Detailed Description

A Species represents a set of chemically similar molecules.

A description of the structure of a molecule of this species.
A capacity, which is the maximum allowed number of Molecules of this Species, or the number for which space should be allocated.

The chemical structure of each molecule within a Species is defined by specifying the type of each atom and constructing a list of bond, angle and dihedral covalent groups. Information about covalent groups is stored internally in a set of SpeciesGroup<N> objects with N=2,3, and 4. This chemical structure is defined within the virtual protected readSpeciesParam(std::istream&) function, which is called by readParam.

Implementations of readSpeciesParam() must read whatever parameters are required to define the chemical structure of some class of molecular structures. The default implementation of Species::readSpeciesParam() is general enough to describe any molecular structure, and simply reads all of the required information about atom types and groups from file. Subclasses of Species generally hard-code some or all of the information required to describe a structure into the class definition, and require correspondingly less information to to be specified in the parameter file. For example, the parameter file format for a class that represents a flexible linear homopolymer might require only the number of monomers per chain, a single atom type index and a single bond type index. A subclass that represents a specific chemical structure (e.g., a water molecule) might not require any data from the parameter file.

A subclass of Species that is defined in the McMd namespace may also represent a "mutable" species. A mutable species is one in which each molecule can be in any of a finite number of different internal states, in which the chemical structure is slightly different in different states. A mutable species could, for example, be used implement a semi-grand ensemble for a polymer mixture, in which each polymer can be of either of two types. A subclass that represents a mutable species must have an associated McMd::SpeciesMutator object. See documentation for the Species::setMutatorPtr() function.

See also: parameter file format

Definition at line 71 of file simp/species/Species.h.

#include <Species.h>

Inheritance diagram for Simp::Species:

Public Types
typedef SpeciesGroup< 2 >	SpeciesBond
	A SpeciesBond has the local atom ids and a type id for one bond. More...

typedef FSArray< int, MaxBondPerAtom >	AtomBondIdArray
	An array of local integer bond ids for all bonds containing one atom. More...

typedef SpeciesGroup< 3 >	SpeciesAngle
	A SpeciesAngle has local atom ids and a type id for one angle. More...

typedef FSArray< int, MaxAnglePerAtom >	AtomAngleIdArray
	An array of local angle ids for all angles containing one atom. More...

typedef SpeciesGroup< 4 >	SpeciesDihedral
	A SpeciesDihedral has local atom ids and a type id for one dihedral. More...

typedef FSArray< int, MaxDihedralPerAtom >	AtomDihedralIdArray
	An array of local angle ids for all dihedrals containing one atom. More...

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...

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

virtual	~Species ()
	Destructor. More...

Initialization
void	setId (int id)
	Set integer id for this Species. More...

virtual void	readParameters (std::istream &in)
	Read parameters and initialize structure for this species. More...

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

void	readStructure (std::istream &in)
	Read structure from config/topology file format. More...

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

void	writeStructure (std::ostream &out, std::string indent=std::string())
	Write molecular structure in config/topology file format. More...

bool	matchStructure (std::istream &in)
	Read structure, return true iff it matches existing structure. More...

Chemical Structure Accessors
int	nAtom () const
	Get number of atoms per molecule for this Species. More...

int	atomTypeId (int iAtom) const
	Get atom type index for a specific atom, by local atom index. More...

int	nBond () const
	Get number of bonds per molecule for this Species. More...

const SpeciesBond &	speciesBond (int iBond) const
	Get a specific SpeciesBond object, by local bond index. More...

const AtomBondIdArray &	atomBondIds (int atomId) const
	Get array of ids for Bonds that contain one Atom. More...

int	nAngle () const
	Get number of angles per molecule for this Species. More...

const SpeciesAngle &	speciesAngle (int iAngle) const
	Get a specific SpeciesAngle object, by local angle index. More...

const AtomAngleIdArray &	atomAngleIds (int atomId) const
	Get array of ids for angles that contain one Atom. More...

int	nDihedral () const
	Get number of dihedrals per molecule for this Species. More...

const SpeciesDihedral &	speciesDihedral (int iDihedral) const
	Get a specific SpeciesDihedral object, by local angle index. More...

const AtomDihedralIdArray &	atomDihedralIds (int atomId) const
	Get array of ids for dihedrals that contain one Atom. More...

