BALL::MolecularDynamics Class Reference

#include <BALL/MOLMEC/MDSIMULATION/molecularDynamics.h>

Inheritance diagram for BALL::MolecularDynamics:

Classes
struct	Default
struct	Option

Public Member Functions
Constructors and Destructors
	MolecularDynamics ()
	MolecularDynamics (ForceField &force_field)
	MolecularDynamics (const MolecularDynamics &rhs)
virtual	~MolecularDynamics ()
Assignments
const MolecularDynamics &	operator= (const MolecularDynamics &rhs)
void	set (const MolecularDynamics &rhs)
Debugging and Diagnostics
bool	isValid () const
Setup methods
virtual bool	setup (ForceField &force_field, SnapShotManager *snapshot_man)
virtual bool	setup (ForceField &forcefield, SnapShotManager *snapshot_man, const Options &myoptions)
virtual bool	specificSetup ()
Accessors
void	setNumberOfIteration (Size number)
void	setMaximalNumberOfIterations (Size number)
void	setMaximalSimulationTime (double time)
virtual void	setTimeStep (double step)
void	setReferenceTemperature (double temperature)
void	setCurrentTime (double time)
void	setEnergyOutputFrequency (Size number)
void	setSnapShotFrequency (Size number)
Size	getEnergyOutputFrequency () const
Size	getNumberOfIterations () const
Size	getMaximalNumberOfIterations () const
double	getMaximalSimulationTime () const
double	getTimeStep () const
Size	getSnapShotFrequency () const
double	getTemperature () const
double	getTime () const
double	getTotalEnergy () const
double	getPotentialEnergy () const
double	getKineticEnergy () const
ForceField *	getForceField () const
bool	simulate (bool restart=false)
bool	simulateTime (double simulation_time, bool restart=false)
virtual bool	simulateIterations (Size number, bool restart=false)
void	enableEnergyAbortCondition (bool state)
bool	energyAbortConditionEnabled () const
	Query if the MDSimulation aborts if the Energy is greater than abort_energy_. More...
void	setEnergyToAbort (float value)
float	getEnergyToAbort () const

Public Attributes
Public Attributes
Options	options

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.

Definition at line 42 of file molecularDynamics.h.

Constructor & Destructor Documentation

BALL::MolecularDynamics::MolecularDynamics

(

)

Default constructor.

BALL::MolecularDynamics::MolecularDynamics

(

ForceField &

force_field

)

Constructor. It expects the forcefield

BALL::MolecularDynamics::MolecularDynamics

(

const MolecularDynamics &

rhs

)

Copy constructor

virtual BALL::MolecularDynamics::~MolecularDynamics ( )

virtual

Destructor.

Member Function Documentation

void BALL::MolecularDynamics::enableEnergyAbortCondition

(

bool

state

)

Specify if the MDSimulation aborts if the Energy is greater than abort_energy_

bool BALL::MolecularDynamics::energyAbortConditionEnabled

(

)

const

Query if the MDSimulation aborts if the Energy is greater than abort_energy_.

Size BALL::MolecularDynamics::getEnergyOutputFrequency

(

)

const

Get the energy output frequency

float BALL::MolecularDynamics::getEnergyToAbort

(

)

const

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

ForceField* BALL::MolecularDynamics::getForceField

(

)

const

Get the force field the MD simulation is bound to

double BALL::MolecularDynamics::getKineticEnergy

(

)

const

Get the current kinetic energy of the system

Size BALL::MolecularDynamics::getMaximalNumberOfIterations

(

)

const

Get the maximal number of iterations of the MD simulation

double BALL::MolecularDynamics::getMaximalSimulationTime

(

)

const

Get the maximal simulation time of the MD simulation

Size BALL::MolecularDynamics::getNumberOfIterations

(

)

const

Get the current iteration of the MD simulation

double BALL::MolecularDynamics::getPotentialEnergy

(

)

const

Get the current potential energy of the system

Size BALL::MolecularDynamics::getSnapShotFrequency

(

)

const

Get the snapshot frequency

double BALL::MolecularDynamics::getTemperature

(

)

const

Get the current temperature of the system

double BALL::MolecularDynamics::getTime

(

)

const

Get the current time of the MD simulation

double BALL::MolecularDynamics::getTimeStep

(

)

const

Get the current time step

double BALL::MolecularDynamics::getTotalEnergy

(

)

const

Get the current total energy of the system

bool BALL::MolecularDynamics::isValid

(

)

const

Has the molecular dynamics class been successfully set up?

