glotzmd::Simulation Class Reference
[Molecular Dynamics]

Implements a molecular dynamics (MD) - like simulation. More...

#include <Simulation.h>

Inheritance diagram for glotzmd::Simulation:

List of all members.

Public Member Functions
	Simulation ()
	Constructor.
	Simulation (const Simulation &)
	Copy constructor.
virtual Simulation *	Clone ()
	Clone function.
virtual	~Simulation ()
	Destructor.
void	operator++ (const int)
	Step the simulation forward one timestep.
void	operator+= (const int)
	Step the simulation forward "n" timesteps.
void	operator-- (const int)
	Step the simulation backward one timestep.
void	operator-= (const int)
	Step the simulation backward n timesteps.
void	StepForward (const int)
	Step the simulation forward "n" timesteps.
void	StepBackward (const int)
	Step the simulation backward "n" timesteps.
void	RescaleSystem (const glotz_flt)
void	RescaleSystem (const glotz_vec)
void	RescaleSystem (const glotz_flt, const glotz_flt, const glotz_flt)
void	RescaleVelocities (const glotz_flt)
void	InvertVelocities ()
void	ZeroLinearMomentum ()
int	Fail ()
	Get a boolean value indicating whether or not the simulation has failed.
void	Save (const char *)
	Save the current state of the simulation.
void	Restore (const char *)
	Restore the simulaiton from a previous state.
void	Save ()
	Save the current state of the simulation.
void	Load (const char *)
	Restore the simulaiton from a previous state.
void	Serialize (glotzutil::Archive &)
virtual glotz_flt	ComputePotentialEnergy ()
	Compute the system potential energy.
virtual glotz_flt	ComputeKineticEnergy ()
	Compute the system kinetic energy.
virtual glotz_flt	ComputeLinearKineticEnergy ()
	Compute kinetic energy from translation.
virtual glotz_flt	ComputeAngularKineticEnergy ()
	Compute kinetic energy from rotation.
virtual glotz_flt	ComputeVirial ()
	Compute the system viral.
virtual glotz_flt	ComputeTemperature ()
	Compute the system temperature.
virtual glotz_flt	ComputePressure ()
	Compute the system pressure.
virtual glotz_flt	ComputeTotalEnergy ()
	Compute the system total energy.
virtual glotz_flt	ComputeNumberDensity ()
	Compute the number density.
virtual glotz_flt	ComputeVolumeFraction ()
	Compute the volume fraction.
virtual int	ComputeDegreesOfFreedom ()
	Compute the system's degrees of freedom.
void	AddParticle (Particle *)
	Add a new particle to the system.
void	AddInteraction (const int, const int, Potential *)
	Add a new set of particle interactions to the system.
void	AddSimulationModifier (SimulationModifier *)
	Add a new modifier the the simulation.
void	RemoveParticle (Particle *)
	Remove an existing particle from the system.
void	RemoveSimulationModifier (SimulationModifier *)
	Remove an existing modifier from the simulation.
void	RemoveInteraction (Potential *)
	Remove an existing set of particle interactions from the system.
void	SetForceRoutine (ForceRoutine *)
	Set the force calculation method.
void	SetIntegrationScheme (IntegrationScheme *)
	Set the scheme used to integrate Newton's equations of motion.
void	SetBoundaryConditions (BoundaryConditions *)
	Set the type of boundary conditions.
void	SetUnits (Units *)
	Set the type of units (reduced, real, etc.).
void	SetDimensions (const int)
	Set the number of dimensions.
void	SetTimestep (const glotz_flt)
	Set the integration timestep.
void	SetConfiguration (glotzdatasources::Lattice *)
	Set the initial configuration (requires datasources enabled).
BoundaryConditions *	GetBoundaryConditions ()
	Get a pointer to the boundary conditions.
std::string	GetEnsemble ()
	Get a string describing the ensmeble being sampled.
glotz_flt	GetTargetTemperature ()
	Get thermostat temperature.
glotz_flt	GetTargetPressure ()
	Get barostat pressure.
glotz_flt	GetTimestep ()
	Get the size of the simulation timestep.
ErrorList	GetErrorList ()
	Get the list of errors that the simulation has encountered.
ObjectList &	GetObjects ()
	Get a list of interacting objects.
ParticleList &	GetParticleList ()
	Get a list of particles.
BeadList &	GetBeadList ()
	Get a list of particles.
int	GetNumberOfObjects ()
	Get the number of interacting objects.
int	GetNumberOfBeads ()
	Get the number of beads.
int	GetNumberOfParticles ()
	Get the number of particles.
int	GetNumberOfRigidBodies ()
	Get the number of rigid bodies.
int	GetNumberOfSprings ()
	Get the number of springs.
int	GetDimensions ()
	Get the dimensionality.
int	GetNumberOfSimulationModifiers ()
	Get the number of simulation modifiers.
int	GetNumberOfPotentials ()
	Get the number of potentials.
int	GetTimesteps ()
	Get the number of timesteps the simulation has performed.
void	PrintPotentialEnergy (std::ostream &)
void	PrintPotentialEnergies (std::ostream &)
void	PrintPositions (std::ostream &)
void	PrintVelocities (std::ostream &)
void	PrintForces (std::ostream &)
void	PrintVis3d (std::ostream &)
void	PrintVis3dTemplate (std::ostream &)
void	PrintParticles (std::ostream &, std::string &)
void	PrintParticles (std::ostream &, const char *)
Public Attributes
ParticleList	gParticle
	Global vector of particles.
ObjectList	gInteractingObject
	Global vector of objects.
BeadList	gBead
	Global vector of beads.
RigidBodyList	gRigidBody
	Global vector of rigid bodies.
SpringList	gSpring
	Global vector of springs.
PotentialMap	gPotentialMap
	Global map of potentials.
PotentialList	gPotential
	Global list of potentials.
SimulationModifierList	gSimulationModifier
	Global map of simulation components.
ForceRoutine *	gForceRoutine
	Global pointer to the force routine.
IntegrationScheme *	gIntegrationScheme
	Global pointer to the integration scheme.
BoundaryConditions *	gBoundaryConditions
	Global pointer to simulation boundary conditions.
Units *	gUnits
	Global pointer to the simulation units.
int	gDimensions
	Simulation dimensions.
glotz_flt	gTimestep
	Simulation timestep.
SimulationEventManager *	gEventManager
	Manages "events" or changes to the simulation.
BaseObjectList	gBaseObject
	List of pointers to all objects (force routines, integrators, particles, etc.).
Protected Types
enum	{ BACKWARD = -1, FORWARD = 1 }
Protected Member Functions
void	FinalizeUnserialization ()
void	CheckForErrors ()
	Check the simulation for errors.
void	HandleEvents ()
	Handle Events.
virtual void	OnEvent ()
	Perform when an event occurs.
void	Timestep ()
Protected Attributes
int	mDirectionOfTime
bool	mIsFirstTimeVis3d
RigidBodyUpdater *	mRigidBodyUpdater
SimulationEvent	mPossibleEvents
	A list of events that the simulation reacts to.

