Inheritance diagram for MoleculeInterface:

Public Member Functions
virtual unsigned long	getID () const =0

virtual void	setid (unsigned long id)=0

virtual void	setComponent (Component *component)=0

virtual void	setr (unsigned short d, double r)=0

virtual void	setv (unsigned short d, double v)=0

virtual void	setF (unsigned short d, double F)=0

unsigned int	componentid () const

virtual Component *	component () const =0

virtual unsigned	getComponentLookUpID () const

virtual double	r (unsigned short d) const =0

std::array< double, 3 >	r_arr () const

virtual double	v (unsigned short d) const =0

std::array< double, 3 >	v_arr () const

virtual double	mass () const

virtual double	F (unsigned short d) const =0

virtual std::array< double, 3 >	F_arr ()

virtual std::array< double, 3 >	M_arr ()

virtual std::array< double, 3 >	Vi_arr ()

virtual const Quaternion &	q () const =0

virtual void	setq (Quaternion q)=0

virtual double	D (unsigned short d) const =0

std::array< double, 3 >	D_arr () const

virtual double	M (unsigned short d) const =0

virtual double	Vi (unsigned short d) const =0

virtual void	setD (unsigned short d, double D)=0

virtual void	move (int d, double dr)=0

virtual double	getI (unsigned short d) const =0

virtual double	v2 () const

virtual double	F2 () const

virtual double	L2 () const

virtual double	M2 () const

virtual double	U_trans () const

virtual double	U_trans_2 () const

virtual double	U_rot ()=0

virtual double	U_rot_2 ()=0

virtual double	U_kin ()

virtual void	updateMassInertia ()=0

virtual void	setupSoACache (CellDataSoABase *const s, unsigned iLJ, unsigned iC, unsigned iD, unsigned iQ)=0

virtual void	setSoA (CellDataSoABase *const s)=0

virtual void	setStartIndexSoA_LJ (unsigned i)=0

virtual void	setStartIndexSoA_C (unsigned i)=0

virtual void	setStartIndexSoA_D (unsigned i)=0

virtual void	setStartIndexSoA_Q (unsigned i)=0

virtual unsigned int	numSites () const =0

virtual unsigned int	numOrientedSites () const =0

virtual unsigned int	numLJcenters () const =0

virtual unsigned int	numCharges () const =0

virtual unsigned int	numDipoles () const =0

virtual unsigned int	numQuadrupoles () const =0

virtual std::array< double, 3 >	site_d (unsigned int i) const =0

virtual std::array< double, 3 >	ljcenter_d (unsigned int i) const =0

virtual std::array< double, 3 >	charge_d (unsigned int i) const =0

virtual std::array< double, 3 >	dipole_d (unsigned int i) const =0

virtual std::array< double, 3 >	quadrupole_d (unsigned int i) const =0

virtual std::array< double, 3 >	site_d_abs (unsigned int i) const =0

virtual std::array< double, 3 >	ljcenter_d_abs (unsigned int i) const =0

virtual std::array< double, 3 >	charge_d_abs (unsigned int i) const =0

virtual std::array< double, 3 >	dipole_d_abs (unsigned int i) const =0

virtual std::array< double, 3 >	quadrupole_d_abs (unsigned int i) const =0

virtual std::array< double, 3 >	dipole_e (unsigned int i) const =0

virtual std::array< double, 3 >	quadrupole_e (unsigned int i) const =0

virtual std::array< double, 3 >	site_F (unsigned int i) const =0

virtual std::array< double, 3 >	ljcenter_F (unsigned int i) const =0

virtual std::array< double, 3 >	charge_F (unsigned int i) const =0

virtual std::array< double, 3 >	dipole_F (unsigned int i) const =0

virtual std::array< double, 3 >	quadrupole_F (unsigned int i) const =0

virtual void	normalizeQuaternion ()=0

virtual std::array< double, 3 >	computeLJcenter_d (unsigned int i) const =0

virtual std::array< double, 3 >	computeCharge_d (unsigned int i) const =0

virtual std::array< double, 3 >	computeDipole_d (unsigned int i) const =0

virtual std::array< double, 3 >	computeQuadrupole_d (unsigned int i) const =0

virtual std::array< double, 3 >	computeDipole_e (unsigned int i) const =0

virtual std::array< double, 3 >	computeQuadrupole_e (unsigned int i) const =0

virtual unsigned long	totalMemsize () const =0

double	dist2 (const MoleculeInterface &molecule2, double dr[3]) const

double	orientationAngle (const MoleculeInterface &molecule2, double dr[3], double d2) const

virtual void	setF (double F[3])=0

virtual void	setM (double M[3])=0

virtual void	setVi (double Vi[3])=0

void	scale_v (double s)