Interface for mutable species.
bool	isMutable () const
	Is this a mutable Species? More...

McMd::SpeciesMutator &	mutator ()
	Return the species mutator object by reference. More...

Miscellaneous Accessors
int	id () const
	Get integer id of this Species. More...

int	capacity () const
	Maximum allowed number of molecules for this Species. More...

bool	isValid () const
	Return true if Species is valid, or throw an Exception. 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...

Static Public Attributes
static const int	MaxBondPerAtom = 4
	Maximum number of bonds that can be connected to one atom. More...

static const int	MaxAnglePerAtom = 18
	Maximum number of angles groups that can contain one atom. More...

static const int	MaxDihedralPerAtom = 72
	Maximum number of dihedral groups that can contain one atom. More...

Protected Member Functions
virtual void	readSpeciesParam (std::istream &in)
	Define chemical structure for this Species. More...

virtual void	loadSpeciesParam (Serializable::IArchive &ar)
	Define chemical structure for this Species. More...

void	allocate ()
	Allocate chemical structure arrays. More...

void	allocateAtoms ()
	Allocate and initialize array of atom type Ids. More...

void	setAtomType (int atomId, int atomType)
	Set the type for one atom in a generic molecule of this Species. More...

void	allocateBonds ()
	Allocate arrays associated with Bonds. More...

void	makeBond (int bondId, int atomId1, int atomId2, int bondType)
	Add a bond to the chemical structure of a generic molecule. More...

void	allocateAngles ()
	Allocate arrays associated with angles. More...

void	makeAngle (int angleId, int atomId1, int atomId2, int atomId3, int angleType)
	Add an angle to the chemical structure of a generic molecule. More...

void	allocateDihedrals ()
	Allocate arrays associated with dihedrals. More...

void	makeDihedral (int dihedralId, int atomId1, int atomId2, int atomId3, int atomId4, int dihedralType)
	Add a dihedral to the chemical structure of a generic molecule. More...

void	initializeAtomGroupIdArrays ()
	Initialize all atom groupId arrays (point from atoms to groups). More...

void	setMutatorPtr (McMd::SpeciesMutator *mutatorPtr)
	Set pointer to associated McMd::SpeciesMutator for a mutable species. 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 Attributes
int	id_
	Integer index for this Species. More...

int	moleculeCapacity_
	Number of molecules associated with the species. More...

int	nAtom_
	Number of atoms per molecule. More...

DArray< int >	atomTypeIds_
	Array of atom type Ids, indexed by local atom id. More...

int	nBond_
	Number of bonds per molecule. More...

DArray< SpeciesBond >	speciesBonds_
	Array of SpeciesBonds for all bonds, indexed by local bond id. More...

int	nAngle_
	Number of angles per molecule. More...

DArray< SpeciesAngle >	speciesAngles_
	Array of SpeciesAngles for all angles, indexed by local angle id. More...

int	nDihedral_
	Number of dihedrals per molecule. More...

DArray< SpeciesDihedral >	speciesDihedrals_
	Array of SpeciesDihedrals, indexed by local dihedral id. More...

Static Protected Attributes
static const int	NullIndex = -1
	Null (unknown) value for any non-negative index. More...

Additional Inherited Members
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...

Member Typedef Documentation

typedef SpeciesGroup<2> Simp::Species::SpeciesBond

A SpeciesBond has the local atom ids and a type id for one bond.

Definition at line 81 of file simp/species/Species.h.

typedef FSArray<int, MaxBondPerAtom> Simp::Species::AtomBondIdArray

An array of local integer bond ids for all bonds containing one atom.

Definition at line 84 of file simp/species/Species.h.

typedef SpeciesGroup<3> Simp::Species::SpeciesAngle

A SpeciesAngle has local atom ids and a type id for one angle.

Definition at line 92 of file simp/species/Species.h.

typedef FSArray<int, MaxAnglePerAtom> Simp::Species::AtomAngleIdArray

An array of local angle ids for all angles containing one atom.

Definition at line 95 of file simp/species/Species.h.

typedef SpeciesGroup<4> Simp::Species::SpeciesDihedral

A SpeciesDihedral has local atom ids and a type id for one dihedral.

Definition at line 103 of file simp/species/Species.h.

typedef FSArray<int, MaxDihedralPerAtom> Simp::Species::AtomDihedralIdArray

An array of local angle ids for all dihedrals containing one atom.

Definition at line 106 of file simp/species/Species.h.

Constructor & Destructor Documentation

Tools::Species::Species ( )

Constructor.

Definition at line 22 of file simp/species/Species.cpp.

References Util::ParamComposite::setClassName().

Tools::Species::~Species ( )

virtual

Destructor.

Definition at line 45 of file simp/species/Species.cpp.

Member Function Documentation

void Tools::Species::setId ( int id )

Set integer id for this Species.

Parameters

id	integer id

Definition at line 452 of file simp/species/Species.cpp.

References id(), id_, and UTIL_THROW.

Referenced by McMd::Simulation::loadParameters(), and McMd::Simulation::readParameters().

void Simp::Species::readParameters ( std::istream & in )

virtual

Read parameters and initialize structure for this species.

This function reads the parameter moleculeCapacity (the maximum allowed number of molecules of this Species) and invokes the virtual Species::readSpeciesParam() function to define the chemical structure of the Species.

Parameters

in	input stream.

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::LinearSG, and McMd::HomopolymerSG.

Definition at line 51 of file simp/species/Species.cpp.

References isValid(), moleculeCapacity_, and readSpeciesParam().

Referenced by McMd::HomopolymerSG::readParameters(), and McMd::LinearSG::readParameters().

void Simp::Species::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 65 of file simp/species/Species.cpp.

References isValid(), loadSpeciesParam(), and moleculeCapacity_.

void Simp::Species::readStructure ( std::istream & in )

Read structure from config/topology file format.

Parameters

in	file from which to read structure.

Definition at line 160 of file simp/species/Species.cpp.

References allocateAngles(), allocateAtoms(), allocateBonds(), allocateDihedrals(), atomTypeIds_, initializeAtomGroupIdArrays(), Util::Label::isClear(), isValid(), nAngle_, nAtom_, nBond_, nDihedral_, speciesAngles_, speciesBonds_, speciesDihedrals_, and UTIL_CHECK.

void Simp::Species::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::LinearSG, McMd::HomopolymerSG, Simp::Homopolymer, Simp::HomoRing, Simp::Diblock, Simp::Multiblock, and Simp::Point.

Definition at line 312 of file simp/species/Species.cpp.

References atomTypeIds_, moleculeCapacity_, nAngle_, nAtom_, nBond_, nDihedral_, speciesAngles_, speciesBonds_, and speciesDihedrals_.

void Simp::Species::writeStructure	(	std::ostream &	out,
		std::string	indent = `std::string()`
	)

Write molecular structure in config/topology file format.

Parameters

out	file to which to write structure.
indent	indentation string (sequence of spaces)

Definition at line 340 of file simp/species/Species.cpp.

References atomTypeIds_, Util::ParamComponent::indent(), nAngle_, nAtom_, nBond_, nDihedral_, speciesAngles_, speciesBonds_, and speciesDihedrals_.

Referenced by McMd::SmpConfigIo::write().

bool Simp::Species::matchStructure ( std::istream & in )

Read structure, return true iff it matches existing structure.

Throw exception if structure is not parseable. Return false if it is parseable but does not match.

Parameters

in	file from which to read structure.

Definition at line 387 of file simp/species/Species.cpp.

References atomTypeIds_, nAngle(), nAngle_, nAtom(), nAtom_, nBond(), nBond_, nDihedral(), nDihedral_, speciesAngles_, speciesBonds_, and speciesDihedrals_.

Referenced by McMd::SmpConfigIo::read().

int Tools::Species::nAtom ( ) const

inline

Get number of atoms per molecule for this Species.

Definition at line 591 of file simp/species/Species.h.

References nAtom_.

int Simp::Species::atomTypeId ( int iAtom ) const

inline

Get atom type index for a specific atom, by local atom index.

Parameters

iAtom local index for an atom within a molecule.

Definition at line 597 of file simp/species/Species.h.

References atomTypeIds_.

Referenced by McMd::CfbLinear::addAtom(), McMd::Simulation::isValid(), McMd::McMuExchange::loadParameters(), McMd::SmpConfigIo::read(), McMd::CfbReptationMove::readParameters(), McMd::McMuExchange::readParameters(), and McMd::Simulation::save().

int Simp::Species::nBond ( ) const

inline

Get number of bonds per molecule for this Species.

