Detailed Description

A Homopolymer species of chain molecules.

A hompolymer is a chemically homogeneous linear chain of nAtom atoms. All atoms are of the same atom type, with all bonds of the same bond type. A Homopolymer may optionally have angle potentials for each sequences of three susbseuqent atoms, in which case all angle potentials must be of the same angle type. A Homopolymer may also optionally have dihedral potentials among all sequences of four subsequent atoms, which (if present) must all be of the same dihedral type.

See also: parameter file format

Definition at line 34 of file Homopolymer.h.

#include <Homopolymer.h>

Inheritance diagram for Simp::Homopolymer:

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

Public Member Functions inherited from Simp::Linear
	Linear ()
	Constructor. More...

virtual	~Linear ()
	Destructor. More...

Public Member Functions inherited from Simp::Species
	Species ()
	Constructor. More...

virtual	~Species ()
	Destructor. More...

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...

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...

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...

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

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

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...

Protected Member Functions
virtual void	readSpeciesParam (std::istream &in)
	Read nAtom_ and the chain type. More...

virtual void	loadSpeciesParam (Serializable::IArchive &ar)
	Load species structure from an Archive. More...

virtual int	calculateAtomTypeId (int index) const
	Return the same type for any particle in any chain. More...

virtual int	calculateBondTypeId (int index) const
	Return same bond type for any bond in any chain. More...

virtual int	calculateAngleTypeId (int index) const
	Return same angle type for any angle in any chain. More...

virtual int	calculateDihedralTypeId (int index) const
	Return same dihedral type for any dihedral in any chain. More...

Protected Member Functions inherited from Simp::Linear
void	buildLinear ()
	Build the chemical structure for a linear molecule. More...

Protected Member Functions inherited from Simp::Species
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	atomType_
	Particle type id for every particle of every molecule of this species. More...

int	bondType_
	Bond type id for every bond of this species. More...

int	angleType_
	Angle type id for every angle of this species. More...

int	dihedralType_
	Dihedral type id for every dihedral of this species. More...

Protected Attributes inherited from Simp::Linear
int	hasAngles_
	Does this chain have angle potentials (0 = false, 1 = true). More...

int	hasDihedrals_
	Does this chain have dihedral potentials (0 = false, 1 = true). More...

Protected Attributes inherited from Simp::Species
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...

Additional Inherited Members
Public Types inherited from Simp::Species
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...

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...

Static Public Attributes inherited from Simp::Species
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...

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

Member Function Documentation

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Simp::Species.

Definition at line 115 of file Homopolymer.cpp.

References Util::Parameter::saveOptional().

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

protectedvirtual

Read nAtom_ and the chain type.

Parameters

in	input stream

Reimplemented from Simp::Species.

Definition at line 33 of file Homopolymer.cpp.

References UTIL_THROW.

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

protectedvirtual

Load species structure from an Archive.

Parameters

ar	input/loading archive

Reimplemented from Simp::Species.

Definition at line 74 of file Homopolymer.cpp.

int Simp::Homopolymer::calculateAtomTypeId ( int index ) const

protectedvirtual

Return the same type for any particle in any chain.

Parameters

index atom index, in range 0,...,nAtom_ - 1

Returns: atom type index

Implements Simp::Linear.

Definition at line 138 of file Homopolymer.cpp.

int Simp::Homopolymer::calculateBondTypeId ( int index ) const

protectedvirtual

Return same bond type for any bond in any chain.

Parameters

index bond index, in range 0,...,nBond_ - 1

Returns: bond type index

Implements Simp::Linear.

Definition at line 144 of file Homopolymer.cpp.

int Simp::Homopolymer::calculateAngleTypeId ( int index ) const

protectedvirtual

Return same angle type for any angle in any chain.

Parameters

index angle index, in range 0,...,nAngle_ - 1

Returns: angle type index

Implements Simp::Linear.

Definition at line 151 of file Homopolymer.cpp.

int Simp::Homopolymer::calculateDihedralTypeId ( int index ) const

protectedvirtual

Return same dihedral type for any dihedral in any chain.

Parameters

index angle index, in range 0,...,nDihedral_ - 1

Returns: dihedral type index

Implements Simp::Linear.

Definition at line 159 of file Homopolymer.cpp.

Member Data Documentation

int Simp::Homopolymer::atomType_

protected

Particle type id for every particle of every molecule of this species.

Definition at line 62 of file Homopolymer.h.

int Simp::Homopolymer::bondType_

protected

Bond type id for every bond of this species.

Definition at line 67 of file Homopolymer.h.

int Simp::Homopolymer::angleType_

protected

Angle type id for every angle of this species.

Definition at line 73 of file Homopolymer.h.

int Simp::Homopolymer::dihedralType_

protected

Dihedral type id for every dihedral of this species.

Definition at line 80 of file Homopolymer.h.

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

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation

Member Data Documentation