CanonicalMD Class Reference
[Molecular Dynamics Simulation]

A MD simulation in the canoncial ensemble. More...

#include <canonicalMD.h>

Inheritance diagram for CanonicalMD:

List of all members.

Public Member Functions
Constructors and Destructor
	CanonicalMD (ForceField &myforcefield) throw ()
	This constructor expects a force field .
	CanonicalMD (ForceField &force_field, SnapShotManager *ssm) throw ()
	This constructor expects a force field and a snapshot manager.
	CanonicalMD (ForceField &myforcefield, SnapShotManager *ssm, const Options &options) throw ()
	This constructor wants a force field, a snapshot manager and new options.
	CanonicalMD (const CanonicalMD &rhs) throw ()
	Copy constructor.
virtual	~CanonicalMD () throw ()
	Destructor.
Assignment
CanonicalMD &	operator= (const CanonicalMD &rhs) throw ()
	Assignment operator.
Setup methods
virtual bool	setup (ForceField &force_field, SnapShotManager *ssm=0) throw ()
	This method does general setup things.
virtual bool	setup (ForceField &force_field, SnapShotManager *ssm, const Options &options) throw ()
	This method does general setup things.
virtual bool	specificSetup () throw ()
	This method is meant for additional preparations apart from those done in setup.
Accessors
void	setBathRelaxationTime (double time) throw ()
	This method sets a new relaxation time for the coupling to an external heat bath.
double	getBathRelaxationTime () const throw ()
	This method gets the current value for heat bath coupling.
virtual void	setTimeStep (double time) throw ()
	Set a new time step for the numerical integration.
virtual bool	simulateIterations (Size number, bool restart=false) throw ()
	This method does the actual simulation stuff.
Protected Member Functions
Protected methods
void	calculateFactors_ () throw ()
	A protected method for calculating some factors that are needed all the time.
Protected Attributes
Protected Attributes
double	bath_relaxation_time_
	The coupling parameter to the heat bath.
std::vector< AuxFactors >	mass_factor_
	This vector contains special precomputed factors.

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Detailed Description

A MD simulation in the canoncial ensemble.

A class for doing molecular dynamics simulations according to the principle of a canonical ensemble (NVT), i.e., the temperature is kept constant. This is achieved via the velocity rescaling proposed by Berendsen et al., J. Chem. Physics, 81:3684, 1984. Note that this approach does not give all properties of a true canonical system. In particular, the heat capacity cannot be calculated!

The temperature is set through the method.

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Constructor & Destructor Documentation

CanonicalMD::CanonicalMD (  ForceField &  myforcefield  )  throw ()

This constructor expects a force field . The force field's options are used and no saving of snapshots is done. Parameters: myforcefield  the forcefield we need for the simulation

CanonicalMD::CanonicalMD (  ForceField &  force_field, SnapShotManager *  ssm )  throw ()

This constructor expects a force field and a snapshot manager. The force field's options are used. Parameters: myforcefield  the forcefield to use in the simulation ssm  a pointer to the SnapShotManager which will be used to create trajectory files

CanonicalMD::CanonicalMD (  ForceField &  myforcefield, SnapShotManager *  ssm, const Options &  options )  throw ()

This constructor wants a force field, a snapshot manager and new options. Parameters: myforcefield  the forcefield which is to be used in the simulation ssm  a pointer to the SnapShotManager used for creating trajectory files myoptions  arbitrary options that are to be used by this instance instead of those defined therein

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Member Function Documentation

double CanonicalMD::getBathRelaxationTime (   )  const throw ()

This method gets the current value for heat bath coupling. Returns: the bath relaxation time in ps

void CanonicalMD::setBathRelaxationTime (  double  time  )  throw ()

This method sets a new relaxation time for the coupling to an external heat bath. The readjustment to the external bath is not done after every step in order to save compute time. Instead, it is coupled periodically after the time specified here has elapsed. Parameters: time  the time in ps

virtual bool CanonicalMD::setup (  ForceField &  force_field, SnapShotManager *  ssm, const Options &  options )  throw () [virtual]

This method does general setup things. This method also allows the assignment of options for the setup. Reimplemented from MolecularDynamics.

virtual bool CanonicalMD::setup (  ForceField &  force_field, SnapShotManager *  ssm = 0 )  throw () [virtual]

This method does general setup things. Parameters: ssm  if no snapshots during the simulations are required, leave this at the default (NULL pointer) force_field  the forcefield, which has to be bound to a system Reimplemented from MolecularDynamics.

virtual bool CanonicalMD::simulateIterations (  Size  number, bool  restart = false )  throw () [virtual]

This method does the actual simulation stuff. It runs for the indicated number of iterations. If restart is true, the counting of iterations starts with the number of the last iteration in the previous run. Parameters: number  the number of iterations that have to be simulated restart  flag for restarting the simulation Reimplemented from MolecularDynamics.

virtual bool CanonicalMD::specificSetup (   )  throw () [virtual]

This method is meant for additional preparations apart from those done in setup. Returns: bool, true if specificSetup() was successful Reimplemented from MolecularDynamics.