Definition at line 604 of file simp/species/Species.h.

References nBond_.

Referenced by McMd::BondPotentialImpl< Interaction >::addForces(), Simp::Linear::buildLinear(), Simp::Ring::buildRing(), McMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::Activate::deactivate(), McMd::Simulation::isValid(), McMd::CfbReptationMove::loadParameters(), McMd::CfbReptateMove::loadParameters(), McMd::IntraBondStressAutoCorr< SystemType >::loadParameters(), McMd::IntraBondTensorAutoCorr< SystemType >::loadParameters(), matchStructure(), McMd::Activate::reactivate(), McMd::DdMdConfigIo::read(), McMd::LammpsConfigIo::read(), McMd::CfbReptationMove::readParameters(), McMd::CfbReptateMove::readParameters(), McMd::IntraBondStressAutoCorr< SystemType >::readParameters(), McMd::IntraBondTensorAutoCorr< SystemType >::readParameters(), McMd::Simulation::save(), McMd::DdMdConfigIo::write(), and McMd::LammpsConfigIo::write().

const Species::SpeciesBond & Simp::Species::speciesBond ( int iBond ) const

inline

Get a specific SpeciesBond object, by local bond index.

Parameters

iBond local index of a SpeciesBond within a molecule.

Definition at line 611 of file simp/species/Species.h.

References speciesBonds_.

Referenced by initializeAtomGroupIdArrays(), isValid(), McMd::Simulation::isValid(), McMd::CfbReptationMove::loadParameters(), McMd::CfbReptateMove::loadParameters(), McMd::CfbReptationMove::readParameters(), and McMd::Simulation::save().

const Species::AtomBondIdArray & Simp::Species::atomBondIds ( int atomId ) const

inline

Get array of ids for Bonds that contain one Atom.

Parameters

atomId local index for atom of interest

Definition at line 618 of file simp/species/Species.h.

Referenced by McMd::Activate::deactivate(), McMd::getAtomBonds(), and McMd::Activate::reactivate().

int Simp::Species::nAngle ( ) const

inline

Get number of angles per molecule for this Species.

Definition at line 626 of file simp/species/Species.h.

References nAngle_.

Referenced by McMd::AnglePotentialImpl< Interaction >::addForces(), Simp::Linear::buildLinear(), Simp::Ring::buildRing(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), McMd::Activate::deactivate(), McMd::Simulation::isValid(), matchStructure(), McMd::Activate::reactivate(), McMd::Simulation::save(), McMd::DdMdConfigIo::write(), McMd::LammpsConfigIo::write(), and McMd::CfbLinear::~CfbLinear().

const Species::SpeciesAngle & Simp::Species::speciesAngle ( int iAngle ) const

inline

Get a specific SpeciesAngle object, by local angle index.

Parameters

iAngle local index of a SpeciesAngle within a molecule.

Definition at line 633 of file simp/species/Species.h.

References speciesAngles_.

Referenced by initializeAtomGroupIdArrays(), isValid(), McMd::Simulation::isValid(), and McMd::Simulation::save().

const Species::AtomAngleIdArray & Simp::Species::atomAngleIds ( int atomId ) const

inline

Get array of ids for angles that contain one Atom.

Parameters

atomId local index for atom of interest

Definition at line 640 of file simp/species/Species.h.

Referenced by McMd::Activate::deactivate(), McMd::getAtomAngles(), and McMd::Activate::reactivate().

int Simp::Species::nDihedral ( ) const

inline

Get number of dihedrals per molecule for this Species.

Definition at line 648 of file simp/species/Species.h.

References nDihedral_.

Referenced by McMd::DihedralPotentialImpl< Interaction >::addForces(), Simp::Linear::buildLinear(), Simp::Ring::buildRing(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::Activate::deactivate(), McMd::Simulation::isValid(), matchStructure(), McMd::Activate::reactivate(), McMd::Simulation::save(), McMd::DdMdConfigIo::write(), McMd::LammpsConfigIo::write(), and McMd::CfbLinear::~CfbLinear().

const Species::SpeciesDihedral & Simp::Species::speciesDihedral ( int iDihedral ) const

inline

Get a specific SpeciesDihedral object, by local angle index.

Parameters

iDihedral local index of a SpeciesDihedral within a molecule.

Definition at line 655 of file simp/species/Species.h.

