

private

Definition at line 81 of file Value.h.

double PLMD::Value::min

private

Definition at line 80 of file Value.h.

std::string PLMD::Value::name

private

The name of this quantiy.

Definition at line 73 of file Value.h.

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

Is this quantity periodic.

std::string PLMD::Value::str_max

private

Definition at line 79 of file Value.h.

std::string PLMD::Value::str_min

private

Various quantities that describe the domain of this value.

Definition at line 79 of file Value.h.

double PLMD::Value::value

private

The value of the quantity.

Definition at line 64 of file Value.h.

bool PLMD::Value::value_set

private

Had the value been set.

Definition at line 62 of file Value.h.

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation