MolecularDynamics Class Reference
[Molecular Dynamics Simulation]

Molecular Dynamics base class. More...

#include <molecularDynamics.h>

Inheritance diagram for MolecularDynamics:


Public Member Functions
Constructors and Destructors
	MolecularDynamics ()
	Default constructor.
	MolecularDynamics (ForceField &force_field)
	Constructor.
	MolecularDynamics (const MolecularDynamics &rhs)
	Copy constructor.
virtual	~MolecularDynamics ()
	Destructor.
Assignments
const MolecularDynamics &	operator= (const MolecularDynamics &rhs)
	Assignment operator.
void	set (const MolecularDynamics &rhs)
	Assign a molecular dynamics objects.
Debugging and Diagnostics
bool	isValid () const
	Has the molecular dynamics class been successfully set up?
Setup methods
virtual bool	setup (ForceField &force_field, SnapShotManager *snapshot_man)
	Set up the molecular dynamics.
virtual bool	setup (ForceField &forcefield, SnapShotManager *snapshot_man, const Options &myoptions)
	Set up the molecular dynamics.
virtual bool	specificSetup ()
	Specific setup; derived class can use this method for additional preparations if necessary.
Accessors
void	setNumberOfIteration (Size number)
	Set the number of the current iteration.
void	setMaximalNumberOfIterations (Size number)
	Set the maximal number of iterations that will be carried out.
void	setMaximalSimulationTime (double time)
	Set the maximal simulation time in ps that will be carried out.
virtual void	setTimeStep (double step)
	Set the time step in ps.
void	setReferenceTemperature (double temperature)
	Set the reference temperature for the system.
void	setCurrentTime (double time)
	Set the current time of the MD run in picoseconds.
void	setEnergyOutputFrequency (Size number)
	Set the energy output frequency.
void	setSnapShotFrequency (Size number)
	Set the snapshot frequency.
Size	getEnergyOutputFrequency () const
	Get the energy output frequency.
Size	getNumberOfIterations () const
	Get the current iteration of the MD simulation.
Size	getMaximalNumberOfIterations () const
	Get the maximal number of iterations of the MD simulation.
double	getMaximalSimulationTime () const
	Get the maximal simulation time of the MD simulation.
double	getTimeStep () const
	Get the current time step.
Size	getSnapShotFrequency () const
	Get the snapshot frequency.
double	getTemperature () const
	Get the current temperature of the system.
double	getTime () const
	Get the current time of the MD simulation.
double	getTotalEnergy () const
	Get the current total energy of the system.
double	getPotentialEnergy () const
	Get the current potential energy of the system.
double	getKineticEnergy () const
	Get the current kinetic energy of the system.
ForceField *	getForceField () const
	Get the force field the MD simulation is bound to.
bool	simulate (bool restart=false)
	Start the molecular dynamics simulation.
bool	simulateTime (double simulation_time, bool restart=false)
	Simulate a given time interval.
virtual bool	simulateIterations (Size number, bool restart=false)
	Start the molecular dynamics simulation and carry out the given number of iterations.
void	enableEnergyAbortCondition (bool state)
	Specify if the MDSimulation aborts if the Energy is greater than abort_energy_.
bool	energyAbortConditionEnabled () const
	Query if the MDSimulation aborts if the Energy is greater than abort_energy_.
void	setEnergyToAbort (float value)
	Specify the energy to abort the simulation.
float	getEnergyToAbort () const
	Query the energy to abort the simulation.
Public Attributes
Public Attributes
Options	options
	The options for this class.
Protected Member Functions
void	updateInstantaneousTemperature ()
Protected Attributes
bool	valid_
ForceField *	force_field_ptr_
System *	system_ptr_
AtomVector	atom_vector_
Size	number_of_iteration_
Size	maximal_number_of_iterations_
double	time_step_
double	reference_temperature_
double	current_temperature_
double	kinetic_energy_
double	total_energy_
double	current_time_
Size	energy_output_frequency_
Size	snapshot_frequency_
SnapShotManager *	snapshot_manager_ptr_
bool	abort_by_energy_enabled_
float	abort_energy_

Detailed Description

Molecular Dynamics base class.

This class is the base class for classical molecular dynamics simulations. Actual MD classes are derived from this class and then implement the actual simulation classes for the different ensembles or methods.

Constructor & Destructor Documentation

MolecularDynamics::MolecularDynamics ( )

Default constructor.

MolecularDynamics::MolecularDynamics ( ForceField & force_field )

Constructor.
It expects the forcefield

virtual MolecularDynamics::~MolecularDynamics ( ) [virtual]

Destructor.

Member Function Documentation

float MolecularDynamics::getEnergyToAbort ( ) const

Query the energy to abort the simulation.
The default value is 10^8.

void MolecularDynamics::set ( const MolecularDynamics & rhs )

Assign a molecular dynamics objects.

void MolecularDynamics::setEnergyOutputFrequency ( Size number )

Set the energy output frequency.
The current energies during the simulation will be printed every number steps.

void MolecularDynamics::setEnergyToAbort ( float value )

Specify the energy to abort the simulation.
The default value is 10^8.

void MolecularDynamics::setMaximalNumberOfIterations ( Size number )

Set the maximal number of iterations that will be carried out.
If the number of the start iteration is 0 (which is the default), this method sets the total number of simulated iterations.

void MolecularDynamics::setMaximalSimulationTime ( double time )

Set the maximal simulation time in ps that will be carried out.
If the start time is zero(which is the default), then this method sets the total simulation time.

void MolecularDynamics::setReferenceTemperature ( double temperature )

Set the reference temperature for the system.
In isothermal ensembles, this is the simulation temperature set set by the thermostat.

virtual void MolecularDynamics::setTimeStep ( double step ) [virtual]

Set the time step in ps.
Note that this will change the maximum simulation time.
Reimplemented in CanonicalMD, and MicroCanonicalMD.

bool MolecularDynamics::simulate ( bool restart = false )

Start the molecular dynamics simulation.
This method calls simulateIterations with the maximum number of iterations.
See also:
setMaximumNumberOfIterations

Returns:
false if an error occured, e.g. the energy was too high

virtual bool MolecularDynamics::simulateIterations ( Size number,

bool restart = false

) [virtual]

Start the molecular dynamics simulation and carry out the given number of iterations.
This is the proper simulation method, which is implemented in the derived classes only. The implementation provided by MolecularDynamics is simply empty.
Returns:
false if an error occured, e.g. the energy was too high

Reimplemented in CanonicalMD, and MicroCanonicalMD.

bool MolecularDynamics::simulateTime ( double simulation_time,

bool restart = false

)

Simulate a given time interval.
This method determines the number of steps necessary to simulate a given time interval and executes a simulation for that interval by calling simulateIterations .
Returns:
false if an error occured, e.g. the energy was too high

MolecularDynamics Class Reference [Molecular Dynamics Simulation]

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

MolecularDynamics Class Reference
[Molecular Dynamics Simulation]