References speciesDihedrals_.

Referenced by initializeAtomGroupIdArrays(), isValid(), McMd::Simulation::isValid(), and McMd::Simulation::save().

const Species::AtomDihedralIdArray & Simp::Species::atomDihedralIds ( int atomId ) const

inline

Get array of ids for dihedrals that contain one Atom.

Parameters

atomId local index for atom of interest

Definition at line 663 of file simp/species/Species.h.

Referenced by McMd::Activate::deactivate(), McMd::getAtomDihedrals(), and McMd::Activate::reactivate().

bool Simp::Species::isMutable ( ) const

inline

Is this a mutable Species?

Definition at line 671 of file simp/species/Species.h.

Referenced by McMd::Generator::generate(), isValid(), McMd::Simulation::isValid(), McMd::SemiGrandDistribution::loadParameters(), McMd::TypeDistribution::loadParameters(), McMd::EndSwapMove::loadParameters(), McMd::McMdConfigIo::read(), and McMd::McMdConfigIo::write().

McMd::SpeciesMutator & Simp::Species::mutator ( )

inline

Return the species mutator object by reference.

Definition at line 677 of file simp/species/Species.h.

Referenced by McMd::Generator::generate(), McMd::System::loadConfig(), McMd::SemiGrandDistribution::loadParameters(), McMd::TypeDistribution::loadParameters(), McMd::HomopolymerSG::loadSpeciesParam(), McMd::LinearSG::loadSpeciesParam(), McMd::HomopolymerSemiGrandMove::move(), McMd::McMdConfigIo::read(), McMd::HomopolymerSG::readSpeciesParam(), McMd::LinearSG::readSpeciesParam(), McMd::System::saveConfig(), and McMd::McMdConfigIo::write().

int Tools::Species::id ( ) const

inline

Get integer id of this Species.

Definition at line 579 of file simp/species/Species.h.

References id_.

Referenced by McMd::System::addMolecule(), McMd::Generator::generate(), isValid(), Tools::Species::molecule(), McMd::System::moleculeId(), McMd::System::removeMolecule(), McMd::Simulation::returnMolecule(), McMd::MdPairEnergyCoefficients::sample(), McMd::Simulation::save(), McMd::RingOctaRebridgeMove::scanBridge(), setId(), and McMd::McMdConfigIo::write().

int Tools::Species::capacity ( ) const

inline

Maximum allowed number of molecules for this Species.

Definition at line 585 of file simp/species/Species.h.

References moleculeCapacity_.

bool Tools::Species::isValid ( ) const

Return true if Species is valid, or throw an Exception.

Definition at line 649 of file simp/species/Species.cpp.

References Simp::SpeciesGroup< NAtom >::atomId(), atomTypeIds_, Util::Array< Data >::capacity(), id(), Util::DArray< Data >::isAllocated(), isMutable(), moleculeCapacity_, nAngle_, nAtom_, nBond_, nDihedral_, speciesAngle(), speciesAngles_, speciesBond(), speciesBonds_, speciesDihedral(), speciesDihedrals_, UTIL_CHECK, and UTIL_THROW.

Referenced by Tools::ConfigReader::addAtomsToSpecies(), Tools::Species::begin(), McMd::Simulation::isValid(), loadParameters(), readParameters(), and readStructure().

void Simp::Species::readSpeciesParam ( std::istream & in )

protectedvirtual

Define chemical structure for this Species.

This virtual function must define the structure of a molecule of this species, and read any data required to do so. The default implementation Species::readSpeciesParam reads nAtom_, nBond_, nAngle_, and the elements of the arrays atomTypeIds_ and speciesBonds_, speciesAngles_.

Re-implementations of this function by subclasses may hard-code some or all of the information contained in these variables, and may define a more compact file format for any parameters that are read from file.

Parameters

in	input parameter file stream.

Reimplemented in Simp::Homopolymer, Simp::Multiblock, McMd::LinearSG, McMd::HomopolymerSG, Simp::Diblock, Simp::HomoRing, and Simp::Point.

Definition at line 79 of file simp/species/Species.cpp.

References allocateAngles(), allocateAtoms(), allocateBonds(), allocateDihedrals(), atomTypeIds_, initializeAtomGroupIdArrays(), nAngle_, nAtom_, nBond_, nDihedral_, speciesAngles_, speciesBonds_, and speciesDihedrals_.

