AutoPasSimpleMolecule Class Reference

#include <AutoPasSimpleMolecule.h>

Inheritance diagram for AutoPasSimpleMolecule:

Public Types
enum	AttributeNames : int {   ptr , id , posX , posY ,   posZ , forceX , forceY , forceZ ,   typeId , ownershipState }
using	SoAArraysType = typename autopas::utils::SoAType< AutoPasSimpleMolecule *, size_t, double, double, double, double, double, double, size_t, autopas::OwnershipState >::Type

Public Member Functions
	AutoPasSimpleMolecule (unsigned long id=0, Component *component=nullptr, double rx=0., double ry=0., double rz=0., double vx=0., double vy=0., double vz=0., double q0=1., double q1=1., double q2=0., double q3=0., double Dx=0., double Dy=0., double Dz=0.)
	AutoPasSimpleMolecule (const AutoPasSimpleMolecule &m)=default
template<AttributeNames attribute>
constexpr std::tuple_element< static_cast< size_t >(attribute), SoAArraysType >::type::value_type	get ()
template<AttributeNames attribute>
constexpr void	set (typename std::tuple_element< static_cast< size_t >(attribute), SoAArraysType >::type::value_type value)
unsigned long	getID () const override
void	setid (unsigned long id) override
void	setComponent (Component *component) override
void	setr (unsigned short d, double r) override
void	setv (unsigned short d, double v) override
void	setF (unsigned short d, double F) override
Component *	component () const override
double	r (unsigned short d) const override
double	v (unsigned short d) const override
double	F (unsigned short d) const override
const Quaternion &	q () const override
void	setq (Quaternion q) override
double	D (unsigned short d) const override
double	M (unsigned short d) const override
double	Vi (unsigned short d) const override
void	setD (unsigned short d, double D) override
void	move (int d, double dr) override
double	getI (unsigned short d) const override
double	U_rot () override
double	U_rot_2 () override
void	updateMassInertia () override
void	setupSoACache (CellDataSoABase *const s, unsigned iLJ, unsigned iC, unsigned iD, unsigned iQ) override
void	setSoA (CellDataSoABase *const s) override
void	setStartIndexSoA_LJ (unsigned i) override
void	setStartIndexSoA_C (unsigned i) override
void	setStartIndexSoA_D (unsigned i) override
void	setStartIndexSoA_Q (unsigned i) override
unsigned int	numSites () const override
unsigned int	numOrientedSites () const override
unsigned int	numLJcenters () const override
unsigned int	numCharges () const override
unsigned int	numDipoles () const override
unsigned int	numQuadrupoles () const override
std::array< double, 3 >	site_d (unsigned int i) const override
std::array< double, 3 >	ljcenter_d (unsigned int i) const override
std::array< double, 3 >	charge_d (unsigned int i) const override
std::array< double, 3 >	dipole_d (unsigned int i) const override
std::array< double, 3 >	quadrupole_d (unsigned int i) const override
std::array< double, 3 >	site_d_abs (unsigned int i) const override
std::array< double, 3 >	ljcenter_d_abs (unsigned int i) const override
std::array< double, 3 >	charge_d_abs (unsigned int i) const override
std::array< double, 3 >	dipole_d_abs (unsigned int i) const override
std::array< double, 3 >	quadrupole_d_abs (unsigned int i) const override
std::array< double, 3 >	dipole_e (unsigned int i) const override
std::array< double, 3 >	quadrupole_e (unsigned int i) const override
std::array< double, 3 >	site_F (unsigned int i) const override
std::array< double, 3 >	ljcenter_F (unsigned int i) const override
std::array< double, 3 >	charge_F (unsigned int i) const override
std::array< double, 3 >	dipole_F (unsigned int i) const override
std::array< double, 3 >	quadrupole_F (unsigned int i) const override
void	normalizeQuaternion () override
std::array< double, 3 >	computeLJcenter_d (unsigned int i) const override
std::array< double, 3 >	computeCharge_d (unsigned int i) const override
std::array< double, 3 >	computeDipole_d (unsigned int i) const override
std::array< double, 3 >	computeQuadrupole_d (unsigned int i) const override
std::array< double, 3 >	computeDipole_e (unsigned int i) const override
std::array< double, 3 >	computeQuadrupole_e (unsigned int i) const override
unsigned long	totalMemsize () const override
void	setF (double F[3]) override
void	setF (const std::array< double, 3 > &f)
void	setM (double M[3]) override
void	setVi (double Vi[3]) override
void	Fadd (const double F[]) override
void	Madd (const double a[]) override
void	Viadd (const double a[]) override
void	vadd (const double ax, const double ay, const double az) override
void	vsub (const double ax, const double ay, const double az) override
void	Fljcenteradd (unsigned int i, double a[]) override
void	Fljcentersub (unsigned int i, double a[]) override
void	Fchargeadd (unsigned int i, double a[]) override
void	Fchargesub (unsigned int i, double a[]) override
void	Fdipoleadd (unsigned int i, double a[]) override
void	Fdipolesub (unsigned int i, double a[]) override
void	Fquadrupoleadd (unsigned int i, double a[]) override
void	Fquadrupolesub (unsigned int i, double a[]) override
void	upd_preF (double dt) override
void	upd_postF (double dt_halve, double &summv2, double &sumIw2) override
void	calculate_mv2_Iw2 (double &summv2, double &sumIw2) override
void	calculate_mv2_Iw2 (double &summv2, double &sumIw2, double offx, double offy, double offz) override
void	write (std::ostream &ostrm) const override
void	writeBinary (std::ostream &ostrm) const override
void	clearFM () override
void	calcFM () override
void	check (unsigned long id) override
void	buildOwnSoA () override
void	releaseOwnSoA () override
bool	inBox (const double rmin[3], const double rmax[3]) const override
	test whether molecule is inside a cuboid region More...
bool	inBox (const std::array< double, 3 > &rmin, const std::array< double, 3 > &rmax) const
size_t	getTypeId () const
Public Member Functions inherited from MoleculeInterface
unsigned int	componentid () const
virtual unsigned	getComponentLookUpID () const
std::array< double, 3 >	r_arr () const
std::array< double, 3 >	v_arr () const
virtual double	mass () const
virtual std::array< double, 3 >	F_arr ()
virtual std::array< double, 3 >	M_arr ()
virtual std::array< double, 3 >	Vi_arr ()
std::array< double, 3 >	D_arr () const
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_kin ()
double	dist2 (const MoleculeInterface &molecule2, double dr[3]) const
double	orientationAngle (const MoleculeInterface &molecule2, double dr[3], double d2) const
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)
void	ee_upd_preF (double dt)
void	ee_upd_postF (double dt, double &summv2)
bool	isLessThan (const MoleculeInterface &m2) const
	find out whether m1 is before m2 (in some global ordering) More...