void	scale_v (double s, double offx, double offy, double offz)

void	scale_F (double s)

void	scale_D (double s)

void	scale_M (double s)

virtual void	Fadd (const double a[])=0

virtual void	Madd (const double a[])=0

virtual void	Viadd (const double a[])=0

virtual void	vadd (const double ax, const double ay, const double az)=0

virtual void	vsub (const double ax, const double ay, const double az)=0

virtual void	Fljcenteradd (unsigned int i, double a[])=0

virtual void	Fljcentersub (unsigned int i, double a[])=0

virtual void	Fchargeadd (unsigned int i, double a[])=0

virtual void	Fchargesub (unsigned int i, double a[])=0

virtual void	Fdipoleadd (unsigned int i, double a[])=0

virtual void	Fdipolesub (unsigned int i, double a[])=0

virtual void	Fquadrupoleadd (unsigned int i, double a[])=0

virtual void	Fquadrupolesub (unsigned int i, double a[])=0

virtual void	upd_preF (double dt)=0

virtual void	upd_postF (double dt_halve, double &summv2, double &sumIw2)=0

void	ee_upd_preF (double dt)

void	ee_upd_postF (double dt, double &summv2)

virtual void	calculate_mv2_Iw2 (double &summv2, double &sumIw2)=0

virtual void	calculate_mv2_Iw2 (double &summv2, double &sumIw2, double offx, double offy, double offz)=0

virtual void	write (std::ostream &ostrm) const =0

virtual void	writeBinary (std::ostream &ostrm) const =0

virtual void	clearFM ()=0

virtual void	calcFM ()=0

virtual void	check (unsigned long id)=0

bool	isLessThan (const MoleculeInterface &m2) const
	find out whether m1 is before m2 (in some global ordering) More...

virtual bool	inBox (const double l[3], const double u[3]) const
	test whether molecule is inside a cuboid region More...

virtual void	buildOwnSoA ()=0

virtual void	releaseOwnSoA ()=0

Static Public Member Functions
static std::array< vcp_real_calc, 3 >	convert_double_to_vcp_real_calc (const std::array< double, 3 > &v)

static std::string	getWriteFormat ()

Member Function Documentation

◆ buildOwnSoA()

virtual void MoleculeInterface::buildOwnSoA ( )

pure virtual

In almost all cases, molecule's caches are stored in SoAs. In some rare instances (e.g. ParticleContainer::getEnergy()) a molecule should rather better exist alone and not be part of a particleCell. This function allocates a new SoA. Remember to release it when no longer necessary!

Implemented in AutoPasSimpleMolecule, FullMolecule, and MoleculeRMM.

◆ calcFM()

virtual void MoleculeInterface::calcFM ( )

pure virtual

Implemented in FullMolecule.

◆ calculate_mv2_Iw2()

virtual void MoleculeInterface::calculate_mv2_Iw2	(	double &	summv2,
		double &	sumIw2
	)

pure virtual

Implemented in FullMolecule.

◆ check()

virtual void MoleculeInterface::check ( unsigned long id )

pure virtual

Implemented in FullMolecule.

◆ clearFM()

virtual void MoleculeInterface::clearFM ( )

pure virtual

Implemented in FullMolecule.

◆ component()

virtual Component* MoleculeInterface::component ( ) const

pure virtual

Implemented in FullMolecule.

◆ D()

virtual double MoleculeInterface::D ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ F()

virtual double MoleculeInterface::F ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ F2()

virtual double MoleculeInterface::F2 ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ getComponentLookUpID()

virtual unsigned MoleculeInterface::getComponentLookUpID ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ getI()

virtual double MoleculeInterface::getI ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ getID()

virtual unsigned long MoleculeInterface::getID ( ) const

pure virtual

Implemented in FullMolecule.

◆ inBox()

virtual bool MoleculeInterface::inBox	(	const double	l[3],
		const double	u[3]
	)		const

inlinevirtual

test whether molecule is inside a cuboid region

Parameters

l	lower left front corner of cube (equality allowed)
u	upper right back corner of cube (equality not allowed)

Returns: true if molecule is contained in the box, false otherwise

Reimplemented in AutoPasSimpleMolecule.

◆ isLessThan()

bool MoleculeInterface::isLessThan ( const MoleculeInterface & m2 ) const

find out whether m1 is before m2 (in some global ordering)

NOTE: Vectorized force calculation doesn't use this anymore

Compares this molecule to m2 based on their coordinates.

