Detailed Description

template<int NAtom>
class Simp::SpeciesGroup< NAtom >

A Group of covalently interacting atoms within any molecule of one Species.

Class SpeciesGroup is used in the implementation of class Species to define the covalent chemical structure for any molecule of a particular species. The chemical structure of a Species is defined by a set of SpeciesGroup<2> (bond), SpeciesGroup<3> (angle), and SpeciesGroup<4> (dihedral) objects. Each SpeciesGroup<NAtom> object contains an array of NAtom local integer atom indices, which identities a group of atoms that are involved in a an NAtom-body covalent interaction. Each local atom index i must lie in the range 0 <= i < nAtom. A local atom index identifies the position of of an Atom within a generic molecule of the associated species. Each SpeciesGroup also has an integer group type index to distinguish different types of bonds, angles, and dihedrals, with different potential parameters.

The difference between a SpeciesGroup and a Group is that a Group contains an array of pointers to specific Atom objects that all belong to a specific Molecule. Each SpeciesGroup is thus a prototype for constructing one Group for each Molecule within a Species.

A SpeciesGroup<N> object can be input or output to file using overloaded inserter (<<) and extractor (>>) operators, like a built in type. The text representation contains a sequence of atom ids followed by the group type id, as described in a separate file.

See also: text representation

Definition at line 20 of file SpeciesGroup.h.

#include <SpeciesGroup.h>

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

void	setAtomId (int i, int atomId)
	Set index for one atom in the group. More...

void	setTypeId (int typeId)
	Set the group type id for this group. More...

int	atomId (int i) const
	Get the local id for a specific Atom. More...

int	typeId () const
	Get the type id for this covalent group. More...

Static Public Member Functions
static void	commitMpiType ()
	Commit associated MPI DataType. More...

Static Public Attributes
static const int	NullIndex = -1
	Null (unknown) value for non-negative atom and group type indices. More...

Friends
std::istream &	operator>> (std::istream &in, SpeciesGroup< NAtom > &speciesGroup)
	istream extractor for a SpeciesGroup. More...

std::ostream &	operator<< (std::ostream &out, const SpeciesGroup< NAtom > &speciesGroup)
	ostream inserter for a SpeciesGroup. More...

template<class Archive >
void	serialize (Archive &ar, SpeciesGroup< NAtom > &speciesGroup, const unsigned int version)
	Serialize one SpeciesGroup<NAtom>. More...

template<class Archive >
void	serialize (Archive &ar, SpeciesGroup< NAtom > &speciesGroup, const unsigned int version)
	Serialize one SpeciesGroup<NAtom>. More...

Constructor & Destructor Documentation

template<int NAtom>

Simp::SpeciesGroup< NAtom >::SpeciesGroup ( )

inline

Constructor.

Definition at line 156 of file SpeciesGroup.h.

References Simp::SpeciesGroup< NAtom >::NullIndex.

Member Function Documentation

template<int NAtom>

void Simp::SpeciesGroup< NAtom >::setAtomId	(	int	i,
		int	atomId
	)

inline

Set index for one atom in the group.

Parameters

i	index of atom within group (0, .., NAtom - 1)
atomId	index of atom to be added.

Definition at line 168 of file SpeciesGroup.h.

References Simp::SpeciesGroup< NAtom >::atomId().

template<int NAtom>

void Simp::SpeciesGroup< NAtom >::setTypeId ( int typeId )

inline

Set the group type id for this group.

Parameters

typeId value of covalent group typeId

Definition at line 175 of file SpeciesGroup.h.

References Simp::SpeciesGroup< NAtom >::typeId().

template<int NAtom>

int Simp::SpeciesGroup< NAtom >::atomId ( int i ) const

inline

Get the local id for a specific Atom.

Parameters

i	index within group (0, ..., NAtom - 1)

Definition at line 182 of file SpeciesGroup.h.

Referenced by Simp::Species::initializeAtomGroupIdArrays(), Simp::Species::isValid(), McMd::Simulation::isValid(), McMd::Simulation::save(), and Simp::SpeciesGroup< NAtom >::setAtomId().

template<int NAtom>

int Simp::SpeciesGroup< NAtom >::typeId ( ) const

inline

Get the type id for this covalent group.

Definition at line 189 of file SpeciesGroup.h.

References Simp::SpeciesGroup< NAtom >::operator>>, and Simp::SpeciesGroup< NAtom >::serialize.

Referenced by McMd::Simulation::isValid(), McMd::CfbReptationMove::loadParameters(), McMd::CfbReptateMove::loadParameters(), McMd::CfbReptationMove::readParameters(), McMd::Simulation::save(), and Simp::SpeciesGroup< NAtom >::setTypeId().

template<int NAtom>

void Simp::SpeciesGroup< NAtom >::commitMpiType ( )

static

Commit associated MPI DataType.

Commit MPI Datatype.

Definition at line 57 of file SpeciesGroup.tpp.

References Util::MpiStructBuilder::addMember(), Util::MpiStructBuilder::commit(), and Util::MpiStructBuilder::setBase().

Referenced by Simp::commitMpiSpeciesGroupTypes().

Friends And Related Function Documentation

template<int NAtom>

std::istream& operator>>	(	std::istream &	in,
		SpeciesGroup< NAtom > &	speciesGroup
	)

friend

istream extractor for a SpeciesGroup.

The format is as follows:

 atomIds[0] atomIds[1] ...  atomId[NAtom-1]  typeId

Parameters

in	input stream
speciesGroup	SpeciesGroup to be read from stream

Returns: modified input stream

Definition at line 27 of file SpeciesGroup.tpp.

Referenced by Simp::SpeciesGroup< NAtom >::typeId().

template<int NAtom>

std::ostream& operator<<	(	std::ostream &	out,
		const SpeciesGroup< NAtom > &	speciesGroup
	)

friend

ostream inserter for a SpeciesGroup.

The format is as follows, output one one line with no line break:

 atomIds[0] atomIds[1] ...  atomId[NAtom-1] typeId

Parameters

out	output stream
speciesGroup	SpeciesGroup to be written to stream

Returns: modified output stream

Definition at line 41 of file SpeciesGroup.tpp.

template<int NAtom>

template<class Archive >

void serialize	(	Archive &	ar,
		SpeciesGroup< NAtom > &	speciesGroup,
		const unsigned int	version
	)

friend

Serialize one SpeciesGroup<NAtom>.

Default implementation calls serialize member function of data object. Can be overridden by any explicit specialization.

Parameters

ar	archive object
speciesGroup	object to be serialized
version	archive version id

Referenced by Simp::SpeciesGroup< NAtom >::typeId().

template<int NAtom>

template<class Archive >

void serialize	(	Archive &	ar,
		SpeciesGroup< NAtom > &	speciesGroup,
		const unsigned int	version
	)

friend

Serialize one SpeciesGroup<NAtom>.

Default implementation calls serialize member function of data object. Can be overridden by any explicit specialization.

Parameters

ar	archive object
speciesGroup	object to be serialized
version	archive version id

Member Data Documentation

template<int NAtom>

const int Simp::SpeciesGroup< NAtom >::NullIndex = -1

static

Null (unknown) value for non-negative atom and group type indices.

Definition at line 83 of file SpeciesGroup.h.

Referenced by Simp::SpeciesGroup< NAtom >::SpeciesGroup().

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

Detailed Description

template<int NAtom> class Simp::SpeciesGroup< NAtom >

Public Member Functions

Static Public Member Functions

Static Public Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<int NAtom>
class Simp::SpeciesGroup< NAtom >