---

Detailed Description

Implements a molecular dynamics (MD) - like simulation.

Author:

Aaron Keys

Tony Sheh

Performs a molecular dynamics (MD) simulation. Can also perform Brownian Dynamics (BD) and Dissipative Particle Dynamics (DPD) simulations as well. For more information on simulation methods, see:

• Simulation Methods:
  1. MD Simulation ( http://matdl.org/matdlwiki/index.php/softmatter:Molecular_Dynamics_Simulation_%28MD%29 )
  2. BD Simulation ( http://matdl.org/matdlwiki/index.php/softmatter:Brownian_Dynamics_Simulation_%28BD%29 )
  3. DPD Simulation ( http://matdl.org/matdlwiki/index.php/softmatter:Dissipative_Particle_Dynamics_Simulation_%28DPD%29 )

An MD Simulation needs several inputs in order to run.

• Required Inputs
  1. One or more Particle
  2. One or more set of particle Interaction (s)
  3. A ForceRoutine
  4. An IntegrationScheme
  5. A set of BoundaryConditions

• Optional Inputs
  1. One or more SimulationModifier
  2. A set of Units

---

Member Enumeration Documentation

anonymous enum [protected]

Enumerator:

BACKWARD
FORWARD

---

Constructor & Destructor Documentation

glotzmd::Simulation::Simulation

(

)

Constructor.

