Detailed Description

Interface for a Dihedral Potential.

Definition at line 35 of file mcMd/potentials/dihedral/DihedralPotential.h.

#include <DihedralPotential.h>

Inheritance diagram for McMd::DihedralPotential:

Public Member Functions
	DihedralPotential ()
	Constructor. More...

virtual	~DihedralPotential ()
	Destructor (does nothing) More...

Dihedral interaction interface
virtual double	energy (const Vector &R1, const Vector &R2, const Vector &R3, int type) const =0
	Returns potential energy for one dihedral. More...

virtual void	force (const Vector &R1, const Vector &R2, const Vector &R3, Vector &F1, Vector &F2, Vector &F3, int type) const =0
	Returns derivatives of energy with respect to bond vectors. More...

virtual void	set (std::string name, int type, double value)=0
	Modify an interaction parameter, identified by a string. More...

virtual double	get (std::string name, int type) const =0
	Get an interaction parameter value, identified by a string. More...

virtual std::string	interactionClassName () const =0
	Get name of pair interaction class (e.g., "HarmonicDihedral"). More...

System Forces and Energy
virtual void	addForces ()=0
	Add dihedral potential forces to all atomic forces. More...

virtual double	atomEnergy (const Atom &atom) const
	Compute and return the dihedral potential energy for one Atom. More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Public Member Functions inherited from McMd::EnergyCalculator
virtual void	computeEnergy ()=0
	Calculate the total nonBonded pair energy for the associated System. More...

virtual void	unsetEnergy ()
	Mark the energy as unknown. More...

double	energy ()
	Return the energy contribution, compute if necessary. More...

Public Member Functions inherited from McMd::StressCalculator
virtual void	computeStress ()
	Compute and store the stress tensor. More...

virtual void	unsetStress ()
	Mark the stress as unknown. More...

void	computeStress (Tensor &stress)
	Get pair stress tensor. More...

void	computeStress (Vector &pressures)
	Get the xx, yy, zz non-Coulomb pair pressures. More...

void	computeStress (double &pressure)
	Get the scalar pressure. More...

bool	createsStress () const
	Return false if subclass does not generate stress. More...

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string. More...

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag. More...

void	setIsActive (bool isActive)
	Set or unset the isActive flag. More...

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array. More...

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	addCArray (std::istream &in, const char label, Type value, int n, bool isRequired=true)
	Add (but do not read) a required C array parameter. More...

template<typename Type >
DArrayParam< Type > &	addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
	Add (but do not read) a DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
	Add (but do not read) a FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	addCArray2D (std::istream &in, const char label, Type value, int m, int n, int np, bool isRequired=true)
	Add (but do not read) a CArray2DParam < Type > 2D C-array. More...

template<typename Type >
DMatrixParam< Type > &	addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
	Add and read a required DMatrix < Type > matrix parameter. More...

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor. More...

	ParamComponent (const ParamComponent &other)
	Copy constructor. More...

Protected Member Functions inherited from McMd::StressCalculator
	StressCalculator (bool createsStress=true)
	Constructor (protected to prevent direct instantiation). More...

Constructor & Destructor Documentation

McMd::DihedralPotential::DihedralPotential ( )

Constructor.

Definition at line 18 of file mcMd/potentials/dihedral/DihedralPotential.cpp.

McMd::DihedralPotential::~DihedralPotential ( )

virtual

Destructor (does nothing)

Definition at line 24 of file mcMd/potentials/dihedral/DihedralPotential.cpp.

Member Function Documentation

virtual double McMd::DihedralPotential::energy	(	const Vector &	R1,
		const Vector &	R2,
		const Vector &	R3,
		int	type
	)		const

pure virtual

Returns potential energy for one dihedral.

0 2 3 o o-—o \ / o 1

Parameters

R1	bond vector r1 - r0 from atom 0 to 1
R2	bond vector r2 - r1 from atom 1 to 2
R3	bond vector r3 - r2 from atom 2 to 3
type	type index for dihedral

Implemented in McMd::DihedralPotentialImpl< Interaction >.

Referenced by McMd::McNVTChemicalPotential::load(), McMd::McSystem::potentialEnergy(), McMd::MdSystem::potentialEnergy(), McMd::MdEnergyOutput::sample(), McMd::McEnergyOutput::sample(), McMd::McEnergyAnalyzer::sample(), and McMd::MdEnergyAnalyzer::sample().

virtual void McMd::DihedralPotential::force	(	const Vector &	R1,
		const Vector &	R2,
		const Vector &	R3,
		Vector &	F1,
		Vector &	F2,
		Vector &	F3,
		int	type
	)		const

pure virtual

Returns derivatives of energy with respect to bond vectors.

Parameters

R1	bond vector from atom 0 to 1 (input)
R2	bond vector from atom 1 to 2 (input)
R3	bond vector from atom 2 to 3 (input)
F1	derivative of energy w/respect to R1 (output)
F2	derivative of energy w/respect to R2 (output)
F3	derivative of energy w/respect to R3 (output)
type	type index for dihedral

Implemented in McMd::DihedralPotentialImpl< Interaction >.

virtual void McMd::DihedralPotential::set	(	std::string	name,
		int	type,
		double	value
	)

pure virtual

Modify an interaction parameter, identified by a string.

Parameters

name	parameter name
type	dihedral type index
value	new value of parameter

Implemented in McMd::DihedralPotentialImpl< Interaction >.

Referenced by McMd::McCommandManager::readStandardCommand(), and McMd::MdCommandManager::readStandardCommand().

virtual double McMd::DihedralPotential::get	(	std::string	name,
		int	type
	)		const

pure virtual

Get an interaction parameter value, identified by a string.

Parameters

name	parameter name
type	dihedral type index

Returns: value of parameter

Implemented in McMd::DihedralPotentialImpl< Interaction >.

virtual std::string McMd::DihedralPotential::interactionClassName ( ) const

pure virtual

Get name of pair interaction class (e.g., "HarmonicDihedral").

Implemented in McMd::DihedralPotentialImpl< Interaction >.

virtual void McMd::DihedralPotential::addForces ( )

pure virtual

Add dihedral potential forces to all atomic forces.

Implemented in McMd::DihedralPotentialImpl< Interaction >.

Referenced by McMd::MdSystem::calculateForces().

virtual double McMd::DihedralPotential::atomEnergy ( const Atom & atom ) const

inlinevirtual

Compute and return the dihedral potential energy for one Atom.

Default implementation throws an exception.This allows testing of subclasses that only work for MD simulation, and crash gracefully if used for MC.

Parameters

atom	Atom object of interest

Returns: bond potential energy of atom

Reimplemented in McMd::DihedralPotentialImpl< Interaction >.

Definition at line 130 of file mcMd/potentials/dihedral/DihedralPotential.h.

References UTIL_THROW.

Referenced by McMd::McSystem::atomPotentialEnergy().

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

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation