Simp::OrthorhombicBoundary Class Reference

Detailed Description

An orthorhombic periodic unit cell.

Definition at line 38 of file OrthorhombicBoundary.h.

#include <OrthorhombicBoundary.h>

Inheritance diagram for Simp::OrthorhombicBoundary:

Public Member Functions
	OrthorhombicBoundary ()
	Constructor. More...
void	setOrthorhombic (const Vector &lengths)
	Set unit cell dimensions for orthorhombic boundary. More...
void	setTetragonal (double a, double bc)
	Set unit cell dimensions for tetragonal boundary. More...
void	setCubic (double a)
	Set unit cell dimensions for a cubic boundary. More...
template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize to/from an archive. More...
Periodic Boundary Conditions - Primitive Cell
void	shift (Vector &r) const
	Shift Cartesian Vector r to its primary image. More...
void	shift (Vector &r, IntVector &shift) const
	Shift Cartesian Vector r to its primary image. More...
void	applyShift (Vector &r, int i, int t) const
	Shift Cartesian Vector r by multiple t of a Bravais lattice vector. More...
void	shiftGen (Vector &r) const
	Shift generalized Vector r to its primary image. More...
void	shiftGen (Vector &r, IntVector &shift) const
	Shift generalized Vector r to its image within the primary unit cell. More...
Minimum Image Pair Separations for Cartesian Vectors
double	distanceSq (const Vector &r1, const Vector &r2) const
	Return square distance between positions r1 and r2. More...
double	distanceSq (const Vector &r1, const Vector &r2, IntVector &shift) const
	Return square distance between positions r1 and r2. More...
double	distanceSq (const Vector &r1, const Vector &r2, Vector &dr) const
	Compute distance and separation between r1 and r2. More...
Minimum Image Vector Tests
bool	isMinImageGen (const Vector &dr)
	Is a generalized separation vector a minimimum image of itself? More...
bool	isMinImageCart (const Vector &dr)
	Is a Cartesian separation vector a minimimum image of itself? More...
Coordinate Transformations
void	transformCartToGen (const Vector &Rc, Vector &Rg) const
	Transform Cartesian Vector to scaled / generalized coordinates. More...
void	transformGenToCart (const Vector &Rg, Vector &Rc) const
	Transform Vector of generalized coordinates to Cartesian Vector. More...
Accessors
LatticeSystem	latticeSystem ()
	Return actual lattice system. More...
const Vector &	lengths () const
	Get Vector of unit cell lengths by const reference. More...
double	length (int i) const
	Get length in Cartesian direction i. More...
double	minLength () const
	Get minimum length across primitive unit cell. More...
double	volume () const
	Return unit cell volume. More...
const Vector &	bravaisBasisVector (int i) const
	Return Bravais lattice vector i. More...
const Vector &	reciprocalBasisVector (int i) const
	Return reciprocal lattice basis vector i. More...
void	randomPosition (Random &random, Vector &r) const
	Generate random position within the primary unit cell. More...
bool	isValid ()
	Return true if valid, or throw Exception. More...

Friends
class	::OrthorhombicBoundaryTest
	Unit test. More...
std::istream &	operator>> (std::istream &in, Simp::OrthorhombicBoundary &boundary)
	istream extractor More...
std::ostream &	operator<< (std::ostream &out, const Simp::OrthorhombicBoundary &boundary)
	ostream inserter More...

Constructor & Destructor Documentation

Simp::OrthorhombicBoundary::OrthorhombicBoundary

(

)

Constructor.

Definition at line 25 of file OrthorhombicBoundary.cpp.

References Util::Dimension, Simp::OrthoRegion::lengths_, Util::Constants::Pi, and Util::Vector::Zero.

Member Function Documentation

void Simp::OrthorhombicBoundary::setOrthorhombic

(

const Vector &

lengths

)

Set unit cell dimensions for orthorhombic boundary.

Also sets all related lengths and volume.

Parameters

lengths

Vector of unit cell lengths

Definition at line 47 of file OrthorhombicBoundary.cpp.

References lengths(), and Simp::OrthoRegion::maxima_.