Referenced by readParameters().

void Simp::Species::loadSpeciesParam ( Serializable::IArchive & ar )

protectedvirtual

Define chemical structure for this Species.

Analogous to readSpeciesParam, but reads data from a Serializable::IArchive rather than an input stream. This function must define the same parameter file format as readSpeciesParam.

Parameters

ar	input parameter file stream.

Reimplemented in Simp::Homopolymer, Simp::Multiblock, McMd::LinearSG, McMd::HomopolymerSG, Simp::Diblock, Simp::HomoRing, and Simp::Point.

Definition at line 121 of file simp/species/Species.cpp.

References allocateAngles(), allocateAtoms(), allocateBonds(), allocateDihedrals(), atomTypeIds_, initializeAtomGroupIdArrays(), nAngle_, nAtom_, nBond_, nDihedral_, speciesAngles_, speciesBonds_, and speciesDihedrals_.

Referenced by loadParameters().

void Simp::Species::allocate ( )

protected

Allocate chemical structure arrays.

This function allocates the arrays that are used to define the chemical structure of a generic molecule, such as atomTypeIds_, speciesBonds_, atomBondIdArrays_, speciesAngles_, etc.

Precondition: nAtom_, nBond_, nAngles_, etc. must have been assigned final values on entry.

Definition at line 470 of file simp/species/Species.cpp.

References allocateAngles(), allocateAtoms(), allocateBonds(), and allocateDihedrals().

Referenced by Simp::Linear::buildLinear(), Simp::Ring::buildRing(), Simp::Point::loadSpeciesParam(), and Simp::Point::readSpeciesParam().

void Simp::Species::allocateAtoms ( )

protected

Allocate and initialize array of atom type Ids.

Precondition: nAtom_ must be assigned a positive value

Definition at line 487 of file simp/species/Species.cpp.

References Util::DArray< Data >::allocate(), atomTypeIds_, Util::DArray< Data >::isAllocated(), nAtom_, and UTIL_CHECK.

Referenced by allocate(), loadSpeciesParam(), readSpeciesParam(), and readStructure().

void Simp::Species::setAtomType	(	int	atomId,
		int	atomType
	)

protected

Set the type for one atom in a generic molecule of this Species.

Parameters

atomId	local atom id, in range 0,..., nAtom - 1;
atomType	atom type index

Definition at line 503 of file simp/species/Species.cpp.

References atomTypeIds_.

Referenced by Simp::Linear::buildLinear(), and Simp::Ring::buildRing().

void Simp::Species::allocateBonds ( )

protected

Allocate arrays associated with Bonds.

Precondition: nAtom_ > 0 and nBond_ >= 0.

Definition at line 510 of file simp/species/Species.cpp.

References nAtom_, nBond_, speciesBonds_, and UTIL_CHECK.

Referenced by allocate(), loadSpeciesParam(), readSpeciesParam(), and readStructure().

void Simp::Species::makeBond	(	int	bondId,
		int	atomId1,
		int	atomId2,
		int	bondType
	)

protected

Add a bond to the chemical structure of a generic molecule.

This function creates and adds a SpeciesBond object, and also adds a reference to the list of bonds that are connected to each atom.

Parameters

bondId	local index of bond within a molecule
atomId1	local index of 1st atom in bond
atomId2	local index of 2nd atom in bond
bondType	bond type index

Definition at line 526 of file simp/species/Species.cpp.

References nAtom_, nBond_, and speciesBonds_.

Referenced by Simp::Linear::buildLinear(), and Simp::Ring::buildRing().

void Simp::Species::allocateAngles ( )

protected

Allocate arrays associated with angles.

Precondition: nAtom_ > 0 and nAngle_ >= 0.

Definition at line 553 of file simp/species/Species.cpp.

References nAngle_, nAtom_, speciesAngles_, and UTIL_CHECK.

Referenced by allocate(), loadSpeciesParam(), readSpeciesParam(), and readStructure().

void Simp::Species::makeAngle	(	int	angleId,
		int	atomId1,
		int	atomId2,
		int	atomId3,
		int	angleType
	)

protected

Add an angle to the chemical structure of a generic molecule.

This function creates and adds a SpeciesAngle object, and also adds a reference to the list of angles that are connected to each atom.