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

Detailed Description

class that implements additional functions to make the molecule compatible with autopas

Member Typedef Documentation

SoAArraysType

using AutoPasSimpleMolecule::SoAArraysType = typename autopas::utils::SoAType<AutoPasSimpleMolecule *, size_t , double , double , double , double , double , double , size_t , autopas::OwnershipState >::Type

The type for the SoA storage.

Note

The attribute owned is of type float but treated as a bool. This means it shall always only take values 0.0 (=false) or 1.0 (=true). The reason for this is the easier use of the value in calculations (See LJFunctor "energyFactor")

Member Enumeration Documentation

AttributeNames

enum AutoPasSimpleMolecule::AttributeNames : int

Enums used as ids for accessing and creating a dynamically sized SoA.

Member Function Documentation

buildOwnSoA()

void AutoPasSimpleMolecule::buildOwnSoA ( )

inlineoverridevirtual

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!

Implements MoleculeInterface.

calcFM()

void AutoPasSimpleMolecule::calcFM ( )

inlineoverridevirtual

Implements MoleculeInterface.

calculate_mv2_Iw2() [1/2]

void AutoPasSimpleMolecule::calculate_mv2_Iw2 ( double &  summv2, double &  sumIw2  )

inlineoverridevirtual

Implements MoleculeInterface.

calculate_mv2_Iw2() [2/2]

void AutoPasSimpleMolecule::calculate_mv2_Iw2 ( double &  summv2, double &  sumIw2, double  offx, double  offy, double  offz  )

inlineoverridevirtual

Implements MoleculeInterface.

charge_d()

std::array<double, 3> AutoPasSimpleMolecule::charge_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

charge_d_abs()

std::array<double, 3> AutoPasSimpleMolecule::charge_d_abs ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

charge_F()

std::array<double, 3> AutoPasSimpleMolecule::charge_F ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

check()

void AutoPasSimpleMolecule::check ( unsigned long  id )

inlineoverridevirtual

Implements MoleculeInterface.

clearFM()

void AutoPasSimpleMolecule::clearFM ( )

inlineoverridevirtual

Implements MoleculeInterface.

component()

Component* AutoPasSimpleMolecule::component ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeCharge_d()

std::array<double, 3> AutoPasSimpleMolecule::computeCharge_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeDipole_d()

std::array<double, 3> AutoPasSimpleMolecule::computeDipole_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeDipole_e()

std::array<double, 3> AutoPasSimpleMolecule::computeDipole_e ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeLJcenter_d()

std::array<double, 3> AutoPasSimpleMolecule::computeLJcenter_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeQuadrupole_d()

std::array<double, 3> AutoPasSimpleMolecule::computeQuadrupole_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

computeQuadrupole_e()

std::array<double, 3> AutoPasSimpleMolecule::computeQuadrupole_e ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

D()

double AutoPasSimpleMolecule::D ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

dipole_d()

std::array<double, 3> AutoPasSimpleMolecule::dipole_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

dipole_d_abs()

std::array<double, 3> AutoPasSimpleMolecule::dipole_d_abs ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

dipole_e()

std::array<double, 3> AutoPasSimpleMolecule::dipole_e ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

dipole_F()

std::array<double, 3> AutoPasSimpleMolecule::dipole_F ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

F()

double AutoPasSimpleMolecule::F ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

Fadd()

void AutoPasSimpleMolecule::Fadd ( const double  F[] )

inlineoverridevirtual

Implements MoleculeInterface.

Fchargeadd()

void AutoPasSimpleMolecule::Fchargeadd ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fchargesub()

void AutoPasSimpleMolecule::Fchargesub ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fdipoleadd()

void AutoPasSimpleMolecule::Fdipoleadd ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fdipolesub()

void AutoPasSimpleMolecule::Fdipolesub ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fljcenteradd()

void AutoPasSimpleMolecule::Fljcenteradd ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fljcentersub()

void AutoPasSimpleMolecule::Fljcentersub ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fquadrupoleadd()

void AutoPasSimpleMolecule::Fquadrupoleadd ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

Fquadrupolesub()

void AutoPasSimpleMolecule::Fquadrupolesub ( unsigned int  i, double  a[]  )

inlineoverridevirtual

Implements MoleculeInterface.

get()

template<AttributeNames attribute>

constexpr std::tuple_element<static_cast<size_t>(attribute),SoAArraysType>::type::value_type AutoPasSimpleMolecule::get ( )

inlineconstexpr

Getter, which allows access to an attribute using the corresponding attribute name (defined in AttributeNames).

Template Parameters

attribute

Attribute name.

Returns

Value of the requested attribute.