Reimplemented in glotzlammps::Simulation.

glotzmd::Simulation::Simulation

(

const Simulation &

rhs

)

Copy constructor.

glotzmd::Simulation::~Simulation

(

)

[virtual]

Destructor.

Reimplemented in glotzlammps::Simulation.

---

Member Function Documentation

Simulation * glotzmd::Simulation::Clone

(

)

[virtual]

Clone function.

Clone() creates a new simulation that is identical to the current one and returns a pointer to it. This type of routine is particularly useful when trying to run multiple parallel simulations (i.e. parallel tempering, replica exchange, etc.

Returns:

a pointer to a new identical simulation.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::operator++

(

const

int

)

[virtual]

Step the simulation forward one timestep.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::operator+=

(

const

int

)

[virtual]

Step the simulation forward "n" timesteps.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::operator--

(

const

int

)

[virtual]

Step the simulation backward one timestep.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::operator-=

(

const

int

)

[virtual]

Step the simulation backward n timesteps.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::StepForward

(

const

int

)

[virtual]

Step the simulation forward "n" timesteps.

Parameters:

timesteps

is the number of timesteps to integrate forward

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::StepBackward

(

const

int

)

[virtual]

Step the simulation backward "n" timesteps.

Reimplemented from glotzsimapi::SimulationApi.

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::RescaleSystem

(

const

glotz_flt

)

void glotzmd::Simulation::RescaleSystem

(

const

glotz_vec

)

void glotzmd::Simulation::RescaleSystem	(	const	glotz_flt,
		const	glotz_flt,
		const	glotz_flt
	)

void glotzmd::Simulation::RescaleVelocities

(

const

glotz_flt

)

void glotzmd::Simulation::InvertVelocities

(

)

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::ZeroLinearMomentum

(

)

int glotzmd::Simulation::Fail

(

)

Get a boolean value indicating whether or not the simulation has failed.

Returns:

the error code if there is an error, zero otherwise

void glotzmd::Simulation::Save

(

const char *

filename

)

Save the current state of the simulation.

Parameters:

filename

is the filename to save the simulation to

void glotzmd::Simulation::Restore

(

const char *

filename

)

Restore the simulaiton from a previous state.

Parameters:

filename

is the filename to load the simulation from

void glotzmd::Simulation::Save

(

)

Save the current state of the simulation.

Save to default filename

void glotzmd::Simulation::Load

(

const char *

filename

)

Restore the simulaiton from a previous state.

Parameters:

filename

is the filename to load the simulation from

void glotzmd::Simulation::Serialize

(

glotzutil::Archive &

ar

)

[virtual]

Reimplemented from glotzutil::Serializable.

glotz_flt glotzmd::Simulation::ComputePotentialEnergy

(

)

[virtual]

Compute the system potential energy.

Reimplemented in glotzlammps::Simulation.

glotz_flt glotzmd::Simulation::ComputeKineticEnergy

(

)

[virtual]

Compute the system kinetic energy.

Reimplemented in glotzlammps::Simulation.

glotz_flt glotzmd::Simulation::ComputeLinearKineticEnergy

(

)

[virtual]

Compute kinetic energy from translation.

glotz_flt glotzmd::Simulation::ComputeAngularKineticEnergy

(

)

[virtual]

Compute kinetic energy from rotation.

glotz_flt glotzmd::Simulation::ComputeVirial

(

)

[virtual]

Compute the system viral.

glotz_flt glotzmd::Simulation::ComputeTemperature

(

)

[virtual]

Compute the system temperature.

Reimplemented in glotzlammps::Simulation.

glotz_flt glotzmd::Simulation::ComputePressure

(

)

[virtual]

Compute the system pressure.

Reimplemented in glotzlammps::Simulation.

glotz_flt glotzmd::Simulation::ComputeTotalEnergy

(

)

[virtual]

Compute the system total energy.

