Detailed Description

template<class Interaction>
class DdMd::DihedralPotentialImpl< Interaction >

Implementation template for a DihedralPotential.

Definition at line 34 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

#include <DihedralPotentialImpl.h>

Inheritance diagram for DdMd::DihedralPotentialImpl< Interaction >:

Public Member Functions
	DihedralPotentialImpl (Simulation &simulation)
	Constructor. More...

	DihedralPotentialImpl ()
	Default constructor. More...

virtual	~DihedralPotentialImpl ()
	Destructor. More...

Initialization and Serialization
virtual void	setNDihedralType (int nAtomType)
	Set the maximum number of atom types. More...

virtual void	readParameters (std::istream &in)
	Read potential energy parameters. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

Interaction interface
void	set (std::string name, int type, double value)
	Modify an dihedral parameter, identified by a string. More...

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

virtual double	dihedralEnergy (const Vector &R1, const Vector &R2, const Vector &R3, int type) const
	Returns potential energy for one dihedral. More...

virtual void	dihedralForce (const Vector &R1, const Vector &R2, const Vector &R3, Vector &F1, Vector &F2, Vector &F3, int type) const
	Returns derivatives of energy with respect to bond vectors forming the dihedral group. More...

virtual std::string	interactionClassName () const
	Return pair interaction class name (e.g., "CosineDihedral"). More...

Interaction &	interaction ()
	Return dihedral interaction by reference. More...

const Interaction &	interaction () const
	Return dihedral interaction by const reference. More...

Total Energy, Force and Stress
virtual void	computeForces ()
	Add the dihedral forces for all atoms. More...

virtual void	computeEnergy (MPI::Intracomm &communicator)
	Compute the total dihedral energy for all processors. More...

virtual void	computeStress (MPI::Intracomm &communicator)
	Compute the covalent dihedral stress. More...

Public Member Functions inherited from DdMd::DihedralPotential
	DihedralPotential (Simulation &simulation)
	Constructor. More...

	DihedralPotential ()
	Default constructor (for unit testing). More...

	~DihedralPotential ()
	Destructor. More...

void	associate (Boundary &boundary, GroupStorage< 4 > &storage)
	Create associations with related objects. More...

Public Member Functions inherited from DdMd::Potential
	Potential ()
	Constructor. More...

virtual	~Potential ()
	Destructor. More...

void	setReverseUpdateFlag (bool reverseUpdateFlag)
	Set flag to identify if reverse communication is enabled. More...

bool	reverseUpdateFlag () const
	Get flag to identify if reverse communication is enabled. More...

double	energy () const
	Return the total potential, from all processors. More...

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

bool	isEnergySet () const
	Is the energy set (known)? More...

virtual void	computeForcesAndStress (MPI::Intracomm &communicator)
	Compute forces and stress for all processors. More...

Tensor	stress () const
	Return the stress tensor. More...

double	pressure () const
	Return the pressure. More...

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

bool	isStressSet () const
	Is the stress set (known)? More...

virtual bool	isValid (MPI::Intracomm &communicator) const
	Is the potential in a valid internal state? 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	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...

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...

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 DdMd::DihedralPotential
Boundary &	boundary () const
	Return boundary by reference. More...

GroupStorage< 4 > &	storage () const
	Return bond storage by reference. More...

Protected Member Functions inherited from DdMd::Potential
void	setEnergy (double energy)
	Set a value for the total energy. More...

void	setStress (const Tensor &stress)
	Set a value for the total stress. More...

void	incrementPairStress (const Vector &f, const Vector &dr, Tensor &stress) const
	Add a pair contribution to the stress tensor. More...

void	reduceEnergy (double localEnergy, MPI::Intracomm &communicator)
	Add local energies from all processors, set energy on master. More...

void	reduceStress (Tensor &localStress, MPI::Intracomm &communicator)
	Add local stresses from all processors, set total on master. 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...

Constructor & Destructor Documentation

template<class Interaction >

DdMd::DihedralPotentialImpl< Interaction >::DihedralPotentialImpl ( Simulation & simulation )

Constructor.

Primary constructor, for use in a simulation.

Parameters

simulation parent Simulation object.