Note

The value of owned is return as floating point number (true = 1.0, false = 0.0).

getI()

double AutoPasSimpleMolecule::getI ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

getID()

unsigned long AutoPasSimpleMolecule::getID ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

inBox()

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

inlineoverridevirtual

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 from MoleculeInterface.

ljcenter_d()

std::array<double, 3> AutoPasSimpleMolecule::ljcenter_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

ljcenter_d_abs()

std::array<double, 3> AutoPasSimpleMolecule::ljcenter_d_abs ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

ljcenter_F()

std::array<double, 3> AutoPasSimpleMolecule::ljcenter_F ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

M()

double AutoPasSimpleMolecule::M ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

Madd()

void AutoPasSimpleMolecule::Madd ( const double  a[] )

inlineoverridevirtual

Implements MoleculeInterface.

move()

void AutoPasSimpleMolecule::move ( int  d, double  dr  )

inlineoverridevirtual

Implements MoleculeInterface.

normalizeQuaternion()

void AutoPasSimpleMolecule::normalizeQuaternion ( )

inlineoverridevirtual

Implements MoleculeInterface.

numCharges()

unsigned int AutoPasSimpleMolecule::numCharges ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

numDipoles()

unsigned int AutoPasSimpleMolecule::numDipoles ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

numLJcenters()

unsigned int AutoPasSimpleMolecule::numLJcenters ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

numOrientedSites()

unsigned int AutoPasSimpleMolecule::numOrientedSites ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

numQuadrupoles()

unsigned int AutoPasSimpleMolecule::numQuadrupoles ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

numSites()

unsigned int AutoPasSimpleMolecule::numSites ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

q()

const Quaternion& AutoPasSimpleMolecule::q ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

quadrupole_d()

std::array<double, 3> AutoPasSimpleMolecule::quadrupole_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

quadrupole_d_abs()

std::array<double, 3> AutoPasSimpleMolecule::quadrupole_d_abs ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

quadrupole_e()

std::array<double, 3> AutoPasSimpleMolecule::quadrupole_e ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

quadrupole_F()

std::array<double, 3> AutoPasSimpleMolecule::quadrupole_F ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

r()

double AutoPasSimpleMolecule::r ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

releaseOwnSoA()

void AutoPasSimpleMolecule::releaseOwnSoA ( )

inlineoverridevirtual

See above comment.

Implements MoleculeInterface.

set()

template<AttributeNames attribute>

constexpr void AutoPasSimpleMolecule::set ( typename std::tuple_element< static_cast< size_t >(attribute), SoAArraysType >::type::value_type  value )

inlineconstexpr

Setter, which allows set an attribute using the corresponding attribute name (defined in AttributeNames).

Template Parameters

attribute

Attribute name.

Parameters

value

New value of the requested attribute.

Note

The value of owned is extracted from a floating point number (true = 1.0, false = 0.0).

setComponent()

void AutoPasSimpleMolecule::setComponent ( Component *  component )

inlineoverridevirtual

Implements MoleculeInterface.

setD()

void AutoPasSimpleMolecule::setD ( unsigned short  d, double  D  )

inlineoverridevirtual

Implements MoleculeInterface.

setF() [1/2]

void AutoPasSimpleMolecule::setF ( double  F[3] )

inlineoverridevirtual

Implements MoleculeInterface.

setF() [2/2]

void AutoPasSimpleMolecule::setF ( unsigned short  d, double  F  )

inlineoverridevirtual

Implements MoleculeInterface.

setid()

void AutoPasSimpleMolecule::setid ( unsigned long  id )

inlineoverridevirtual

Implements MoleculeInterface.

setM()

void AutoPasSimpleMolecule::setM ( double  M[3] )

inlineoverridevirtual

Implements MoleculeInterface.

setq()

void AutoPasSimpleMolecule::setq ( Quaternion  q )

inlineoverridevirtual

Implements MoleculeInterface.

setr()

void AutoPasSimpleMolecule::setr ( unsigned short  d, double  r  )

inlineoverridevirtual

Implements MoleculeInterface.

