AtomSubsystem Class Reference

#include <AtomSubsystem.h>

Inheritance diagram for AtomSubsystem:

List of all members.

Classes
class	Atom
class	AtomsByBody
class	Bond
class	PairIterator
Public Types
enum	NeighborAlgorithm { N_SQUARED, VOXEL_HASH, AUTOMATIC }
typedef SimTK::units::md::mass_t	mass_t
typedef SimTK::units::md::length_t	length_t
typedef SimTK::units::md::location_t	location_t
typedef SimTK::units::md::area_t	area_t
typedef std::vector< AtomIndex >	AtomIndexList
typedef std::vector< AtomsByBody >	AtomicBodies
Public Member Functions
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (AtomSubsystem, AtomIndex)
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (AtomSubsystem, BodyAtomIndex)
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (AtomSubsystem, LocalBodyIndex)
	SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE (AtomSubsystem, BondIndex)
PairIterator	pairBegin (const State &state, length_t cutoff=0.0 *nanometers, NeighborAlgorithm algorithm=AUTOMATIC) const
PairIterator	pairEnd () const
	AtomSubsystem (SimTK::MultibodySystem &system)
MultibodySystem &	updMultibodySystem ()
const MultibodySystem &	getMultibodySystem () const
AtomSubsystem &	setAtomMobilizedBodyIndex (AtomIndex atomIx, MobilizedBodyIndex bodyIx)
const AtomIndexList &	getBodyAtoms (LocalBodyIndex bodyIx) const
const AtomIndexList &	getBodyAtoms (SimTK::MobilizedBodyIndex bodyIx) const
AtomIndex	addAtom (mass_t mass=0.0 *daltons)
size_t	getNumAtoms () const
const Vec3 &	getAtomLocationInGround (const SimTK::State &state, AtomIndex atom) const
const Vec3 &	getAtomVelocityInGround (const SimTK::State &state, AtomIndex atom) const
const Vec3 &	getAtomBodyStationInGround (const SimTK::State &state, AtomIndex atom) const
const Atom &	getAtom (AtomIndex ix) const
Atom &	updAtom (AtomIndex ix)
BondIndex	addBond (AtomIndex a1, AtomIndex a2)
size_t	getNumBonds () const
const Bond &	getBond (BondIndex ix) const
Bond &	updBond (BondIndex ix)
size_t	getNumBodies () const
void	addBodyExclusion (MobilizedBodyIndex bodyIx1, MobilizedBodyIndex bodyIx2)
SimbodyMatterSubsystem &	updMatterSubsystem ()
Protected Member Functions
const Impl &	getRep () const
Impl &	updRep ()

---

Member Typedef Documentation

typedef SimTK::units::md::area_t area_t

typedef std::vector<AtomsByBody> AtomicBodies

typedef std::vector<AtomIndex> AtomIndexList

typedef SimTK::units::md::length_t length_t

typedef SimTK::units::md::location_t location_t

typedef SimTK::units::md::mass_t mass_t

---

Member Enumeration Documentation

enum NeighborAlgorithm

Enumerator:

N_SQUARED
VOXEL_HASH
AUTOMATIC

---

Constructor & Destructor Documentation

AtomSubsystem

(

SimTK::MultibodySystem &

system

)

---

Member Function Documentation

AtomIndex addAtom

(

mass_t

mass = 0.0 *daltons

)

void addBodyExclusion	(	MobilizedBodyIndex	bodyIx1,
		MobilizedBodyIndex	bodyIx2
	)

BondIndex addBond	(	AtomIndex	a1,
		AtomIndex	a2
	)

const Atom& getAtom

(

AtomIndex

ix

)

const

Referenced by VanDerWaalsForce::calcForce(), VanDerWaalsForce::calcPotentialEnergy(), and VanDerWaalsForce::decorateAtoms().

const Vec3& getAtomBodyStationInGround	(	const SimTK::State &	state,
		AtomIndex	atom
	)			const

Referenced by VanDerWaalsForce::calcForce().

const Vec3& getAtomLocationInGround	(	const SimTK::State &	state,
		AtomIndex	atom
	)			const

Referenced by VanDerWaalsForce::calcForce(), and VanDerWaalsForce::calcPotentialEnergy().

const Vec3& getAtomVelocityInGround	(	const SimTK::State &	state,
		AtomIndex	atom
	)			const

const AtomIndexList& getBodyAtoms

(

SimTK::MobilizedBodyIndex

bodyIx

)

const

const AtomIndexList& getBodyAtoms

(

LocalBodyIndex

bodyIx

)

const

const Bond& getBond

(

BondIndex

ix

)

const

const MultibodySystem& getMultibodySystem

(

)

const

Referenced by VanDerWaalsForce::decorateBoundingSpheres().

size_t getNumAtoms

(

)

const

size_t getNumBodies

(

)

const

size_t getNumBonds

(

)

const

const Impl& getRep

(

)

const [protected]

PairIterator pairBegin	(	const State &	state,
		length_t	cutoff = 0.0 *nanometers,
		NeighborAlgorithm	algorithm = AUTOMATIC
	)			const

Referenced by VanDerWaalsForce::calcForce(), and VanDerWaalsForce::calcPotentialEnergy().

PairIterator pairEnd

(

)

const

Referenced by VanDerWaalsForce::calcForce(), and VanDerWaalsForce::calcPotentialEnergy().

AtomSubsystem& setAtomMobilizedBodyIndex	(	AtomIndex	atomIx,
		MobilizedBodyIndex	bodyIx
	)

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	AtomSubsystem	,
		BondIndex
	)

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	AtomSubsystem	,
		LocalBodyIndex
	)

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	AtomSubsystem	,
		BodyAtomIndex
	)

SimTK_DEFINE_UNIQUE_LOCAL_INDEX_TYPE	(	AtomSubsystem	,
		AtomIndex
	)

Atom& updAtom

(

AtomIndex

ix

)

Bond& updBond

(

BondIndex

ix

)

SimbodyMatterSubsystem& updMatterSubsystem

(

)

MultibodySystem& updMultibodySystem

(

)

Impl& updRep

(

)

[protected]

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

• AtomSubsystem.h