Referenced by DdMd::NphIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::LammpsConfigIo::read(), DdMd::LammpsConfigIo::readConfig(), Tools::HoomdConfigReader::readConfig(), McMd::LammpsDumpReader::readFrame(), McMd::DCDTrajectoryReader::readFrame(), and McMd::NphIntegrator::step().

void Simp::OrthorhombicBoundary::setTetragonal	(	double	a,
		double	bc
	)

Set unit cell dimensions for tetragonal boundary.

Parameters

a	unit cell dimensions in unique x-direction
bc	unit cell length in y and z directions

Definition at line 57 of file OrthorhombicBoundary.cpp.

References Simp::OrthoRegion::maxima_.

void Simp::OrthorhombicBoundary::setCubic

(

double

a

)

Set unit cell dimensions for a cubic boundary.

Parameters

a	unit cell length in x, y, and z directions.

Definition at line 69 of file OrthorhombicBoundary.cpp.

References Util::Dimension, Simp::OrthoRegion::lengths_, Simp::OrthoRegion::maxima_, Util::Constants::Pi, and Simp::OrthoRegion::resetRegion().

template<class Archive >

void Simp::OrthorhombicBoundary::serialize	(	Archive &	ar,
		const unsigned int	version
	)

Serialize to/from an archive.

Parameters

ar	saving or loading archive
version	archive version id

Definition at line 645 of file OrthorhombicBoundary.h.

References isValid(), Simp::OrthoRegion::serialize(), and Util::serializeEnum().

void Simp::OrthorhombicBoundary::shift ( Vector &  r ) const

inline

Shift Cartesian Vector r to its primary image.

Upon completion, each component r[i] of Vector r is shifted by a multiple of length[i] so as to lie within the allowed range minima_[i] <= r[i] < maxima_[i].

Precondition: The algorithm assumes that on input, for each i, minima_[i] - lengths_[i] < r[i] < maxima_[i] + lengths_[i]

Parameters

r	Vector of Cartesian coordinates

Definition at line 432 of file OrthorhombicBoundary.h.

References Util::Dimension, Simp::OrthoRegion::lengths_, Simp::OrthoRegion::maxima_, and Simp::OrthoRegion::minima_.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::CfbRebridgeBase::addMiddleAtom(), McMd::Generator::attemptPlaceAtom(), McMd::McPairPotential::buildCellList(), McMd::MdPairPotential::buildPairList(), McMd::Cluster::clusterCOM(), McMd::CfbLinear::deleteAtom(), McMd::CfbEndBase::deleteEndAtom(), McMd::CfbRebridgeBase::deleteMiddleAtom(), McMd::ClusterIdentifier::identifyClusters(), McMd::McNVTChemicalPotential::load(), McMd::System::loadConfig(), McMd::AtomDisplaceMove::move(), McMd::RigidDisplaceMove::move(), McMd::SmpConfigIo::read(), McMd::MdConfigIo::readAtom(), McMd::McConfigIo::readAtom(), Tools::HoomdConfigReader::readConfig(), McMd::LammpsDumpReader::readFrame(), McMd::DCDTrajectoryReader::readFrame(), Tools::ChainMaker::readParam(), McMd::Crosslinker::sample(), McMd::G1MSD::sample(), McMd::McNVTChemicalPotential::sample(), Tools::AtomMSD::sample(), McMd::AtomMSD::sample(), McMd::ComMSD::sample(), McMd::System::saveConfig(), McMd::G1MSD::setup(), Tools::AtomMSD::setup(), McMd::AtomMSD::setup(), McMd::ComMSD::setup(), McMd::MdSystem::shiftAtoms(), and Tools::HoomdConfigWriter::writeConfig().

void Simp::OrthorhombicBoundary::shift ( Vector &  r, IntVector &  shift  ) const

inline

Shift Cartesian Vector r to its primary image.

This function maps an atomic position to its primary image, and also increments the atomic shift IntVector:

If r[i] -> r[i] - t*length_[i], then shift[i] -> shift[i] + t.

See also

Atom:shift()

Parameters

r	Vector of Cartesian coordinates
shift	integer shifts required to obtain "true" coordinates.

Definition at line 449 of file OrthorhombicBoundary.h.