const MolecularDynamics& BALL::MolecularDynamics::operator=

(

const MolecularDynamics &

rhs

)

Assignment operator

void BALL::MolecularDynamics::set

(

const MolecularDynamics &

rhs

)

Assign a molecular dynamics objects.

void BALL::MolecularDynamics::setCurrentTime

(

double

time

)

Set the current time of the MD run in picoseconds

void BALL::MolecularDynamics::setEnergyOutputFrequency

(

Size

number

)

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

void BALL::MolecularDynamics::setEnergyToAbort

(

float

value

)

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

void BALL::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 BALL::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 BALL::MolecularDynamics::setNumberOfIteration

(

Size

number

)

Set the number of the current iteration

void BALL::MolecularDynamics::setReferenceTemperature

(

double

temperature

)

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

void BALL::MolecularDynamics::setSnapShotFrequency

(

Size

number

)

Set the snapshot frequency

virtual void BALL::MolecularDynamics::setTimeStep ( double  step )

virtual

Set the time step in ps. Note that this will change the maximum simulation time.

Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.

virtual bool BALL::MolecularDynamics::setup ( ForceField &  force_field, SnapShotManager *  snapshot_man  )

virtual

Set up the molecular dynamics

Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.

virtual bool BALL::MolecularDynamics::setup ( ForceField &  forcefield, SnapShotManager *  snapshot_man, const Options &  myoptions  )

virtual

Set up the molecular dynamics

Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.

bool BALL::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 BALL::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 BALL::CanonicalMD, and BALL::MicroCanonicalMD.

bool BALL::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

virtual bool BALL::MolecularDynamics::specificSetup ( )

virtual

Specific setup; derived class can use this method for additional preparations if necessary

Reimplemented in BALL::CanonicalMD, and BALL::MicroCanonicalMD.

void BALL::MolecularDynamics::updateInstantaneousTemperature ( )

protected

Member Data Documentation

bool BALL::MolecularDynamics::abort_by_energy_enabled_

protected

Definition at line 422 of file molecularDynamics.h.

float BALL::MolecularDynamics::abort_energy_

protected

Definition at line 425 of file molecularDynamics.h.

AtomVector BALL::MolecularDynamics::atom_vector_

protected

Definition at line 374 of file molecularDynamics.h.

double BALL::MolecularDynamics::current_temperature_

protected

Definition at line 395 of file molecularDynamics.h.

double BALL::MolecularDynamics::current_time_

protected

Definition at line 407 of file molecularDynamics.h.

Size BALL::MolecularDynamics::energy_output_frequency_

protected

Definition at line 411 of file molecularDynamics.h.

ForceField* BALL::MolecularDynamics::force_field_ptr_

protected

Definition at line 366 of file molecularDynamics.h.

double BALL::MolecularDynamics::kinetic_energy_

protected

Definition at line 399 of file molecularDynamics.h.

Size BALL::MolecularDynamics::maximal_number_of_iterations_

protected

Definition at line 383 of file molecularDynamics.h.

Size BALL::MolecularDynamics::number_of_iteration_

protected

Definition at line 378 of file molecularDynamics.h.

Options BALL::MolecularDynamics::options

The options for this class

Definition at line 340 of file molecularDynamics.h.

double BALL::MolecularDynamics::reference_temperature_

protected

Definition at line 391 of file molecularDynamics.h.

Size BALL::MolecularDynamics::snapshot_frequency_

protected

Definition at line 415 of file molecularDynamics.h.

SnapShotManager* BALL::MolecularDynamics::snapshot_manager_ptr_

protected

Definition at line 419 of file molecularDynamics.h.

System* BALL::MolecularDynamics::system_ptr_

protected

Definition at line 370 of file molecularDynamics.h.

double BALL::MolecularDynamics::time_step_

protected

Definition at line 387 of file molecularDynamics.h.

double BALL::MolecularDynamics::total_energy_

protected

Definition at line 403 of file molecularDynamics.h.

bool BALL::MolecularDynamics::valid_

protected

Definition at line 362 of file molecularDynamics.h.