Definition at line 243 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::Simulation::nDihedralType(), and DdMd::DihedralPotentialImpl< Interaction >::setNDihedralType().

template<class Interaction >

DdMd::DihedralPotentialImpl< Interaction >::DihedralPotentialImpl ( )

Default constructor.

Provided to simplify unit testing.

Definition at line 256 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

template<class Interaction >

DdMd::DihedralPotentialImpl< Interaction >::~DihedralPotentialImpl ( )

virtual

Destructor.

Definition at line 266 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

Member Function Documentation

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::setNDihedralType ( int nAtomType )

virtual

Set the maximum number of atom types.

This function must be called iff this object was instantiated with the default constructor. It is called automatically by the constructor DihedralPotentialImpl(Simulation& ).

Implements DdMd::DihedralPotential.

Definition at line 277 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::DihedralPotentialImpl< Interaction >::interaction().

Referenced by DdMd::DihedralPotentialImpl< Interaction >::DihedralPotentialImpl().

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::readParameters ( std::istream & in )

virtual

Read potential energy parameters.

This functions reads the dihedral potential Interaction parameter block.

Precondition: nDihedralType must be set.

Parameters

in	parameter file

Reimplemented from Util::ParamComposite.

Definition at line 284 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), DdMd::DihedralPotentialImpl< Interaction >::interaction(), and UTIL_CHECK.

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Precondition: nDihedralType must be set.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 298 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), DdMd::DihedralPotentialImpl< Interaction >::interaction(), and UTIL_CHECK.

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Call only on master processor.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 311 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::DihedralPotentialImpl< Interaction >::interaction(), and DdMd::DihedralPotentialImpl< Interaction >::set().

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::set	(	std::string	name,
		int	type,
		double	value
	)

inlinevirtual

Modify an dihedral parameter, identified by a string.

Parameters

name	parameter variable name
type	type index for dihedral group
value	new value of parameter

Implements DdMd::DihedralPotential.

Definition at line 319 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::DihedralPotentialImpl< Interaction >::get().

Referenced by DdMd::DihedralPotentialImpl< Interaction >::save().

template<class Interaction >

double DdMd::DihedralPotentialImpl< Interaction >::get	(	std::string	name,
		int	type
	)		const

inlinevirtual

Get a parameter value, identified by a string.

Parameters

name	parameter variable name
type	type index of dihedral group

Implements DdMd::DihedralPotential.

Definition at line 327 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::DihedralPotentialImpl< Interaction >::dihedralEnergy().

Referenced by DdMd::DihedralPotentialImpl< Interaction >::set().

template<class Interaction >

double DdMd::DihedralPotentialImpl< Interaction >::dihedralEnergy	(	const Vector &	R1,
		const Vector &	R2,
		const Vector &	R3,
		int	type
	)		const

inlinevirtual

Returns potential energy for one dihedral.

0 2 3 o o-—o \ / o 1

Parameters

R1	bond vector from atom 0 to 1
R2	bond vector from atom 1 to 2
R3	bond vector from atom 2 to 3
type	type of dihedral

Implements DdMd::DihedralPotential.

Definition at line 335 of file ddMd/potentials/dihedral/DihedralPotentialImpl.h.

References DdMd::DihedralPotentialImpl< Interaction >::dihedralForce(), and DdMd::DihedralPotentialImpl< Interaction >::interaction().

Referenced by DdMd::DihedralPotentialImpl< Interaction >::computeEnergy(), and DdMd::DihedralPotentialImpl< Interaction >::get().

template<class Interaction >

void DdMd::DihedralPotentialImpl< Interaction >::dihedralForce	(	const Vector &	R1,
		const Vector &	R2,
		const Vector &	R3,
		Vector &	F1,
		Vector &	F2,
		Vector &	F3,
		int	type
	)		const

inlinevirtual

Returns derivatives of energy with respect to bond vectors forming the dihedral group.

Parameters

R1	bond vector from atom 0 to 1
R2	bond vector from atom 1 to 2
R3	bond vector from atom 2 to 3
F1	force along R1 direction (upon return)
F2	force along R2 direction (upon return)
F3	force along R2 direction (upon return)
type	type of dihedral