setSoA()

void AutoPasSimpleMolecule::setSoA ( CellDataSoABase *const  s )

inlineoverridevirtual

Implements MoleculeInterface.

setStartIndexSoA_C()

void AutoPasSimpleMolecule::setStartIndexSoA_C ( unsigned  i )

inlineoverridevirtual

Implements MoleculeInterface.

setStartIndexSoA_D()

void AutoPasSimpleMolecule::setStartIndexSoA_D ( unsigned  i )

inlineoverridevirtual

Implements MoleculeInterface.

setStartIndexSoA_LJ()

void AutoPasSimpleMolecule::setStartIndexSoA_LJ ( unsigned  i )

inlineoverridevirtual

Implements MoleculeInterface.

setStartIndexSoA_Q()

void AutoPasSimpleMolecule::setStartIndexSoA_Q ( unsigned  i )

inlineoverridevirtual

Implements MoleculeInterface.

setupSoACache()

void AutoPasSimpleMolecule::setupSoACache ( CellDataSoABase *const  s, unsigned  iLJ, unsigned  iC, unsigned  iD, unsigned  iQ  )

inlineoverridevirtual

Implements MoleculeInterface.

setv()

void AutoPasSimpleMolecule::setv ( unsigned short  d, double  v  )

inlineoverridevirtual

Implements MoleculeInterface.

setVi()

void AutoPasSimpleMolecule::setVi ( double  Vi[3] )

inlineoverridevirtual

Implements MoleculeInterface.

site_d()

std::array<double, 3> AutoPasSimpleMolecule::site_d ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

site_d_abs()

std::array<double, 3> AutoPasSimpleMolecule::site_d_abs ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

site_F()

std::array<double, 3> AutoPasSimpleMolecule::site_F ( unsigned int  i ) const

inlineoverridevirtual

Implements MoleculeInterface.

totalMemsize()

unsigned long AutoPasSimpleMolecule::totalMemsize ( ) const

inlineoverridevirtual

Implements MoleculeInterface.

U_rot()

double AutoPasSimpleMolecule::U_rot ( )

inlineoverridevirtual

Implements MoleculeInterface.

U_rot_2()

double AutoPasSimpleMolecule::U_rot_2 ( )

inlineoverridevirtual

Implements MoleculeInterface.

upd_postF()

void AutoPasSimpleMolecule::upd_postF ( double  dt_halve, double &  summv2, double &  sumIw2  )

overridevirtual

Implements MoleculeInterface.

upd_preF()

void AutoPasSimpleMolecule::upd_preF ( double  dt )

overridevirtual

Implements MoleculeInterface.

updateMassInertia()

void AutoPasSimpleMolecule::updateMassInertia ( )

inlineoverridevirtual

Implements MoleculeInterface.

v()

double AutoPasSimpleMolecule::v ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

vadd()

void AutoPasSimpleMolecule::vadd ( const double  ax, const double  ay, const double  az  )

inlineoverridevirtual

Implements MoleculeInterface.

Vi()

double AutoPasSimpleMolecule::Vi ( unsigned short  d ) const

inlineoverridevirtual

Implements MoleculeInterface.

Viadd()

void AutoPasSimpleMolecule::Viadd ( const double  a[] )

inlineoverridevirtual

Implements MoleculeInterface.

vsub()

void AutoPasSimpleMolecule::vsub ( const double  ax, const double  ay, const double  az  )

inlineoverridevirtual

Implements MoleculeInterface.

write()

void AutoPasSimpleMolecule::write ( std::ostream &  ostrm ) const

inlineoverridevirtual

Implements MoleculeInterface.

writeBinary()

void AutoPasSimpleMolecule::writeBinary ( std::ostream &  ostrm ) const

inlineoverridevirtual

Implements MoleculeInterface.

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

• src/molecules/AutoPasSimpleMolecule.h
• src/molecules/AutoPasSimpleMolecule.cpp