Returns: true if this molecule is smaller than m2 (according to the order induced by the coordinates (z,y,x)

At the boundary between two processes (if used in parallel mode), the forces for pairs which cross the boundary are calculated twice (once by each proc who owns one of the particles). But the contribution to macroscopic value must be counted only once, which is done by the process who owns the "first" particle. As order criterion, the spacial position is used int this method. The particles with lower x-coordinate is first (if equal, then y- or z-coordinate). For pairs which are completely on one process, the first particle can be determined from the cell structure. But for pairs on different procs, the corresponding cell discretisations might be different as well, and therefore the cell structure must not be used to determine the order.

◆ L2()

virtual double MoleculeInterface::L2 ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ M()

virtual double MoleculeInterface::M ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ M2()

virtual double MoleculeInterface::M2 ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ mass()

virtual double MoleculeInterface::mass ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ numSites()

virtual unsigned int MoleculeInterface::numSites ( ) const

pure virtual

Implemented in FullMolecule.

◆ q()

virtual const Quaternion& MoleculeInterface::q ( ) const

pure virtual

Implemented in FullMolecule.

◆ r()

virtual double MoleculeInterface::r ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ releaseOwnSoA()

virtual void MoleculeInterface::releaseOwnSoA ( )

pure virtual

See above comment.

Implemented in AutoPasSimpleMolecule, FullMolecule, and MoleculeRMM.

◆ setComponent()

virtual void MoleculeInterface::setComponent ( Component * component )

pure virtual

Implemented in FullMolecule.

◆ setF()

virtual void MoleculeInterface::setF ( double F[3] )

pure virtual

Implemented in FullMolecule.

◆ setid()

virtual void MoleculeInterface::setid ( unsigned long id )

pure virtual

Implemented in FullMolecule.

◆ setM()

virtual void MoleculeInterface::setM ( double M[3] )

pure virtual

Implemented in FullMolecule.

◆ setq()

virtual void MoleculeInterface::setq ( Quaternion q )

pure virtual

Implemented in FullMolecule.

◆ setr()

virtual void MoleculeInterface::setr	(	unsigned short	d,
		double	r
	)

pure virtual

Implemented in FullMolecule.

◆ setv()

virtual void MoleculeInterface::setv	(	unsigned short	d,
		double	v
	)

pure virtual

Implemented in FullMolecule.

◆ totalMemsize()

virtual unsigned long MoleculeInterface::totalMemsize ( ) const

pure virtual

Implemented in FullMolecule.

◆ U_kin()

virtual double MoleculeInterface::U_kin ( )

inlinevirtual

Reimplemented in FullMolecule.

◆ U_rot()

virtual double MoleculeInterface::U_rot ( )

pure virtual

Implemented in FullMolecule.

◆ U_trans()

virtual double MoleculeInterface::U_trans ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ upd_postF()

virtual void MoleculeInterface::upd_postF	(	double	dt_halve,
		double &	summv2,
		double &	sumIw2
	)

pure virtual

Implemented in FullMolecule.

◆ upd_preF()

virtual void MoleculeInterface::upd_preF ( double dt )

pure virtual

Implemented in FullMolecule.

◆ updateMassInertia()

virtual void MoleculeInterface::updateMassInertia ( )

pure virtual

Implemented in FullMolecule.

◆ v()

virtual double MoleculeInterface::v ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ v2()

virtual double MoleculeInterface::v2 ( ) const

inlinevirtual

Reimplemented in FullMolecule.

◆ Vi()

virtual double MoleculeInterface::Vi ( unsigned short d ) const

pure virtual

Implemented in FullMolecule.

◆ write()

virtual void MoleculeInterface::write ( std::ostream & ostrm ) const

pure virtual

Implemented in FullMolecule.

◆ writeBinary()

virtual void MoleculeInterface::writeBinary ( std::ostream & ostrm ) const

pure virtual

Implemented in FullMolecule.

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

src/molecules/MoleculeInterface.h
src/molecules/MoleculeInterface.cpp

Public Member Functions

Static Public Member Functions

Member Function Documentation

◆ buildOwnSoA()

◆ calcFM()

◆ calculate_mv2_Iw2()

◆ check()

◆ clearFM()

◆ component()

◆ D()

◆ F()

◆ F2()

◆ getComponentLookUpID()

◆ getI()

◆ getID()

◆ inBox()

◆ isLessThan()

◆ L2()

◆ M()

◆ M2()

◆ mass()

◆ numSites()

◆ q()

◆ r()

◆ releaseOwnSoA()

◆ setComponent()

◆ setF()

◆ setid()

◆ setM()

◆ setq()

◆ setr()

◆ setv()

◆ totalMemsize()

◆ U_kin()

◆ U_rot()

◆ U_trans()

◆ upd_postF()

◆ upd_preF()

◆ updateMassInertia()

◆ v()

◆ v2()

◆ Vi()

◆ write()

◆ writeBinary()