#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, const std::vector< unsigned > &ss=std::vector< unsigned >())
	A constructor that is used throughout the code to setup the value poiters. More...

	Value (const std::string &name)
	A constructor that can be used to make Vectors of named values. More...

void	add (const std::size_t &n, const double &v)
	Add something to the ith element of the data array. More...

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

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

void	addForce (const std::size_t &ival, double f, const bool trueind=true)
	Add some force on the ival th component of this value. More...

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

void	addGridDerivatives (const unsigned &n, const unsigned &j, const double &val)
	Add the derivatives of the grid to the corner. 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	bringBackInPbc (double d1) const
	Bring back one value into the correct pbc if needed, else give back the value. More...

void	buildDataStore (const bool forprint=false)
	This turns on storing of vectors/matrices. More...

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

void	clearDerivatives (const bool force=false)
	Set all the derivatives to zero. More...

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

void	clearInputForce (const std::vector< AtomNumber > &index)
	Special method for clearing forces on variables used by DataPassingObject. More...

void	convertIndexToindices (const std::size_t &index, std::vector< unsigned > &indices) const
	Convert the input index to its corresponding indices. More...

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

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

bool	forcesWereAdded () const
	Check if forces have been added on this value. More...

double	get (const std::size_t &ival=0, const bool trueind=true) const
	Get the value of the function. More...

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

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

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

double	getForce (const std::size_t &ival=0) const
	Get the value of the force on this colvar. More...

unsigned	getGoodNumThreads (const unsigned &j, const unsigned &k) const
	Get the number of threads to use when assigning this value. More...

double	getGridDerivative (const unsigned &n, const unsigned &j) const
	get the derivative of a grid at a point n with resepct to argument j More...

unsigned	getMatrixBookeepingStart () const

double	getMaxMinusMin () const
	Get the difference between max and minimum of domain. More...

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

unsigned	getNumberOfColumns () const

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

unsigned	getNumberOfGridDerivatives () const
	Get the number of derivatives that the grid has. More...

unsigned	getNumberOfValues () const
	Get the total number of scalars that are stored here. More...

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

unsigned	getPositionInMatrixStash () const

unsigned	getPositionInStream () const

unsigned	getRank () const
	Get the rank of the object that is contained in this value. More...

unsigned	getRowIndex (const unsigned &irow, const unsigned &jind) const

unsigned	getRowLength (const unsigned &irow) const

const std::vector< unsigned > &	getShape () const
	Get the shape of the object that is contained in this value. More...

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

bool	ignoreStoredValue (const std::string &n) const
	Are we to ignore the stored value. More...

bool	isConstant () const
	These are used for making constant values. More...

bool	isDerivativeZeroWhenValueIsZero () const
	Return a bool that tells us if the derivative is zero when the value is zero. More...

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

bool	isSymmetric () const

void	passGradients (const double &der, std::map< AtomNumber, Vector > &g) const
	This passes gradients from one action to another. More...

void	print (OFile &ofile) const
	Print out all the values in this Value. More...

void	push_back (const double &val)
	Add another value to the end of the data vector held by this value. This is used in COLLECT. More...

void	readBinary (std::istream &i)

void	reshapeMatrixStore (const unsigned &n)
	Reshape the storage for sparse matrices. More...

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

void	retrieveEdgeList (unsigned &nedge, std::vector< std::pair< unsigned, unsigned > > &active, std::vector< double > &elems)
	Retrieve the non-zero edges in a matrix. More...

void	set (const std::size_t &n, const double &v)
	Set the value of the stored data. More...

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

void	setConstant ()

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

void	setDerivativeIsZeroWhenValueIsZero ()
	Set a bool that tells us if the derivative is zero when the value is zero true. More...

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

void	setGradients (ActionAtomistic *aa, unsigned &start)
	This sets up the gradients. More...

void	setGridDerivatives (const unsigned &n, const unsigned &j, const double &val)

void	setMatrixBookeepingElement (const unsigned &i, const unsigned &n)
	Set a matrix element to be non zero. More...

void	setMatrixBookeepingStart (const unsigned &b)
	This stuff handles where to keep the bookeeping stuff for storing the sparse matrix. More...

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

void	setPositionInMatrixStash (const unsigned &p)
	This stuff handles where to look for the start of the row that contains the row of the matrix. More...

void	setShape (const std::vector< unsigned > &ss)
	Set the shape of the Value. More...

void	setSymmetric (const bool &sym)
	Set the symmetric flag equal true for this matrix. More...

