Classes used by all simpatico molecular simulations. More...

Classes
struct	Bend
	A Bend calculates the angle between two vectors. More...

struct	BendForce
	A BendForce computes derivatives of the angle between two vectors. More...

class	BoundaryEnsemble
	Statistical ensemble for changes in the periodic unit cell size. More...

class	BoxExternal
	A repulsive 9-3 potential confining particles within a box. More...

class	CompensatedPair
	Compensated pair potential for transient gel. More...

class	CompositeBond
	Composite bond potential. More...

class	CosineAngle
	A three body angle potential, as a function of angle cosine. More...

class	CosineDihedral
	A dihedral potential proportional to cos(phi). More...

class	CosineSqAngle
	A three body angle potential, as a function of angle cosine. More...

class	Diblock
	A linear diblock copolymer chain. More...

class	DpdPair
	Soft pair potential used in dissipative particle dynamics (DPD) simulations of Groot, Warren et al. More...

class	EnergyEnsemble
	A statistical ensemble for energy. More...

class	EwaldInteraction
	Implementation of r-space and k-space Ewald Coulomb interactions. More...

class	FeneBond
	A finitely-extensible nonlinear element (FENE) bond potential. More...

class	GeneralPeriodicExternal
	A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i. More...

class	HarmonicAngle
	A angle potential that is harmonic in the angle. More...

class	HarmonicBond
	A harmonic covalent bond potential. More...

class	HarmonicL0Bond
	A harmonic bond potential with zero rest length. More...

class	Homopolymer
	A Homopolymer species of chain molecules. More...

class	HomoRing
	A species of homogeneous ring molecules. More...

class	LamellarOrderingExternal
	A clipped cosine potential that induces lamellar ordering along the direction specified by perpDirection_. More...

class	Linear
	A Species of linear polymers (abstract). More...

class	LJPair
	A cutoff, shifted Lennard-Jones nonbonded pair interaction. More...

class	LocalLamellarOrderingExternal
	A clipped cosine potential that induces lamellar ordering along the direction specified by perpDirection_ in only a fraction of box specified by the parameter fraction along box length in parallelDirection_. More...

class	MonoclinicBoundary
	A monoclinic periodic unit cell. More...

class	Multiblock
	A linear MULTIBLOCK copolymer chain. More...

class	MultiHarmonicDihedral
	A truncated Fourier series dihedral potential. More...

class	NucleationExternal
	A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i. More...

class	OrthoBoxExternal
	A repulsive 9-3 potential confining particles inside an orthogonal box along directions specified by indConfine_. More...

struct	OrthoRegion
	A region with orthogonal edges parallel to the x, y, and z axes. More...

class	OrthorhombicBoundary
	An orthorhombic periodic unit cell. More...

class	PeriodicExternal
	A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i. More...

class	Point
	A Species in which each Molecule contains only one Atom. More...

class	Ring
	A Species of ring polymers (abstract). More...

class	SimplePeriodicExternal
	A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i. More...

class	SlitExternal
	A repulsive 9-3 potential confining particles along the z direction. More...

class	Species
	A Species represents a set of chemically similar molecules. More...

class	SpeciesEnsemble
	An ensemble for the number of molecules of one Species. More...

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

class	SphericalTabulatedExternal
	The potential is independent on the type of atoms. More...

struct	Torsion
	Computes dihedral / torsion angle involving 3 bonds. More...

struct	TorsionForce
	Computes derivatives of dihedral angle with respect to bond vectors. More...

class	WcaPair
	A Weeks-Chandler-Anderson (WCA) repulsive LJ interaction. More...

Typedefs
typedef OrthorhombicBoundary	Boundary
	Boundary is an alias for the periodic boundary condition class. More...

Functions
std::istream &	operator>> (std::istream &in, MonoclinicBoundary &boundary)
	istream extractor for a MonoclinicBoundary. More...

std::ostream &	operator<< (std::ostream &out, const MonoclinicBoundary &boundary)
	ostream inserter for an MonoclinicBoundary. More...

std::istream &	operator>> (std::istream &in, OrthorhombicBoundary &boundary)
	istream extractor for a OrthorhombicBoundary. More...

std::ostream &	operator<< (std::ostream &out, const OrthorhombicBoundary &boundary)
	ostream inserter for an OrthorhombicBoundary. More...

std::istream &	operator>> (std::istream &in, BoundaryEnsemble::Type &type)
	istream extractor for an BoundaryEnsemble::Type enum value. More...

std::ostream &	operator<< (std::ostream &out, const BoundaryEnsemble::Type &type)
	ostream inserter for a BoundaryEnsemble::Type enum value. More...

template<class Archive >
void	serialize (Archive &ar, BoundaryEnsemble::Type &data, const unsigned int version)
	Serialize a BoundaryEnsemble::Type enum value. More...

std::istream &	operator>> (std::istream &in, EnergyEnsemble::Type &type)
	istream extractor for an EnergyEnsemble::Type enum value. More...

std::ostream &	operator<< (std::ostream &out, EnergyEnsemble::Type const &type)
	ostream inserter for a EnergyEnsemble::Type enum value. More...

template<class Archive >
void	serialize (Archive &ar, EnergyEnsemble::Type &data, const unsigned int version)
	Serialize a EnergyEnsemble::Type enum value. More...

std::istream &	operator>> (std::istream &in, SpeciesEnsemble::Type &type)
	istream extractor for an SpeciesEnsemble::Type enum value. More...

std::ostream &	operator<< (std::ostream &out, const SpeciesEnsemble::Type &type)
	ostream inserter for a SpeciesEnsemble::Type enum value. More...

template<class Archive >
void	serialize (Archive &ar, SpeciesEnsemble::Type &data, const unsigned int version)
	Serialize a SpeciesEnsemble::Type enum value. More...

void	commitMpiSpeciesGroupTypes ()
	Commit all MPI SpeciesGroup data types. More...