Reimplemented in glotzlammps::Simulation.

glotz_flt glotzmd::Simulation::ComputeNumberDensity

(

)

[virtual]

Compute the number density.

glotz_flt glotzmd::Simulation::ComputeVolumeFraction

(

)

[virtual]

Compute the volume fraction.

int glotzmd::Simulation::ComputeDegreesOfFreedom

(

)

[virtual]

Compute the system's degrees of freedom.

void glotzmd::Simulation::AddParticle

(

Particle *

particle

)

Add a new particle to the system.

Parameters:

particle

is the particle to be added

void glotzmd::Simulation::AddInteraction	(	const	int,
		const	int,
		Potential *	potential
	)

Add a new set of particle interactions to the system.

Parameters:

	type1	is one of the interacting types
	type2	is one of the interacting types
	potential	is the potential function describing the interaction

void glotzmd::Simulation::AddSimulationModifier

(

SimulationModifier *

mod

)

Add a new modifier the the simulation.

Parameters:

mod

is the modifier to be added

void glotzmd::Simulation::RemoveParticle

(

Particle *

particle

)

Remove an existing particle from the system.

Parameters:

particle

is the particle to be removed

void glotzmd::Simulation::RemoveSimulationModifier

(

SimulationModifier *

mod

)

Remove an existing modifier from the simulation.

Parameters:

mod

is the modifier to remove

void glotzmd::Simulation::RemoveInteraction

(

Potential *

potential

)

Remove an existing set of particle interactions from the system.

Parameters:

potential

is the potential function to be removed

void glotzmd::Simulation::SetForceRoutine

(

ForceRoutine *

forceRoutine

)

Set the force calculation method.

Parameters:

forceRoutine

is the force routine that the simulation will use

void glotzmd::Simulation::SetIntegrationScheme

(

IntegrationScheme *

integrationScheme

)

Set the scheme used to integrate Newton's equations of motion.

Parameters:

integrationScheme

is the integration scheme that the simulation will use

void glotzmd::Simulation::SetBoundaryConditions

(

BoundaryConditions *

boundaryConditions

)

Set the type of boundary conditions.

Parameters:

boundaryConditions

is the set of boundary conditions that the simulation will use

void glotzmd::Simulation::SetUnits

(

Units *

units

)

Set the type of units (reduced, real, etc.).

Parameters:

units

is the unit system used for printing data

void glotzmd::Simulation::SetDimensions

(

const

int

)

Set the number of dimensions.

Note:

This routine currently does not do anything, needs to have an effect on integrators -TS

void glotzmd::Simulation::SetTimestep

(

const

glotz_flt

)

Set the integration timestep.

Parameters:

timestep

is the integration timestep

void glotzmd::Simulation::SetConfiguration

(

glotzdatasources::Lattice *

datasource

)

Set the initial configuration (requires datasources enabled).

BoundaryConditions * glotzmd::Simulation::GetBoundaryConditions

(

)

Get a pointer to the boundary conditions.

std::string glotzmd::Simulation::GetEnsemble

(

)

Get a string describing the ensmeble being sampled.

glotz_flt glotzmd::Simulation::GetTargetTemperature

(

)

Get thermostat temperature.

glotz_flt glotzmd::Simulation::GetTargetPressure

(

)

Get barostat pressure.

glotz_flt glotzmd::Simulation::GetTimestep

(

)

Get the size of the simulation timestep.

ErrorList glotzmd::Simulation::GetErrorList

(

)

Get the list of errors that the simulation has encountered.

Returns:

list of error codes

ObjectList & glotzmd::Simulation::GetObjects

(

)

Get a list of interacting objects.

ParticleList & glotzmd::Simulation::GetParticleList

(

)

Get a list of particles.

BeadList & glotzmd::Simulation::GetBeadList

(

)

Get a list of particles.

int glotzmd::Simulation::GetNumberOfObjects

(

)

Get the number of interacting objects.

int glotzmd::Simulation::GetNumberOfBeads

(

)

Get the number of beads.

int glotzmd::Simulation::GetNumberOfParticles

(

)

Get the number of particles.

int glotzmd::Simulation::GetNumberOfRigidBodies

(

)

Get the number of rigid bodies.

int glotzmd::Simulation::GetNumberOfSprings

(

)

Get the number of springs.