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

bool	valueIsStored () const
	Are we storing this value. More...

void	writeBinary (std::ostream &o) const
	These are used for passing around the data in this value when we are doing replica exchange. More...

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

Private Types
enum	{ normal, constant, average, calcFromAverage }
	The way this value is used in the code normal = regular value that is determined during calculate constant = constnt value that is determined during startup and that doesn't change during simulation average = value that is averaged/collected over multiple steps of trajectory calcFromAverage = value that is calculated from an average value. More...

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

Private Member Functions
void	applyPeriodicity (const unsigned &ival)

bool	calculateOnUpdate () const
	This is used by ActionWithValue to determine if we need to calculate on update. More...

void	setupPeriodicity ()
	Complete the setup of the periodicity. More...

void	setValType (const std::string &vtype)
	This is used by ActionWithValue to set the valtype. More...

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

unsigned	book_start

unsigned	bufstart
	Variables for storing data. More...

std::vector< double >	data
	The value of the quantity. More...

bool	derivativeIsZeroWhenValueIsZero
	Is the derivative of this quantity zero when the value is zero. More...

std::map< AtomNumber, Vector >	gradients
	The derivatives of the quantity stored in value. More...

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

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

std::vector< double >	inputForce
	The force acting on this quantity. More...

double	inv_max_minus_min

unsigned	matpos

std::vector< unsigned >	matrix_bookeeping
	This is a bookeeping array that holds the non-zero elements of the "sparse" matrix. More...

double	max

double	max_minus_min

double	min

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

unsigned	ncols

unsigned	ngrid_der

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

std::vector< unsigned >	shape
	What is the shape of the value (0 dimensional=scalar, n dimensional with derivatives=grid, 1 dimensional no derivatives=vector, 2 dimensional no derivatives=matrix) More...

bool	storedata
	Are we storing the data for this value if it is vector or matrix. More...

std::string	str_max

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

unsigned	streampos

bool	symmetric
	If we are storing a matrix is it symmetric? More...

enum PLMD::Value:: { ... }	valtype =normal
	The way this value is used in the code normal = regular value that is determined during calculate constant = constnt value that is determined during startup and that doesn't change during simulation average = value that is averaged/collected over multiple steps of trajectory calcFromAverage = value that is calculated from an average value. More...

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

Friends
class	ActionAtomistic

class	ActionWithArguments

class	ActionWithValue

class	ActionWithVector

class	ActionWithVirtualAtom

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

template<typename T >
class	DataPassingObjectTyped

class	DomainDecomposition

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

anonymous enum

private

The way this value is used in the code normal = regular value that is determined during calculate constant = constnt value that is determined during startup and that doesn't change during simulation average = value that is averaged/collected over multiple steps of trajectory calcFromAverage = value that is calculated from an average value.

Enumerator
normal
constant
average
calcFromAverage

◆ anonymous enum

anonymous enum

private

Is this quantity periodic.

Enumerator
unset
periodic
notperiodic

Constructor & Destructor Documentation

◆ Value() [1/3]

PLMD::Value::Value ( )

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

◆ Value() [2/3]

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

explicit

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

◆ Value() [3/3]

PLMD::Value::Value	(	ActionWithValue *	av,
		const std::string &	name,
		const bool	withderiv,
		const std::vector< unsigned > &	ss = `std::vector<unsigned>()`
	)

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

Member Function Documentation

◆ add() [1/2]

void PLMD::Value::add	(	const std::size_t &	n,
		const double &	v
	)

inline

Add something to the ith element of the data array.

◆ add() [2/2]

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

inline

Add something to the value of the function.

◆ addDerivative()

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

inline

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

◆ addForce() [1/2]

void PLMD::Value::addForce	(	const std::size_t &	ival,
		double	f,
		const bool	trueind = `true`
	)

Add some force on the ival th component of this value.

◆ addForce() [2/2]

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

inline

Add some force on this value.

◆ addGridDerivatives()

void PLMD::Value::addGridDerivatives	(	const unsigned &	n,
		const unsigned &	j,
		const double &	val
	)

inline

Add the derivatives of the grid to the corner.

◆ applyForce()

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)

◆ applyPeriodicity()

void PLMD::Value::applyPeriodicity ( const unsigned & ival )

inlineprivate

◆ bringBackInPbc()

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

inline

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

◆ buildDataStore()

void PLMD::Value::buildDataStore ( const bool forprint = false )

This turns on storing of vectors/matrices.

◆ calculateOnUpdate()

bool PLMD::Value::calculateOnUpdate ( ) const

private

This is used by ActionWithValue to determine if we need to calculate on update.