References Util::Dimension, Simp::OrthoRegion::lengths_, Simp::OrthoRegion::maxima_, and Simp::OrthoRegion::minima_.

void Simp::OrthorhombicBoundary::applyShift ( Vector &  r, int  i, int  t  ) const

inline

Shift Cartesian Vector r by multiple t of a Bravais lattice vector.

This function shifts the Vector r by a specified amount:

r -> r + t*a'[i]

where a[i] is Bravais lattice vector number i.

Parameters

r	Cartesian position Vector
i	direction index
t	multiple of Bravais lattice vector i

Definition at line 468 of file OrthorhombicBoundary.h.

References Simp::OrthoRegion::lengths_.

Referenced by DdMd::Exchanger::update().

void Simp::OrthorhombicBoundary::shiftGen ( Vector &  r ) const

inline

Shift generalized Vector r to its primary image.

One output, each coordinate r[i] is shifted by an integer, so as to lie within the range 0 < r[i] < 1.0

Precondition: The algorithm assumes that on input, for each i=0,..,2, -1.0 < r[i] < 2.0

Parameters

r	Vector of scaled / generalized coordinates

Definition at line 474 of file OrthorhombicBoundary.h.

References Util::Dimension.

Referenced by DdMd::AtomDistributor::addAtom(), McMd::MdSpmePotential::addForces(), and McMd::MdSpmePotential::makeWaves().

void Simp::OrthorhombicBoundary::shiftGen ( Vector &  r, IntVector &  shift  ) const

inline

Shift generalized Vector r to its image within the primary unit cell.

This function maps a vector of generalized coordinates to lie in the primary cell, and also increments the atomic shift IntVector:

If r[i] -> r[i] - t, then shift[i] -> shift[i] + t.

See also

Atom:shift()

Parameters

r	Vector of generalized coordinates (in/out)
shift	integer shifts, modified on output (in/out)

Definition at line 492 of file OrthorhombicBoundary.h.

References Util::Dimension.

double Simp::OrthorhombicBoundary::distanceSq ( const Vector &  r1, const Vector &  r2  ) const

inline

Return square distance between positions r1 and r2.

This function returns the square distance between two Cartesian vectors, using the nearest image convention for the separation Vector.

Parameters

r1	first Cartesian position Vector
r2	second Cartesian position Vector

Returns

square of distance between r1 and r2, using nearest image.

Definition at line 540 of file OrthorhombicBoundary.h.

References Util::Dimension, Simp::OrthoRegion::halfLengths_, and Simp::OrthoRegion::lengths_.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::CfbRebridgeBase::addMiddleAtom(), McMd::LinkPotentialImpl< Interaction >::atomEnergy(), McMd::BondPotentialImpl< Interaction >::atomEnergy(), McMd::DihedralPotentialImpl< Interaction >::atomEnergy(), McMd::AnglePotentialImpl< Interaction >::atomEnergy(), McMd::Generator::attemptPlaceAtom(), McMd::PairList::build(), McMd::Cluster::clusterCOM(), DdMd::BondTensorAutoCorr::computeData(), McMd::LinkPotentialImpl< Interaction >::computeEnergy(), McMd::McPairPotentialImpl< Interaction >::computeEnergy(), DdMd::AnglePotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), DdMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), DdMd::DihedralPotentialImpl< Interaction >::computeEnergy(), DdMd::AnglePotentialImpl< Interaction >::computeForces(), DdMd::BondPotentialImpl< Interaction >::computeForces(), DdMd::DihedralPotentialImpl< Interaction >::computeForces(), DdMd::BondPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::AnglePotentialImpl< Interaction >::computeStress(), DdMd::BondPotentialImpl< Interaction >::computeStress(), DdMd::DihedralPotentialImpl< Interaction >::computeStress(), McMd::CfbLinear::deleteAtom(), McMd::CfbEndBase::deleteEndAtom(), McMd::CfbRebridgeBase::deleteMiddleAtom(), McMd::ClusterIdentifier::initialize(), McMd::PairList::isCurrent(), McMd::McPairPotentialImpl< Interaction >::moleculeEnergy(), McMd::Cluster::momentTensor(), McMd::Sliplinker::move(), McMd::SliplinkerEnd::move(), McMd::SliplinkerAll::move(), McMd::GcSliplinkMove::move(), McMd::SliplinkMove::move(), McMd::CfbDoubleRebridgeMove::move(), McMd::GroupRebridgeBase::octaEnergy(), McMd::ComMSD::output(), McMd::Crosslinker::sample(), McMd::LinkLengthDist::sample(), McMd::G1MSD::sample(), Tools::AtomMSD::sample(), McMd::McMuExchange::sample(), Tools::PairEnergy::sample(), McMd::AtomMSD::sample(), McMd::BondLengthDist::sample(), McMd::MdPairEnergyCoefficients::sample(), McMd::ComMSD::sample(), McMd::RingRouseAutoCorr::sample(), McMd::EndtoEndXYZ::sample(), McMd::LinearRouseAutoCorr::sample(), McMd::EndtoEnd::sample(), McMd::BlockRadiusGyration::sample(), McMd::RDF::sample(), McMd::IntraBondTensorAutoCorr< SystemType >::sample(), McMd::IntraPairAutoCorr::sample(), McMd::RadiusGyration::sample(), McMd::RingOctaRebridgeMove::scanBridge(), McMd::RingTetraRebridgeMove::scanBridge(), McMd::NvtDpdVvIntegrator::setup(), and McMd::GroupRebridgeBase::tetraEnergy().

