#include <group.h>

Inheritance diagram for Faunus::Group:

Collaboration diagram for Faunus::Group:

Public Types
enum	Selectors : unsigned int { ANY = (1U << 1U), ACTIVE = (1U << 2U), INACTIVE = (1U << 3U), NEUTRAL = (1U << 4U), ATOMIC = (1U << 5U), MOLECULAR = (1U << 6U), FULL = (1U << 7U) }
	Selections to filter groups using `getSelectionFilter()` More...

using	base = ElasticRange< Particle >

using	iter = typename base::Titer

Public Types inherited from Faunus::ElasticRange< Particle >
using	Titer = typename std::vector< Particle >::iterator

using	const_iterator = typename std::vector< Particle >::const_iterator

using	base = IterRange< typename std::vector< Particle >::iterator >

Public Member Functions
bool	isAtomic () const
	Is it an atomic group?

bool	isMolecular () const
	is it a molecular group?

bool	isFull () const override
	True of all particles are active.

std::optional< std::reference_wrapper< Point > >	massCenter ()
	Optional reference to mass center. More...

std::optional< std::reference_wrapper< const Point > >	massCenter () const
	Optional ref. to mass center.

template<unsigned int mask>
bool	match () const
	Determines if given `Selectors` bitmask matches group. More...

const MoleculeData &	traits () const
	Convenient access to molecule properties.

	Group (Group &other)

	Group (const Group &other)

	Group (MoleculeData::index_type molid, iter begin, iter end)
	Constructor. More...

Group &	operator= (const Group &other)
	Deep copy contents from another Group. More...

Group &	shallowCopy (const Group &other)
	copy from `other` but not particle data More...

bool	contains (const Particle &particle, bool include_inactive=false) const
	Does particle belong?

double	mass () const
	Sum of all active masses.

auto	positions ()
	Range of positions of active particles.

auto	positions () const
	Range of positions of active particles.

AtomData::index_type	getParticleIndex (const Particle &particle, bool include_inactive=false) const
	Finds index of particle within group. Throws if not part of group.

auto	findAtomID (AtomData::index_type atomid) const
	Range of all (active) elements with matching particle id.

auto &	operator[] (size_t index)
	Returns i'th element in group. More...

const auto &	operator[] (size_t index) const

Particle &	at (size_t index)
	Returns i'th element in group. More...

const Particle &	at (size_t index) const
	Returns i'th element in group. More...

template<std::integral Tint = size_t>
auto	operator[] (std::vector< Tint > &indices)
	Reference to subset of given indices, where 0 is the start of the group. More...

template<typename TdistanceFunc >
void	unwrap (const TdistanceFunc &vector_distance)
	Remove PBC for molecular groups w. More...

void	wrap (Geometry::BoundaryFunction boundary)
	Apply periodic boundaries (Order N complexity).

void	translate (const Point &displacement, Geometry::BoundaryFunction boundary=[](Point &) { })
	Translate particle positions and mass center.

void	rotate (const Eigen::Quaterniond &quaternion, Geometry::BoundaryFunction boundary)
	Rotate particles incl. internal coordinates (dipole moment etc.)

void	updateMassCenter (Geometry::BoundaryFunction boundary, const Point &approximate_mass_center)
	Calculates mass center. More...

void	updateMassCenter (Geometry::BoundaryFunction boundary)
	Calculates mass center. More...

Public Member Functions inherited from Faunus::ElasticRange< Particle >
	ElasticRange (Titer begin, Titer end)

size_t	capacity () const

auto	inactive () const
	Range of inactive elements.

void	deactivate (Titer first, Titer last)
	Deactivate particles by moving to end, reducing the effective size.

void	activate (Titer first, Titer last)
	Activate previously deactivated elements.

Titer &	trueend ()

const Titer &	trueend () const

void	relocate (const_iterator oldorigin, Titer neworigin)
	Shift all iterators to new underlying container; useful when resizing vectors.

auto	numInactive () const
	Number of inactive elements. More...

bool	resizeIsPossible (int number_to_insert_or_delete) const

auto	all ()
	Active and inactive elements.

auto	all () const
	Active and inactive elements.

Public Member Functions inherited from Faunus::IterRange< std::vector< Particle >::iterator >
std::vector< Particle >::iterator &	begin ()

const std::vector< Particle >::iterator &	begin () const

std::vector< Particle >::iterator &	end ()

const std::vector< Particle >::iterator &	end () const

size_t	size () const

void	resize (size_t n)

bool	empty () const

void	clear ()

std::pair< int, int >	to_index (std::vector< Particle >::iterator reference) const
	Returns particle index pair relative to given reference.

Public Attributes
int	id = -1
	Molecule id.

int	conformation_id = 0
	Conformation index / id.

Point	mass_center = {0.0, 0.0, 0.0}
	Mass center.

Detailed Description

End of Group class.

Member Enumeration Documentation

◆ Selectors

enum Faunus::Group::Selectors : unsigned int

Selections to filter groups using getSelectionFilter()

Enumerator
ANY	Match any group (disregards all other flags)
ACTIVE	Only active groups (non-zero size)
INACTIVE	Only inactive groups (zero size)
NEUTRAL	Only groups with zero net charge.
ATOMIC	Only atomic groups.
MOLECULAR	Only molecular groups (atomic=false)
FULL	Only groups where size equals capacity.

Constructor & Destructor Documentation

◆ Group()

Faunus::Group::Group	(	MoleculeData::index_type	molid,
		Group::iter	begin,
		Group::iter	end
	)

Constructor.

Parameters

molid	Molecule id the group points to, i.e. a valid index in global `Faunus::molecules`.
begin	Iterator to first particle
end	Iterator to (beyond) end particle

Exceptions

if	molid is out of range w. respect to `Faunus::molecules`

Member Function Documentation

◆ at() [1/2]

Particle & Faunus::Group::at ( size_t index )

Returns i'th element in group.

Parameters

index index starting at zero

Returns: reference to value at i'th element

Exceptions

if	out of interval `[0:capacity[`

◆ at() [2/2]

const Particle & Faunus::Group::at ( size_t index ) const

Returns i'th element in group.

Parameters

index index starting at zero

Returns: reference to value at i'th element

Exceptions

if	out of interval `[0:capacity[`

◆ massCenter()

std::optional< std::reference_wrapper< Point > > Faunus::Group::massCenter ( )

Optional reference to mass center.

If the group supports mass centers (i.e.

molecular groups), an optional reference will be returned. Example usage:

if (auto mass_center = group.massCenter()) { (*mass_center).get() = Point(0,1,2); }

Returns: Optional reference to stored group mass center

◆ match()

template<unsigned int mask>

bool Faunus::Group::match ( ) const

inline

Determines if given Selectors bitmask matches group.

Template Parameters

mask	Bitmask build from enum `Group::Selectors`

Returns: true if ALL enabled bits in the mask are satisfied

Note that for INACTIVE | NEUTRAL, the criterion is applied to all active and inactive particles, i.e. until trueend().

◆ operator=()

Group & Faunus::Group::operator= ( const Group & other )

Deep copy contents from another Group.

Performs a deep copy from another group.

Exceptions

if	the capacities of the two groups differ

◆ operator[]() [1/2]

auto& Faunus::Group::operator[] ( size_t index )

inline

Returns i'th element in group.

Parameters

i	index starting at zero

Returns: reference to value at i'th element

Note: No range-checking and i must be in interval [0:size[

◆ operator[]() [2/2]

template<std::integral Tint = size_t>

auto Faunus::Group::operator[] ( std::vector< Tint > & indices )

inline

Reference to subset of given indices, where 0 is the start of the group.

Parameters

indices Range of indices relative to group

Warning: Do not change indices to const& which would create a dangling reference

◆ shallowCopy()

Group & Faunus::Group::shallowCopy ( const Group & other )

copy from other but not particle data

This copies size, id, mass center etc.

from another group but does not copy particle data.

Exceptions

if	the capacities of the two groups differ

◆ unwrap()

template<typename TdistanceFunc >

void Faunus::Group::unwrap ( const TdistanceFunc & vector_distance )

inline

Remove PBC for molecular groups w.

respect to mass center

Template Parameters

TdistanceFunc

Parameters

vector_distance Distance calculation function

Remarks: Atomic groups are not touched

Warning: Is this fit for use?

◆ updateMassCenter() [1/2]

void Faunus::Group::updateMassCenter	(	Geometry::BoundaryFunction	boundary_function,
		const Point &	approximate_mass_center
	)

Calculates mass center.

Parameters

boundary_function	Function to apply periodic boundaries
approximate_mass_center	Original or appriximate mass center used for PBC removal

Only active, molecular groups are affected. Before the mass center is calculated, the molecule is translated towards the center of the simulation box to remove possible periodic boundary conditions; then translated back again. The translation is done by subtracting / adding approximate_mass_center. Safely handles empty groups.

◆ updateMassCenter() [2/2]

void Faunus::Group::updateMassCenter ( Geometry::BoundaryFunction boundary_function )

Calculates mass center.

Parameters

boundary_function Function to apply periodic boundaries

This will approximate the existing mass center by the middle particle which for PBC systems is generally safer then using the old mass center.

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

src/group.h
src/group.cpp

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Enumeration Documentation

◆ Selectors

Constructor & Destructor Documentation

◆ Group()

Member Function Documentation

◆ at() [1/2]

◆ at() [2/2]

◆ massCenter()

◆ match()

◆ operator=()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ shallowCopy()

◆ unwrap()

◆ updateMassCenter() [1/2]

◆ updateMassCenter() [2/2]