◆ chainRule()

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

inline

Apply the chain rule to the derivatives.

◆ clearDerivatives()

void PLMD::Value::clearDerivatives ( const bool force = false )

inline

Set all the derivatives to zero.

◆ clearInputForce() [1/2]

void PLMD::Value::clearInputForce ( )

inline

Clear the input force on the variable.

◆ clearInputForce() [2/2]

void PLMD::Value::clearInputForce ( const std::vector< AtomNumber > & index )

inline

Special method for clearing forces on variables used by DataPassingObject.

◆ convertIndexToindices()

void PLMD::Value::convertIndexToindices	(	const std::size_t &	index,
		std::vector< unsigned > &	indices
	)		const

Convert the input index to its corresponding indices.

◆ difference() [1/2]

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

inline

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

d2-d1

◆ difference() [2/2]

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.

◆ forcesWereAdded()

bool PLMD::Value::forcesWereAdded ( ) const

inline

Check if forces have been added on this value.

◆ get()

double PLMD::Value::get	(	const std::size_t &	ival = `0`,
		const bool	trueind = `true`
	)		const

Get the value of the function.

◆ getDerivative()

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

inline

Get the derivative with respect to component n.

◆ getDomain() [1/2]

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

Get the domain of the quantity.

◆ getDomain() [2/2]

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

Get the domain of the quantity.

◆ getForce()

double PLMD::Value::getForce ( const std::size_t & ival = 0 ) const

inline

Get the value of the force on this colvar.

◆ getGoodNumThreads()

unsigned PLMD::Value::getGoodNumThreads	(	const unsigned &	j,
		const unsigned &	k
	)		const

Get the number of threads to use when assigning this value.

◆ getGridDerivative()

double PLMD::Value::getGridDerivative	(	const unsigned &	n,
		const unsigned &	j
	)		const

inline

get the derivative of a grid at a point n with resepct to argument j

◆ getMatrixBookeepingStart()

unsigned PLMD::Value::getMatrixBookeepingStart ( ) const

inline

◆ getMaxMinusMin()

double PLMD::Value::getMaxMinusMin ( ) const

inline

Get the difference between max and minimum of domain.

◆ getName()

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

inline

Get the name of the quantity.

◆ getNumberOfColumns()

unsigned PLMD::Value::getNumberOfColumns ( ) const

inline

◆ getNumberOfDerivatives()

unsigned PLMD::Value::getNumberOfDerivatives ( ) const

inline

Get the number of derivatives that this particular value has.

◆ getNumberOfGridDerivatives()

unsigned PLMD::Value::getNumberOfGridDerivatives ( ) const

inline

Get the number of derivatives that the grid has.

◆ getNumberOfValues()

unsigned PLMD::Value::getNumberOfValues ( ) const

inline

Get the total number of scalars that are stored here.

◆ getPntrToAction()

ActionWithValue * PLMD::Value::getPntrToAction ( )

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

◆ getPositionInMatrixStash()

unsigned PLMD::Value::getPositionInMatrixStash ( ) const

inline

◆ getPositionInStream()

unsigned PLMD::Value::getPositionInStream ( ) const

inline

◆ getRank()

unsigned PLMD::Value::getRank ( ) const

inline

Get the rank of the object that is contained in this value.

◆ getRowIndex()

unsigned PLMD::Value::getRowIndex	(	const unsigned &	irow,
		const unsigned &	jind
	)		const

inline

◆ getRowLength()

unsigned PLMD::Value::getRowLength ( const unsigned & irow ) const

inline

◆ getShape()

const std::vector< unsigned > & PLMD::Value::getShape ( ) const

inline

Get the shape of the object that is contained in this value.

◆ hasDerivatives()

bool PLMD::Value::hasDerivatives ( ) const

inline

Check whether or not this particular quantity has derivatives.

◆ ignoreStoredValue()

bool PLMD::Value::ignoreStoredValue ( const std::string & n ) const

Are we to ignore the stored value.

◆ isConstant()

bool PLMD::Value::isConstant ( ) const

inline

These are used for making constant values.

◆ isDerivativeZeroWhenValueIsZero()

bool PLMD::Value::isDerivativeZeroWhenValueIsZero ( ) const

inline

Return a bool that tells us if the derivative is zero when the value is zero.

◆ isPeriodic()

bool PLMD::Value::isPeriodic ( ) const

Check if the value is periodic.

◆ isSymmetric()

bool PLMD::Value::isSymmetric ( ) const

inline

◆ passGradients()

void PLMD::Value::passGradients	(	const double &	der,
		std::map< AtomNumber, Vector > &	g
	)		const

This passes gradients from one action to another.