Parameters

angleId	local index of angle within a molecule
atomId1	local index of 1st atom in angle
atomId2	local index of 2nd atom in angle
atomId3	local index of 3rd atom in angle
angleType	angle type index

Definition at line 569 of file simp/species/Species.cpp.

References nAngle_, nAtom_, and speciesAngles_.

Referenced by Simp::Linear::buildLinear(), and Simp::Ring::buildRing().

void Simp::Species::allocateDihedrals ( )

protected

Allocate arrays associated with dihedrals.

Definition at line 599 of file simp/species/Species.cpp.

References nAtom_, nDihedral_, speciesDihedrals_, and UTIL_CHECK.

Referenced by allocate(), loadSpeciesParam(), readSpeciesParam(), and readStructure().

void Simp::Species::makeDihedral	(	int	dihedralId,
		int	atomId1,
		int	atomId2,
		int	atomId3,
		int	atomId4,
		int	dihedralType
	)

protected

Add a dihedral to the chemical structure of a generic molecule.

This function creates and adds a SpeciesDihedral object, and also adds a reference to the list of dihedrals that are connected to each atom.

Parameters

dihedralId	local index of dihedral within a molecule
atomId1	local index of 1st atom in dihedral
atomId2	local index of 2nd atom in dihedral
atomId3	local index of 3rd atom in dihedral
atomId4	local index of 4th atom in dihedral
dihedralType	dihedral type index

Definition at line 616 of file simp/species/Species.cpp.

References nAtom_, nDihedral_, and speciesDihedrals_.

Referenced by Simp::Linear::buildLinear(), and Simp::Ring::buildRing().

void Simp::Species::initializeAtomGroupIdArrays ( )

protected

Initialize all atom groupId arrays (point from atoms to groups).

Precondition: Species::allocate() function must have been invoked.; All speciesGroup arrays (speciesBonds, etc.) must be initialized.

Definition at line 229 of file simp/species/Species.cpp.

References Simp::SpeciesGroup< NAtom >::atomId(), atomTypeIds_, Util::Array< Data >::capacity(), Util::DArray< Data >::isAllocated(), nAngle_, nAtom_, nBond_, nDihedral_, speciesAngle(), speciesAngles_, speciesBond(), speciesBonds_, speciesDihedral(), speciesDihedrals_, and UTIL_CHECK.

Referenced by loadSpeciesParam(), readSpeciesParam(), and readStructure().

void Simp::Species::setMutatorPtr ( McMd::SpeciesMutator * mutatorPtr )

protected

Set pointer to associated McMd::SpeciesMutator for a mutable species.

A mutable subclass of Species must have an associated SpeciesMutator object. The constructor of each such subclass should pass a pointer to the SpeciesMutator to setMutatorPtr. After this function is called, Species::isMutator() will return true, the associated SpeciesMutator will be accessible via the Species::mutator() function. If a mutable Species subclass is derived from both Species and SpeciesMutator (recommended), the function setMutatorPtr(this) should be invoked within the subclass constructor to pass the address of the SpeciesMutator sub-object to the Species subobject.

Parameters

mutatorPtr pointer to an associated SpeciesMutator object

Definition at line 464 of file simp/species/Species.cpp.

Referenced by McMd::HomopolymerSG::HomopolymerSG(), and McMd::LinearSG::LinearSG().

Member Data Documentation

const int Simp::Species::MaxBondPerAtom = 4

static

Maximum number of bonds that can be connected to one atom.

Definition at line 78 of file simp/species/Species.h.

const int Simp::Species::MaxAnglePerAtom = 18

static

Maximum number of angles groups that can contain one atom.

Definition at line 89 of file simp/species/Species.h.

const int Simp::Species::MaxDihedralPerAtom = 72

static

Maximum number of dihedral groups that can contain one atom.

Definition at line 100 of file simp/species/Species.h.

const int Simp::Species::NullIndex = -1

staticprotected

Null (unknown) value for any non-negative index.

Definition at line 304 of file simp/species/Species.h.

Referenced by McMd::HomopolymerSG::calculateAtomTypeId(), McMd::LinearSG::calculateAtomTypeId(), and Simp::Diblock::Diblock().

int Simp::Species::id_

protected

Integer index for this Species.

Definition at line 312 of file simp/species/Species.h.