Returns:

the total number of springs (bonds) in the simulation

int glotzmd::Simulation::GetDimensions

(

)

Get the dimensionality.

int glotzmd::Simulation::GetNumberOfSimulationModifiers

(

)

Get the number of simulation modifiers.

int glotzmd::Simulation::GetNumberOfPotentials

(

)

Get the number of potentials.

int glotzmd::Simulation::GetTimesteps

(

)

[virtual]

Get the number of timesteps the simulation has performed.

Reimplemented from glotzsimapi::SimulationApi.

void glotzmd::Simulation::PrintPotentialEnergy

(

std::ostream &

os

)

Reimplemented in glotzlammps::Simulation.

void glotzmd::Simulation::PrintPotentialEnergies

(

std::ostream &

os

)

void glotzmd::Simulation::PrintPositions

(

std::ostream &

os

)

void glotzmd::Simulation::PrintVelocities

(

std::ostream &

os

)

void glotzmd::Simulation::PrintForces

(

std::ostream &

os

)

void glotzmd::Simulation::PrintVis3d

(

std::ostream &

os

)

void glotzmd::Simulation::PrintVis3dTemplate

(

std::ostream &

os

)

void glotzmd::Simulation::PrintParticles	(	std::ostream &	os,
		std::string &	format
	)

void glotzmd::Simulation::PrintParticles	(	std::ostream &	os,
		const char *	format
	)

void glotzmd::Simulation::FinalizeUnserialization

(

)

[protected]

void glotzmd::Simulation::CheckForErrors

(

)

[protected]

Check the simulation for errors.

Prints error messages to the screen.

void glotzmd::Simulation::HandleEvents

(

)

[protected]

Handle Events.

void glotzmd::Simulation::OnEvent

(

)

[protected, virtual]

Perform when an event occurs.

Reimplemented from glotzmd::BaseObject.

void glotzmd::Simulation::Timestep

(

)

[protected]

---

Member Data Documentation

ParticleList glotzmd::Simulation::gParticle

Global vector of particles.

ObjectList glotzmd::Simulation::gInteractingObject

Global vector of objects.

BeadList glotzmd::Simulation::gBead

Global vector of beads.

RigidBodyList glotzmd::Simulation::gRigidBody

Global vector of rigid bodies.

SpringList glotzmd::Simulation::gSpring

Global vector of springs.

PotentialMap glotzmd::Simulation::gPotentialMap

Global map of potentials.

PotentialList glotzmd::Simulation::gPotential

Global list of potentials.

SimulationModifierList glotzmd::Simulation::gSimulationModifier

Global map of simulation components.

ForceRoutine* glotzmd::Simulation::gForceRoutine

Global pointer to the force routine.

IntegrationScheme* glotzmd::Simulation::gIntegrationScheme

Global pointer to the integration scheme.

BoundaryConditions* glotzmd::Simulation::gBoundaryConditions

Global pointer to simulation boundary conditions.

Units* glotzmd::Simulation::gUnits

Global pointer to the simulation units.

int glotzmd::Simulation::gDimensions

Simulation dimensions.

glotz_flt glotzmd::Simulation::gTimestep

Simulation timestep.

SimulationEventManager* glotzmd::Simulation::gEventManager

Manages "events" or changes to the simulation.

BaseObjectList glotzmd::Simulation::gBaseObject

List of pointers to all objects (force routines, integrators, particles, etc.).

int glotzmd::Simulation::mDirectionOfTime [protected]

bool glotzmd::Simulation::mIsFirstTimeVis3d [protected]

RigidBodyUpdater* glotzmd::Simulation::mRigidBodyUpdater [protected]

SimulationEvent glotzmd::Simulation::mPossibleEvents [protected]

A list of events that the simulation reacts to.

---

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

• Glotzilla/src/glotzmd/trunk/SourceCode/Simulation.h
• Glotzilla/src/glotzmd/trunk/SourceCode/Simulation.cpp
• Glotzilla/src/glotzmd/trunk/SourceCode/SimulationIO.cpp

---