◆ print()

void PLMD::Value::print ( OFile & ofile ) const

Print out all the values in this Value.

◆ projection()

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

static

◆ push_back()

void PLMD::Value::push_back ( const double & val )

Add another value to the end of the data vector held by this value. This is used in COLLECT.

◆ readBinary()

void PLMD::Value::readBinary ( std::istream & i )

◆ reshapeMatrixStore()

void PLMD::Value::reshapeMatrixStore ( const unsigned & n )

Reshape the storage for sparse matrices.

◆ resizeDerivatives()

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

inline

Set the number of derivatives.

◆ retrieveEdgeList()

void PLMD::Value::retrieveEdgeList	(	unsigned &	nedge,
		std::vector< std::pair< unsigned, unsigned > > &	active,
		std::vector< double > &	elems
	)

Retrieve the non-zero edges in a matrix.

◆ set() [1/2]

void PLMD::Value::set	(	const std::size_t &	n,
		const double &	v
	)

Set the value of the stored data.

◆ set() [2/2]

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

inline

Set the value of the function.

◆ setConstant()

void PLMD::Value::setConstant ( )

◆ setDerivative()

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

inline

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

◆ setDerivativeIsZeroWhenValueIsZero()

void PLMD::Value::setDerivativeIsZeroWhenValueIsZero ( )

inline

Set a bool that tells us if the derivative is zero when the value is zero true.

◆ setDomain()

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

Set the domain of the function.

◆ setGradients()

void PLMD::Value::setGradients	(	ActionAtomistic *	aa,
		unsigned &	start
	)

This sets up the gradients.

◆ setGridDerivatives()

void PLMD::Value::setGridDerivatives	(	const unsigned &	n,
		const unsigned &	j,
		const double &	val
	)

inline

◆ setMatrixBookeepingElement()

void PLMD::Value::setMatrixBookeepingElement	(	const unsigned &	i,
		const unsigned &	n
	)

inline

Set a matrix element to be non zero.

◆ setMatrixBookeepingStart()

void PLMD::Value::setMatrixBookeepingStart ( const unsigned & b )

inline

This stuff handles where to keep the bookeeping stuff for storing the sparse matrix.

◆ setNotPeriodic()

void PLMD::Value::setNotPeriodic ( )

Set the function not periodic.

◆ setPositionInMatrixStash()

void PLMD::Value::setPositionInMatrixStash ( const unsigned & p )

This stuff handles where to look for the start of the row that contains the row of the matrix.

◆ setShape()

void PLMD::Value::setShape ( const std::vector< unsigned > & ss )

Set the shape of the Value.

◆ setSymmetric()

void PLMD::Value::setSymmetric ( const bool & sym )

Set the symmetric flag equal true for this matrix.

◆ setupPeriodicity()

void PLMD::Value::setupPeriodicity ( )

private

Complete the setup of the periodicity.

◆ setValType()

void PLMD::Value::setValType ( const std::string & vtype )

private

This is used by ActionWithValue to set the valtype.

◆ valueHasBeenSet()

bool PLMD::Value::valueHasBeenSet ( ) const

inline

Find out if the value has been set.

◆ valueIsStored()

bool PLMD::Value::valueIsStored ( ) const

inline

Are we storing this value.

◆ writeBinary()

void PLMD::Value::writeBinary ( std::ostream & o ) const

These are used for passing around the data in this value when we are doing replica exchange.

Friends And Related Function Documentation

◆ ActionAtomistic

friend class ActionAtomistic

friend

◆ ActionWithArguments

friend class ActionWithArguments

friend

◆ ActionWithValue

friend class ActionWithValue

friend

◆ ActionWithVector

friend class ActionWithVector

friend

◆ ActionWithVirtualAtom

friend class ActionWithVirtualAtom

friend

◆ add

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

friend

This adds some derivatives onto the value.

◆ copy [1/2]

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)

◆ copy [2/2]

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

friend

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

◆ DataPassingObjectTyped

template<typename T >

friend class DataPassingObjectTyped

friend

◆ DomainDecomposition

friend class DomainDecomposition

friend

◆ product

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

friend

This calculates val1*val2 and sorts out the derivatives.

◆ quotient

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

friend

This calculates va1/val2 and sorts out the derivatives.

Member Data Documentation

◆ action

ActionWithValue* PLMD::Value::action

private

The action in which this quantity is calculated.

◆ book_start

unsigned PLMD::Value::book_start

private

◆ bufstart

unsigned PLMD::Value::bufstart

private

Variables for storing data.