double Simp::OrthorhombicBoundary::distanceSq ( const Vector &  r1, const Vector &  r2, IntVector &  shift  ) const

inline

Return square distance between positions r1 and r2.

This function returns the square distance between two Cartesian vectors, using the nearest image convention for the separation Vector. On return, the IntVector shift contains the coefficients of the Bravais lattice vectors that were added to r1 to create a nearest image of r2.

Parameters

r1	first Cartesian position Vector
r2	second Cartesian position Vector
shift	shift added to r1 to create nearest image of r2.

Returns

square of distance between r1 and r2, using nearest image.

Definition at line 512 of file OrthorhombicBoundary.h.

References Util::Dimension, Simp::OrthoRegion::halfLengths_, and Simp::OrthoRegion::lengths_.

double Simp::OrthorhombicBoundary::distanceSq ( const Vector &  r1, const Vector &  r2, Vector &  dr  ) const

inline

Compute distance and separation between r1 and r2.

This function returns the square distance between two Cartesian vectors, using the nearest image convention for the separation Vector. Upon return, Vector dr contains the separation r1 - r2 computed using the nearest image convention, and the return value is the square of dr.

Parameters

r1	first Cartesian position Vector
r2	second Cartesian position Vector
dr	separation Vector (upon return)

Returns

square of separation Vector dr

Definition at line 564 of file OrthorhombicBoundary.h.

References Util::Dimension, Simp::OrthoRegion::halfLengths_, and Simp::OrthoRegion::lengths_.

bool Simp::OrthorhombicBoundary::isMinImageGen ( const Vector &  dr )

inline

Is a generalized separation vector a minimimum image of itself?

This function returns true if the scaled separation dr has a Cartesian norm less than or equal to that of any vector that can be produced by adding a Bravais vector to the corresponding Cartesian vector, or false otherwise.

Parameters

dr	separation vector in generalized coordinates.

Returns

true if minimum image, false otherwise

Definition at line 615 of file OrthorhombicBoundary.h.

References Util::Dimension.

bool Simp::OrthorhombicBoundary::isMinImageCart ( const Vector &  dr )

inline

Is a Cartesian separation vector a minimimum image of itself?

This function returns true if the scaled separation dr has a Cartesian norm less than or equal to that of any vector that can be produced by adding a Bravais vector to dr, false otherwise.

Parameters

dr	separation vector in Cartesian coordinates.

Returns

true if minimum image, false otherwise

Definition at line 629 of file OrthorhombicBoundary.h.

References Util::Dimension, and Simp::OrthoRegion::halfLengths_.

void Simp::OrthorhombicBoundary::transformCartToGen ( const Vector &  Rc, Vector &  Rg  ) const

inline

Transform Cartesian Vector to scaled / generalized coordinates.

