ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.

ProtoMol::Modifier Class Reference

#include <Modifier.h>

Inheritance diagram for ProtoMol::Modifier:

List of all members.


Public Member Functions
	Modifier (int order=0)
virtual	~Modifier ()
void	execute ()
virtual bool	isInternal () const=0
int	order () const
void	enable () const
void	disable () const
bool	isEnabled () const
bool	operator< (const Modifier &m) const
void	initialize (GenericTopology topo, Vector3DBlock positions, Vector3DBlock velocities, Vector3DBlock forces, ScalarStructure *energies)
std::string	print () const
Protected Attributes
GenericTopology *	myTopology
Vector3DBlock *	myPositions
Vector3DBlock *	myVelocities
Vector3DBlock *	myForces
ScalarStructure *	myEnergies
Private Member Functions
virtual void	doExecute ()=0
virtual void	doInitialize ()
virtual std::string	doPrint () const=0
Private Attributes
int	myOrder
bool	myEnable

Detailed Description

Base class for all kind of modifier implementation, based on the Observer Pattern. A modifier object can be added at five different stages of a single time step:

before doDriftOrNextIntegrator (pre)
after doDriftOrNextIntegrator (post)
before the force calculation (pre)
between system and extended force calculation (medi)
after the force calculation (post)

Each modifier object performs it changes to the system via the method execute(...) with the implementation details in doExecute(). The execution is defined 1. by an order number and 2. by the pointer of the object. An implementation can be either internal -- added by an integrator -- or external -- added by the user or at application level. Integrator provides all methods add, remove and delete modifiers. Integrators provides also interface to add internal modifiers before/after the initialization of forces. Internal modifiers (isInternal() is true) are removed, if any, by Intergrator under initialize and each integrator has to add its modifiers, if any. To add internal modifier you should override addModifierBeforeInitialize() and/or addModifierAfterInitialize() in order the specify if the modifications should be considered during the (force) initialization or not. Furthermore, it is possible to disable and enable a modifier.

Constructor & Destructor Documentation

ProtoMol::Modifier::Modifier ( int order = 0 ) [inline]

virtual ProtoMol::Modifier::~Modifier ( ) [inline, virtual]

Member Function Documentation

void ProtoMol::Modifier::disable ( ) const [inline]

Deactivate modifier.

virtual void ProtoMol::Modifier::doInitialize ( ) [inline, private, virtual]

Implemenation of initialize.

Reimplemented in ProtoMol::ModifierMetaRattleShake, ProtoMol::ModifierRemoveAngularMomentum, ProtoMol::ModifierRemoveLinearMomentum, and ProtoMol::ModifierISG.

void ProtoMol::Modifier::enable ( ) const [inline]

Activate modifier.

void ProtoMol::Modifier::execute ( ) [inline]

The method, which calls the implemenation.

void ProtoMol::Modifier::initialize ( GenericTopology * topo,

Vector3DBlock * positions,

Vector3DBlock * velocities,

Vector3DBlock * forces,

ScalarStructure * energies

) [inline]

Initialize.