◆ data

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

private

The value of the quantity.

◆ derivativeIsZeroWhenValueIsZero

bool PLMD::Value::derivativeIsZeroWhenValueIsZero

private

Is the derivative of this quantity zero when the value is zero.

◆ gradients

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

private

The derivatives of the quantity stored in value.

◆ hasDeriv

bool PLMD::Value::hasDeriv

private

Does this quanity have derivatives.

◆ hasForce

bool PLMD::Value::hasForce

private

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

◆ inputForce

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

private

The force acting on this quantity.

◆ inv_max_minus_min

double PLMD::Value::inv_max_minus_min

private

◆ matpos

unsigned PLMD::Value::matpos

private

◆ matrix_bookeeping

std::vector<unsigned> PLMD::Value::matrix_bookeeping

private

This is a bookeeping array that holds the non-zero elements of the "sparse" matrix.

◆ max

double PLMD::Value::max

private

◆ max_minus_min

double PLMD::Value::max_minus_min

private

◆ min

double PLMD::Value::min

private

◆ name

std::string PLMD::Value::name

private

The name of this quantiy.

◆ ncols

unsigned PLMD::Value::ncols

private

◆ ngrid_der

unsigned PLMD::Value::ngrid_der

private

◆ periodicity

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

Is this quantity periodic.

◆ shape

std::vector<unsigned> PLMD::Value::shape

private

What is the shape of the value (0 dimensional=scalar, n dimensional with derivatives=grid, 1 dimensional no derivatives=vector, 2 dimensional no derivatives=matrix)

◆ storedata

bool PLMD::Value::storedata

private

Are we storing the data for this value if it is vector or matrix.

◆ str_max

std::string PLMD::Value::str_max

private

◆ str_min

std::string PLMD::Value::str_min

private

Various quantities that describe the domain of this value.

◆ streampos

unsigned PLMD::Value::streampos

private

◆ symmetric

bool PLMD::Value::symmetric

private

If we are storing a matrix is it symmetric?

◆ valtype

enum { ... } PLMD::Value::valtype

The way this value is used in the code normal = regular value that is determined during calculate constant = constnt value that is determined during startup and that doesn't change during simulation average = value that is averaged/collected over multiple steps of trajectory calcFromAverage = value that is calculated from an average value.

◆ value_set

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

◆ anonymous enum

◆ anonymous enum

Constructor & Destructor Documentation

◆ Value() [1/3]

◆ Value() [2/3]

◆ Value() [3/3]

Member Function Documentation

◆ add() [1/2]

◆ add() [2/2]

◆ addDerivative()

◆ addForce() [1/2]

◆ addForce() [2/2]

◆ addGridDerivatives()

◆ applyForce()

◆ applyPeriodicity()

◆ bringBackInPbc()

◆ buildDataStore()

◆ calculateOnUpdate()

◆ chainRule()

◆ clearDerivatives()

◆ clearInputForce() [1/2]

◆ clearInputForce() [2/2]

◆ convertIndexToindices()

◆ difference() [1/2]

◆ difference() [2/2]

◆ forcesWereAdded()

◆ get()

◆ getDerivative()

◆ getDomain() [1/2]

◆ getDomain() [2/2]

◆ getForce()

◆ getGoodNumThreads()

◆ getGridDerivative()

◆ getMatrixBookeepingStart()

◆ getMaxMinusMin()

◆ getName()

◆ getNumberOfColumns()

◆ getNumberOfDerivatives()

◆ getNumberOfGridDerivatives()

◆ getNumberOfValues()

◆ getPntrToAction()

◆ getPositionInMatrixStash()

◆ getPositionInStream()

◆ getRank()

◆ getRowIndex()

◆ getRowLength()

◆ getShape()

◆ hasDerivatives()

◆ ignoreStoredValue()

◆ isConstant()

◆ isDerivativeZeroWhenValueIsZero()

◆ isPeriodic()

◆ isSymmetric()

◆ passGradients()

◆ print()

◆ projection()

◆ push_back()

◆ readBinary()

◆ reshapeMatrixStore()

◆ resizeDerivatives()

◆ retrieveEdgeList()

◆ set() [1/2]

◆ set() [2/2]

◆ setConstant()

◆ setDerivative()

◆ setDerivativeIsZeroWhenValueIsZero()

◆ setDomain()

◆ setGradients()

◆ setGridDerivatives()

◆ setMatrixBookeepingElement()

◆ setMatrixBookeepingStart()

◆ setNotPeriodic()