Generalized coordinates range from 0.0 < Rg[i] < 1.0 within the primitive cell, for i=0,..,2.

Parameters

Rc	Vector of Cartesian coordinates (input)
Rg	Vector of generalized coordinates (output)

Definition at line 591 of file OrthorhombicBoundary.h.

References Util::Dimension.

Referenced by McMd::MdEwaldPotential::addForces(), McMd::MdSpmePotential::addForces(), McMd::CellList::cellIndexFromPosition(), McMd::DeformCommand::execute(), DdMd::SerializeConfigIo::loadConfig(), McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), DdMd::DdMdConfigIo::readConfig(), DdMd::LammpsConfigIo::readConfig(), DdMd::DdMdOrderedConfigIo::readConfig(), McMd::McCommandManager::readStandardCommand(), DdMd::AtomStorage::transformCartToGen(), Tools::HoomdConfigWriter::writeConfig(), DdMd::DdMdTrajectoryWriter::writeFrame(), and DdMd::DdMdGroupTrajectoryWriter::writeFrame().

void Simp::OrthorhombicBoundary::transformGenToCart ( const Vector &  Rg, Vector &  Rc  ) const

inline

Transform Vector of generalized coordinates to Cartesian Vector.

Parameters

Rg	Vector of generalized coordinates (input)
Rc	Vector of Cartesian coordinates (output)

Definition at line 603 of file OrthorhombicBoundary.h.

References Util::Dimension, and Simp::OrthoRegion::lengths_.

Referenced by McMd::DeformCommand::execute(), McMd::DdMdTrajectoryReader::readFrame(), McMd::McCommandManager::readStandardCommand(), DdMd::SerializeConfigIo::saveConfig(), DdMd::AtomStorage::transformGenToCart(), Tools::HoomdConfigWriter::writeConfig(), DdMd::DdMdConfigIo::writeConfig(), DdMd::LammpsConfigIo::writeConfig(), DdMd::DdMdOrderedConfigIo::writeConfig(), and DdMd::LammpsDumpWriter::writeFrame().

LatticeSystem Simp::OrthorhombicBoundary::latticeSystem ( )

inline

Return actual lattice system.

Value can be Cubic, Tetragonal, or Orthorhombic.

Definition at line 584 of file OrthorhombicBoundary.h.

const Vector & Simp::OrthorhombicBoundary::lengths ( ) const

inline

Get Vector of unit cell lengths by const reference.

Definition at line 396 of file OrthorhombicBoundary.h.

References Simp::OrthoRegion::lengths_.

Referenced by Util::bcast< Simp::OrthorhombicBoundary >(), DdMd::Exchanger::exchange(), DdMd::NphIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::VelProf::output(), Util::recv< Simp::OrthorhombicBoundary >(), McMd::G1MSD::sample(), Tools::AtomMSD::sample(), McMd::VelProf::sample(), McMd::CompositionProfile::sample(), McMd::BoundaryAverage::sample(), McMd::AtomMSD::sample(), DdMd::OutputBoxdim::sample(), McMd::ComMSD::sample(), DdMd::OrderParamNucleation::sample(), Util::send< Simp::OrthorhombicBoundary >(), setOrthorhombic(), McMd::VelProf::setup(), Tools::PairEnergy::setup(), McMd::CellList::setup(), McMd::NphIntegrator::step(), McMd::LammpsConfigIo::write(), Tools::HoomdConfigWriter::writeConfig(), DdMd::LammpsConfigIo::writeConfig(), DdMd::LammpsDumpWriter::writeFrame(), and Tools::LammpsDumpWriter::~LammpsDumpWriter().

double Simp::OrthorhombicBoundary::length ( int  i ) const

inline

Get length in Cartesian direction i.

Parameters

i	index of Cartesian direction, 0 <= i < Dimension

Definition at line 402 of file OrthorhombicBoundary.h.

References Simp::OrthoRegion::lengths_.

Referenced by DdMd::PairPotential::buildCellList(), and DdMd::PairPotential::save().

double Simp::OrthorhombicBoundary::minLength ( ) const

inline

Get minimum length across primitive unit cell.

