VanDerWaalsForce Class Reference

#include <VanDerWaalsForce.h>

Inheritance diagram for VanDerWaalsForce:

Classes
struct	ForceAndEnergy
class	VdwAtom
struct	WallSphere
Public Types
typedef AtomSubsystem::AtomIndex	AtomIndex
typedef Real	length_t
typedef Real	area_t
typedef Real	energy_t
typedef Real	inverse_area_t
typedef Vec3	location_t
typedef Vec3	force_t
Public Member Functions
	VanDerWaalsForce (const AtomSubsystem &atomSubsystem, length_t cutoff=0.0 *nanometers)
bool	dependsOnlyOnPositions () const
	Get whether this force depends only on the position variables (q), not on the velocies (u) or auxiliary variables (z).
void	addAtom (AtomSubsystem::AtomIndex atomIndex, length_t rMin, energy_t wellDepth)
void	addBoundarySphere (const location_t &center, length_t radius, length_t vdwRadius, energy_t wellDepth)
void	decorateAtoms (DecorationSubsystem &decorations, Real scale=1.0) const
void	decorateBoundingSpheres (DecorationSubsystem &decorations) const
void	calcForce (const State &state, Vector_< SpatialVec > &bodyForces, Vector_< Vec3 > &particleForces, Vector &mobilityForces) const
	Calculate the force for a given state.
Real	calcPotentialEnergy (const State &state) const
	Calculate this force's contribution to the potential energy of the System.
Protected Member Functions
ForceAndEnergy	calcForceAndEnergy (const location_t &r, Real dij, Real eij) const
void	calcForce (const VdwAtom &vdwAtom1, const VdwAtom &vdwAtom2, const State &state, Vector_< SpatialVec > &bodyForces) const
energy_t	calcPotentialEnergy (const VdwAtom &vdwAtom1, const VdwAtom &vdwAtom2, const State &state) const
void	calcForce (const WallSphere &sphere, const VdwAtom &vdwAtom2, const State &state, Vector_< SpatialVec > &bodyForces) const
energy_t	calcPotentialEnergy (const WallSphere &sphere, const VdwAtom &vdwAtom2, const State &state) const
Protected Attributes
const AtomSubsystem &	atomSubsystem
std::vector< VdwAtom >	vdwAtoms
length_t	cutoff
area_t	cutoffSquared
std::vector< WallSphere >	wallSpheres

Member Typedef Documentation

typedef Real area_t

typedef AtomSubsystem::AtomIndex AtomIndex

typedef Real energy_t

typedef Vec3 force_t

typedef Real inverse_area_t

typedef Real length_t

typedef Vec3 location_t

Constructor & Destructor Documentation

VanDerWaalsForce	(	const AtomSubsystem &	atomSubsystem,
		length_t	cutoff = `0.0 * nanometers`
	)			`[inline]`

Member Function Documentation

void addAtom	(	AtomSubsystem::AtomIndex	atomIndex,
		length_t	rMin,
		energy_t	wellDepth
	)			`[inline]`

References VanDerWaalsForce::vdwAtoms.

void addBoundarySphere	(	const location_t &	center,
		length_t	radius,
		length_t	vdwRadius,
		energy_t	wellDepth
	)			`[inline]`

References WallSphere::center, WallSphere::radius, WallSphere::vdwRadius, VanDerWaalsForce::wallSpheres, and WallSphere::wellDepth.

void calcForce	(	const WallSphere &	sphere,
		const VdwAtom &	vdwAtom2,
		const State &	state,
		Vector_< SpatialVec > &	bodyForces
	)			const `[inline, protected]`

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::calcForceAndEnergy(), WallSphere::center, ForceAndEnergy::force, AtomSubsystem::getAtom(), AtomSubsystem::getAtomBodyStationInGround(), AtomSubsystem::getAtomLocationInGround(), Atom::getMobilizedBodyIndex(), Vec< M, ELT, STRIDE >::norm(), WallSphere::radius, VdwAtom::rMin, WallSphere::vdwRadius, VdwAtom::wellDepth, and WallSphere::wellDepth.

void calcForce	(	const VdwAtom &	vdwAtom1,
		const VdwAtom &	vdwAtom2,
		const State &	state,
		Vector_< SpatialVec > &	bodyForces
	)			const `[inline, protected]`

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::calcForceAndEnergy(), ForceAndEnergy::force, AtomSubsystem::getAtom(), AtomSubsystem::getAtomBodyStationInGround(), AtomSubsystem::getAtomLocationInGround(), Atom::getMobilizedBodyIndex(), VdwAtom::rMin, and VdwAtom::wellDepth.

void calcForce	(	const State &	state,
		Vector_< SpatialVec > &	bodyForces,
		Vector_< Vec3 > &	particleForces,
		Vector &	mobilityForces
	)			const `[inline, virtual]`

Calculate the force for a given state.

Parameters:

	state	the State for which to calculate the force
	bodyForces	spatial forces on MobilizedBodies are accumulated in this. To apply a force to a body, add it to the appropriate element of this vector.
	particleForces	forces on particles are accumulated in this. Since particles are not yet implemented, this is ignored.
	mobilityForces	forces on individual mobilities (elements of the state's u vector) are accumulated in this. To apply a force to a mobility, add it to the appropriate element of this vector.

Implements Implementation.

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::cutoff, AtomSubsystem::pairBegin(), AtomSubsystem::pairEnd(), VanDerWaalsForce::vdwAtoms, and VanDerWaalsForce::wallSpheres.

ForceAndEnergy calcForceAndEnergy	(	const location_t &	r,
		Real	dij,
		Real	eij
	)			const `[inline, protected]`

References VanDerWaalsForce::cutoff, VanDerWaalsForce::cutoffSquared, ForceAndEnergy::energy, and ForceAndEnergy::force.

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

energy_t calcPotentialEnergy	(	const WallSphere &	sphere,
		const VdwAtom &	vdwAtom2,
		const State &	state
	)			const `[inline, protected]`

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::calcForceAndEnergy(), WallSphere::center, ForceAndEnergy::energy, AtomSubsystem::getAtom(), AtomSubsystem::getAtomLocationInGround(), Vec< M, ELT, STRIDE >::norm(), WallSphere::radius, VdwAtom::rMin, WallSphere::vdwRadius, VdwAtom::wellDepth, and WallSphere::wellDepth.

energy_t calcPotentialEnergy	(	const VdwAtom &	vdwAtom1,
		const VdwAtom &	vdwAtom2,
		const State &	state
	)			const `[inline, protected]`

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::calcForceAndEnergy(), ForceAndEnergy::energy, AtomSubsystem::getAtom(), AtomSubsystem::getAtomLocationInGround(), VdwAtom::rMin, and VdwAtom::wellDepth.

Real calcPotentialEnergy ( const State & state ) const [inline, virtual]

Calculate this force's contribution to the potential energy of the System.

Parameters:

state

the State for which to calculate the potential energy

Implements Implementation.

References VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, VanDerWaalsForce::cutoff, SimTK::md::kilojoules_per_mole, AtomSubsystem::pairBegin(), AtomSubsystem::pairEnd(), VanDerWaalsForce::vdwAtoms, and VanDerWaalsForce::wallSpheres.

void decorateAtoms	(	DecorationSubsystem &	decorations,
		Real	scale = `1.0`
	)			const `[inline]`

References DecorationSubsystem::addBodyFixedDecoration(), VdwAtom::atomIndex, VanDerWaalsForce::atomSubsystem, AtomSubsystem::getAtom(), Atom::getMass(), Atom::getMobilizedBodyIndex(), Atom::getStationInBodyFrame(), VdwAtom::rMin, and VanDerWaalsForce::vdwAtoms.

void decorateBoundingSpheres ( DecorationSubsystem & decorations ) const [inline]

References DecorationSubsystem::addBodyFixedDecoration(), VanDerWaalsForce::atomSubsystem, WallSphere::center, SimbodyMatterSubsystem::getGround(), MultibodySystem::getMatterSubsystem(), MobilizedBody::getMobilizedBodyIndex(), AtomSubsystem::getMultibodySystem(), WallSphere::radius, and VanDerWaalsForce::wallSpheres.

bool dependsOnlyOnPositions ( ) const [inline, virtual]

Get whether this force depends only on the position variables (q), not on the velocies (u) or auxiliary variables (z).

The default implementation returns false. If the force depends only on positions, you should override this to return true. This allows force calculations to be optimized in some cases.

Reimplemented from Implementation.