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

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

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

Detailed Description

Classes used by all simpatico molecular simulations.

Function Documentation

std::istream & Simp::operator>>	(	std::istream &	in,
		MonoclinicBoundary &	boundary
	)

istream extractor for a MonoclinicBoundary.

istream extractor

Parameters

in	input stream
boundary	MonoclinicBoundary to be read from stream

Returns: modified input stream

Definition at line 161 of file MonoclinicBoundary.cpp.

References UTIL_THROW.

std::ostream & Simp::operator<<	(	std::ostream &	out,
		const MonoclinicBoundary &	boundary
	)

ostream inserter for an MonoclinicBoundary.

ostream inserter

Parameters

out	output stream
boundary	MonoclinicBoundary to be written to stream

Returns: modified output stream

Definition at line 178 of file MonoclinicBoundary.cpp.

Referenced by operator>>().

std::istream & Simp::operator>>	(	std::istream &	in,
		OrthorhombicBoundary &	boundary
	)

istream extractor for a OrthorhombicBoundary.

istream extractor

Parameters

in	input stream
boundary	OrthorhombicBoundary to be read from stream

Returns: modified input stream

Definition at line 157 of file OrthorhombicBoundary.cpp.

References Simp::OrthoRegion::maxima_, and UTIL_THROW.

std::ostream & Simp::operator<<	(	std::ostream &	out,
		const OrthorhombicBoundary &	boundary
	)

ostream inserter for an OrthorhombicBoundary.

ostream inserter

Parameters

out	output stream
boundary	OrthorhombicBoundary to be written to stream

Returns: modified output stream

Definition at line 189 of file OrthorhombicBoundary.cpp.

References Simp::OrthoRegion::lengths_.

std::istream & Simp::operator>>	(	std::istream &	in,
		BoundaryEnsemble::Type &	type
	)

istream extractor for an BoundaryEnsemble::Type enum value.

Parameters

in	input stream
type	BoundaryEnsemble::Type enum value to be read from stream

Returns: modified input stream

Definition at line 79 of file BoundaryEnsemble.cpp.

References UTIL_THROW.

std::ostream & Simp::operator<<	(	std::ostream &	out,
		const BoundaryEnsemble::Type &	type
	)

ostream inserter for a BoundaryEnsemble::Type enum value.

Parameters

out	output stream
type	BoundaryEnsemble::Type enum value to be written to stream

Returns: modified output stream

Definition at line 97 of file BoundaryEnsemble.cpp.

template<class Archive >

void Simp::serialize	(	Archive &	ar,
		BoundaryEnsemble::Type &	data,
		const unsigned int	version
	)

inline

Serialize a BoundaryEnsemble::Type enum value.

Parameters

ar	archive object
data	enum value to be serialized
version	archive version id

Definition at line 162 of file BoundaryEnsemble.h.

References Util::serializeEnum().

std::istream & Simp::operator>>	(	std::istream &	in,
		EnergyEnsemble::Type &	type
	)

istream extractor for an EnergyEnsemble::Type enum value.

Parameters

in	input stream
type	EnergyEnsemble::Type enum value to be read from stream

Returns: modified input stream

Definition at line 85 of file EnergyEnsemble.cpp.

References operator<<(), and UTIL_THROW.

std::ostream& Simp::operator<<	(	std::ostream &	out,
		EnergyEnsemble::Type const &	type
	)

ostream inserter for a EnergyEnsemble::Type enum value.

Parameters

out	output stream
type	EnergyEnsemble::Type enum value to be written to stream

Returns: modified output stream

template<class Archive >

void Simp::serialize	(	Archive &	ar,
		EnergyEnsemble::Type &	data,
		const unsigned int	version
	)

inline

Serialize a EnergyEnsemble::Type enum value.

Parameters

ar	archive object
data	enum value to be serialized
version	archive version id

Definition at line 175 of file EnergyEnsemble.h.

References Util::serializeEnum().

std::istream & Simp::operator>>	(	std::istream &	in,
		SpeciesEnsemble::Type &	type
	)

istream extractor for an SpeciesEnsemble::Type enum value.

Parameters

in	input stream
type	SpeciesEnsemble::Type enum value to be read from stream

Returns: modified input stream

Definition at line 59 of file SpeciesEnsemble.cpp.

References UTIL_THROW.

std::ostream & Simp::operator<<	(	std::ostream &	out,
		const SpeciesEnsemble::Type &	type
	)

ostream inserter for a SpeciesEnsemble::Type enum value.

Parameters

out	output stream
type	SpeciesEnsemble::Type enum value to be written to stream

Returns: modified output stream

Definition at line 77 of file SpeciesEnsemble.cpp.

template<class Archive >

void Simp::serialize	(	Archive &	ar,
		SpeciesEnsemble::Type &	data,
		const unsigned int	version
	)

inline

Serialize a SpeciesEnsemble::Type enum value.

Parameters

ar	archive object
data	enum value to be serialized
version	archive version id

Definition at line 140 of file SpeciesEnsemble.h.

References Util::serializeEnum().

void Simp::commitMpiSpeciesGroupTypes ( )

Commit all MPI SpeciesGroup data types.

Definition at line 38 of file SpeciesGroup.cpp.

References commitMpiSpeciesGroupTypes(), and Simp::SpeciesGroup< NAtom >::commitMpiType().

Referenced by commitMpiSpeciesGroupTypes(), and McMd::commitMpiTypes().

template<int NAtom>

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

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.

template<int NAtom>

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

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<class Archive , int NAtom>

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

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

Classes

Typedefs

Functions

Detailed Description

Function Documentation