Definition at line 408 of file OrthorhombicBoundary.h.

double Simp::OrthorhombicBoundary::volume ( ) const

inline

Return unit cell volume.

Definition at line 414 of file OrthorhombicBoundary.h.

References Simp::OrthoRegion::volume_.

Referenced by McMd::MdEwaldPotential::addForces(), McMd::MdSpmePotential::addForces(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), McMd::LinkPotentialImpl< Interaction >::computeEnergy(), McMd::McPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), DdMd::BondPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), McMd::MdEwaldPotential::computeStress(), McMd::MdSpmePotential::computeStress(), DdMd::AnglePotentialImpl< Interaction >::computeStress(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), DdMd::BondPotentialImpl< Interaction >::computeStress(), DdMd::DihedralPotentialImpl< Interaction >::computeStress(), DdMd::PairPotentialImpl< Interaction >::computeStress(), DdMd::NphIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), DdMd::NphIntegrator::integrateStep2(), DdMd::NptIntegrator::integrateStep2(), McMd::MdSystem::kineticEnergy(), McMd::HybridNphMdMove::move(), DdMd::OrderParamNucleation::output(), McMd::BoundaryAverage::sample(), DdMd::OutputBoxdim::sample(), DdMd::StressAutoCorr::sample(), McMd::RDF::sample(), McMd::StructureFactor::sample(), DdMd::StructureFactorGrid::sample(), McMd::StructureFactorGrid::sample(), DdMd::StructureFactor::sample(), McMd::StructureFactorP::sample(), McMd::IntraStructureFactor::sample(), and McMd::McSystem::unsetPotentialEnergies().

const Vector & Simp::OrthorhombicBoundary::bravaisBasisVector ( int  i ) const

inline

Return Bravais lattice vector i.

Parameters

i	basis Vector index.

Definition at line 420 of file OrthorhombicBoundary.h.

Referenced by McMd::MdEwaldPotential::makeWaves().

const Vector & Simp::OrthorhombicBoundary::reciprocalBasisVector ( int  i ) const

inline

Return reciprocal lattice basis vector i.

Parameters

i	basis Vector index.

Definition at line 426 of file OrthorhombicBoundary.h.

Referenced by McMd::MdEwaldPotential::addForces(), McMd::MdEwaldPotential::computeStress(), McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), McMd::CompositionProfile::makeWaveVectors(), McMd::StructureFactor::makeWaveVectors(), DdMd::VanHove::makeWaveVectors(), DdMd::StructureFactor::makeWaveVectors(), McMd::StructureFactorP::makeWaveVectors(), McMd::VanHove::sample(), and McMd::IntraStructureFactor::sample().

void Simp::OrthorhombicBoundary::randomPosition	(	Random &	random,
		Vector &	r
	)		const

Generate random position within the primary unit cell.

Generates Vector r[i], i=1,..,3 with minima_[i] < r[i] < maxima_[i].

Parameters

random	random number generator object
r	Vector of random coordinates (upon return)

Definition at line 105 of file OrthorhombicBoundary.cpp.

References Util::Dimension, Simp::OrthoRegion::maxima_, Simp::OrthoRegion::minima_, and Util::Random::uniform().

Referenced by McMd::PointGenerator::attemptPlaceMolecule(), McMd::LinearGenerator::attemptPlaceMolecule(), Tools::ChainMaker::readParam(), and McMd::McNVTChemicalPotential::sample().

bool Simp::OrthorhombicBoundary::isValid

(

)

Return true if valid, or throw Exception.

Definition at line 115 of file OrthorhombicBoundary.cpp.

References Util::Dimension, Util::feq(), Simp::OrthoRegion::isValid(), Simp::OrthoRegion::lengths_, Simp::OrthoRegion::minima_, Util::Constants::Pi, and UTIL_THROW.

Referenced by serialize().

Friends And Related Function Documentation

friend class ::OrthorhombicBoundaryTest

friend

Unit test.

Definition at line 353 of file OrthorhombicBoundary.h.

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

friend

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.

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

friend

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.

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

• OrthorhombicBoundary.h
• OrthorhombicBoundary.cpp