Referenced by Tools::Species::addAtom(), Tools::Species::begin(), id(), Tools::Species::molecule(), Simp::HomoRing::save(), and setId().

int Simp::Species::moleculeCapacity_

protected

Number of molecules associated with the species.

Definition at line 315 of file simp/species/Species.h.

Referenced by capacity(), isValid(), loadParameters(), readParameters(), Simp::Point::save(), Simp::Multiblock::save(), Simp::Diblock::save(), Simp::HomoRing::save(), McMd::HomopolymerSG::save(), McMd::LinearSG::save(), and save().

int Simp::Species::nAtom_

protected

Number of atoms per molecule.

Definition at line 320 of file simp/species/Species.h.

Referenced by Tools::Species::addAtom(), allocateAngles(), allocateAtoms(), allocateBonds(), allocateDihedrals(), Tools::Species::begin(), Tools::Species::initialize(), initializeAtomGroupIdArrays(), isValid(), Simp::HomoRing::loadSpeciesParam(), Simp::Diblock::loadSpeciesParam(), McMd::HomopolymerSG::loadSpeciesParam(), McMd::LinearSG::loadSpeciesParam(), Simp::Multiblock::loadSpeciesParam(), loadSpeciesParam(), makeAngle(), makeBond(), makeDihedral(), matchStructure(), Tools::Species::molecule(), nAtom(), Tools::operator<<(), Tools::operator>>(), Simp::Point::Point(), Simp::HomoRing::readSpeciesParam(), Simp::Diblock::readSpeciesParam(), McMd::HomopolymerSG::readSpeciesParam(), McMd::LinearSG::readSpeciesParam(), Simp::Multiblock::readSpeciesParam(), readSpeciesParam(), readStructure(), Simp::HomoRing::save(), McMd::HomopolymerSG::save(), McMd::LinearSG::save(), save(), Tools::Species::size(), and writeStructure().

DArray<int> Simp::Species::atomTypeIds_

protected

Array of atom type Ids, indexed by local atom id.

Element atomTypeIds_[id] is the atom type index for atom id of any molecule of this species, where 0 <= id < nAtom_.

Definition at line 328 of file simp/species/Species.h.

Referenced by allocateAtoms(), atomTypeId(), initializeAtomGroupIdArrays(), isValid(), Simp::Point::loadSpeciesParam(), loadSpeciesParam(), matchStructure(), Simp::Point::readSpeciesParam(), readSpeciesParam(), readStructure(), save(), setAtomType(), and writeStructure().

int Simp::Species::nBond_

protected

DArray<SpeciesBond> Simp::Species::speciesBonds_

protected

Array of SpeciesBonds for all bonds, indexed by local bond id.

Element speciesBonds_[id] is the SpeciesBond object for bond number id in any molecule of this Species, where 0 <= id < nBond_.

Definition at line 342 of file simp/species/Species.h.

Referenced by allocateBonds(), initializeAtomGroupIdArrays(), isValid(), loadSpeciesParam(), makeBond(), matchStructure(), readSpeciesParam(), readStructure(), save(), speciesBond(), and writeStructure().

int Simp::Species::nAngle_

protected

DArray<SpeciesAngle> Simp::Species::speciesAngles_

protected

Array of SpeciesAngles for all angles, indexed by local angle id.

Element speciesAngles_[id] is the SpeciesAngle object for angle number id in any molecule of this Species, where 0 <= id < nAngle_.

Definition at line 357 of file simp/species/Species.h.

Referenced by allocateAngles(), initializeAtomGroupIdArrays(), isValid(), loadSpeciesParam(), makeAngle(), matchStructure(), readSpeciesParam(), readStructure(), save(), speciesAngle(), and writeStructure().

int Simp::Species::nDihedral_

protected

DArray<SpeciesDihedral> Simp::Species::speciesDihedrals_

protected

Array of SpeciesDihedrals, indexed by local dihedral id.

Element speciesDihedrals_[id] is the SpeciesDihedral object for dihedral number id in any molecule of this Species, where the index satisfies 0 <= id < nAngle_.

Definition at line 373 of file simp/species/Species.h.

Referenced by allocateDihedrals(), initializeAtomGroupIdArrays(), isValid(), loadSpeciesParam(), makeDihedral(), matchStructure(), readSpeciesParam(), readStructure(), save(), speciesDihedral(), and writeStructure().

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

Detailed Description

Public Types

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation