Placeholder for atoms and molecules. More...

#include <space.h>

Collaboration diagram for Faunus::Space:

Public Types
enum	Selection { ALL, ACTIVE, INACTIVE, ALL_NEUTRAL, ACTIVE_NEUTRAL, INACTIVE_NEUTRAL }

using	GeometryType = Geometry::Chameleon

using	GroupType = Group
	Continuous range of particles defining molecules.

using	GroupVector = std::vector< GroupType >

using	GroupRefVector = std::vector< std::reference_wrapper< Group > >

using	ConstGroupRefVector = std::vector< std::reference_wrapper< const Group > >

using	ScaleVolumeTrigger = std::function< void(Space &, double, double)>

using	ChangeTrigger = std::function< void(Space &, const Change &)>

using	SyncTrigger = std::function< void(Space &, const Space &, const Change &)>

Public Member Functions
const std::map< MoleculeData::index_type, std::size_t > &	getImplicitReservoir () const
	Implicit molecules.

std::map< MoleculeData::index_type, std::size_t > &	getImplicitReservoir ()
	Implicit molecules. More...

void	clear ()
	Clears particle and molecule list.

GroupType &	addGroup (MoleculeData::index_type molid, const ParticleVector &particles)
	Append a group. More...

GroupVector::iterator	findGroupContaining (const Particle &particle, bool include_inactive=false)
	Finds the group containing the given atom.

GroupVector::iterator	findGroupContaining (AtomData::index_type atom_index)
	Find group containing atom index.

size_t	numParticles (Selection selection=Selection::ACTIVE) const
	Number of (active) particles.

Point	scaleVolume (double new_volume, Geometry::VolumeMethod method=Geometry::VolumeMethod::ISOTROPIC)
	Scales atoms, molecules, container. More...

GroupVector::iterator	randomMolecule (MoleculeData::index_type molid, Random &rand, Selection selection=Selection::ACTIVE)
	Random group matching molid.

json	info ()

std::size_t	getGroupIndex (const GroupType &group) const
	Get index of given group in the group vector. More...

std::size_t	getFirstParticleIndex (const GroupType &group) const
	Index of first particle in group.

std::size_t	getFirstActiveParticleIndex (const GroupType &group) const
	Index of first particle w. respect to active particles. More...

template<std::forward_iterator iterator, class copy_operation = std::function<void(const Particle&, Particle&)>>
void	updateParticles (const iterator begin, const iterator end, ParticleVector::iterator destination, copy_operation copy_function=[](const Particle &src, Particle &dst) { dst=src;})
	Update particles in Space from a source range. More...

void	updateInternalState (const Change &change)
	This will make sure that the internal state is updated to reflect a change. More...

auto	positions () const
	Iterable range of all particle positions.

auto	positions ()
	Mutable iterable range of all particle positions.

auto	findMolecules (MoleculeData::index_type molid, Selection selection=Selection::ACTIVE)
	Finds all groups of type `molid` (complexity: order N) More...

auto	findMolecules (MoleculeData::index_type molid, Selection selection=Selection::ACTIVE) const

auto	activeParticles ()
	Range with all active particles.

auto	activeParticles () const
	Range with all active particles.

template<std::integral index_type = int>
auto	toIndices (const RequireParticles auto &particle_range) const
	Get vector of indices of given range of particles. More...

auto	findAtoms (AtomData::index_type atomid)
	Find active atoms of type `atomid` (complexity: order N) More...

auto	findAtoms (AtomData::index_type atomid) const
	Find active atoms of type `atomid` (complexity: order N) More...

size_t	countAtoms (AtomData::index_type atomid) const
	Count active particles.

template<unsigned int mask>
auto	numMolecules (MoleculeData::index_type molid) const
	Count number of molecules matching criteria. More...

void	sync (const Space &other, const Change &change)
	Copy differing data from other Space using Change object. More...

Static Public Member Functions
static std::function< bool(const GroupType &)>	getGroupFilter (MoleculeData::index_type molid, const Selection &selection)

Public Attributes
ParticleVector	particles
	All particles are stored here!

GroupVector	groups
	All groups are stored here (i.e. molecules)

GeometryType	geometry
	Container geometry (boundaries, shape, volume)

std::vector< ScaleVolumeTrigger >	scaleVolumeTriggers
	Functions triggered whenever the volume is scaled.

Detailed Description

Placeholder for atoms and molecules.

Space is pervasive in the code as it stores the state of

particles
groups
simulation container (geometry)
implicit particles and groups

It has methods to insert, find, and probe particles, groups, as well as scaling the volume of the system

Member Function Documentation

◆ addGroup()

Space::GroupType & Faunus::Space::addGroup	(	MoleculeData::index_type	molid,
		const ParticleVector &	new_particles
	)

Append a group.

The following is considered:

groups vector is expanded with a new group at the end
if the space particle vector is relocated, all existing group iterators are updated to reflect the new memory positions
for molecular groups, the mass center is calculated and set

Parameters

molid	Molecule id of inserted data
new_particles	Particles to generate group from

Returns: Reference to the inserted group

Exceptions

if	particles is empty or if the given particles do not match the molecule id

◆ findAtoms() [1/2]

auto Faunus::Space::findAtoms ( AtomData::index_type atomid )

inline

Find active atoms of type atomid (complexity: order N)

Parameters

atomid Atom id to look for

Returns: Range of filtered particles

◆ findAtoms() [2/2]

auto Faunus::Space::findAtoms ( AtomData::index_type atomid ) const

inline

Find active atoms of type atomid (complexity: order N)

Parameters

atomid Atom id to look for

Returns: Range of filtered particles

◆ findMolecules()

auto Faunus::Space::findMolecules	(	MoleculeData::index_type	molid,
		Selection	selection = `Selection::ACTIVE`
	)

inline

Finds all groups of type molid (complexity: order N)

Parameters

molid	Molecular id to look for
selection	Selection

Returns: range with all groups of molid

◆ getFirstActiveParticleIndex()

std::size_t Faunus::Space::getFirstActiveParticleIndex ( const GroupType & group ) const

Index of first particle w. respect to active particles.

Returns the index of the first particle of the group in the range returned by activeParticles()

◆ getGroupFilter()

static std::function<bool(const GroupType&)> Faunus::Space::getGroupFilter	(	MoleculeData::index_type	molid,
		const Selection &	selection
	)

inlinestatic

< determines if range of particles is neutral

< Lambda to filter groups according to selection

◆ getGroupIndex()

std::size_t Faunus::Space::getGroupIndex ( const GroupType & group ) const

Get index of given group in the group vector.

Exceptions

If	group is not part of space

◆ getImplicitReservoir()

std::map< MoleculeData::index_type, std::size_t > & Faunus::Space::getImplicitReservoir ( )

Implicit molecules.

Keywords to select particles based on the their active/inactive state and charge neutrality

◆ numMolecules()

template<unsigned int mask>

auto Faunus::Space::numMolecules ( MoleculeData::index_type molid ) const

inline

Count number of molecules matching criteria.

Parameters

molid Molecule id to match

Template Parameters

mask	Selection mask based on `Group::Selectors`

Returns: Number of molecules matching molid and mask

◆ scaleVolume()

Point Faunus::Space::scaleVolume	(	double	Vnew,
		Geometry::VolumeMethod	method = `Geometry::VolumeMethod::ISOTROPIC`
	)

Scales atoms, molecules, container.

Parameters

Vnew	New volume
method	Scaling policy

Returns: Scaling factors in each dimension

Warning: Check new_volume/old_volume for ISOCHORIC in case of external triggers (see end of function)

< unary helper function to scale position and apply PBC

◆ sync()

void Faunus::Space::sync	(	const Space &	other,
		const Change &	change
	)

Copy differing data from other Space using Change object.

Parameters

other	Space to copy from
change	Change object describing the changes beteeen the two Space objects

Copy data from another Space according to Change object. This is typically done after a Monte Carlo move has either been accepted or rejected. The other space must be populated in the exact same way, i.e. must have the same molecules and particles. In DEBUG mode, several assertions are included to ensure this is true.

Copied data includes:

geometry
groups
particles
implicit molecules

◆ toIndices()

template<std::integral index_type = int>

auto Faunus::Space::toIndices ( const RequireParticles auto & particle_range ) const

inline

Get vector of indices of given range of particles.

Returns: std::vector of indices pointing to Space::particles

Exceptions

std::out_of_range if any particle in range does not belong to Space::particles

◆ updateInternalState()

void Faunus::Space::updateInternalState ( const Change & change )

This will make sure that the internal state is updated to reflect a change.

Typically this is called after a modification of the system, e.g. a MC move and will update the following:

mass centers;
particle trackers
cell lists

Todo:: Under construction and currently not in use

◆ updateParticles()

template<std::forward_iterator iterator, class copy_operation = std::function<void(const Particle&, Particle&)>>

void Faunus::Space::updateParticles	(	const iterator	begin,
		const iterator	end,
		ParticleVector::iterator	destination,
		copy_operation	copy_function = `[](const Particle& src, Particle& dst) { dst = src; }`
	)

inline

Update particles in Space from a source range.

Template Parameters

iterator	Iterator for source range
copy_operation	Functor used to copy data from an element in the source range to element in `Space:p`

Parameters

begin	Begin of source particle range
end	End of source particle range
destination	Iterator to target particle vector (should be in `Space::p`)
copy_function	Function used to copy from source range to destination particle

By default a source range of particles is expected and all content is copied. This can be customised to e.g. a position range by giving a copy_function such as [](const auto &pos, auto &particle){particle.pos = pos;}.

The following is updated:

particles
molecular mass centers of affected groups
future: update cell list?

Todo:: Since Space::groups is ordered, binary search could be used to filter

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

src/space.h
src/space.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ addGroup()

◆ findAtoms() [1/2]

◆ findAtoms() [2/2]

◆ findMolecules()

◆ getFirstActiveParticleIndex()

◆ getGroupFilter()

◆ getGroupIndex()

◆ getImplicitReservoir()

◆ numMolecules()

◆ scaleVolume()

◆ sync()

◆ toIndices()

◆ updateInternalState()

◆ updateParticles()