Simulation Class Reference

#include <simulation.hh>

Public Member Functions
	Simulation (const ost::mol::EntityHandle &handle, const SettingsPtr settings)
	Simulation (const ost::mol::mm::TopologyPtr top, const ost::mol::EntityHandle &handle, const SettingsPtr settings)
void	Save (const String &filename)
ost::mol::EntityHandle	GetEntity ()
geom::Vec3List	GetPositions (bool enforce_periodic_box=false, bool in_angstrom=true)
geom::Vec3List	GetVelocities ()
geom::Vec3List	GetForces ()
void	SetPositions (const geom::Vec3List &positions, bool in_angstrom=true)
void	SetVelocities (geom::Vec3List &velocities)
void	UpdatePositions (bool enforce_periodic_box=false)
bool	ApplySD (Real tolerance=100, int max_iterations=1000)
void	ApplyLBFGS (Real tolerance=1, int max_iterations=1000)
Real	GetEnergy ()
Real	GetPotentialEnergy ()
Real	GetKineticEnergy ()
TopologyPtr	GetTopology ()
void	Steps (int steps)
void	Register (ObserverPtr o)
void	ResetHarmonicBond (uint index, Real bond_length, Real force_constant)
void	ResetHarmonicAngle (uint index, Real angle, Real force_constant)
void	ResetUreyBradleyAngle (uint index, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant)
void	ResetPeriodicDihedral (uint index, int multiplicity, Real phase, Real force_constant)
void	ResetPeriodicImproper (uint index, int multiplicity, Real phase, Real force_constant)
void	ResetHarmonicImproper (uint index, Real phase, Real force_constant)
void	ResetLJPair (uint index, Real sigma, Real epsilon)
void	ResetDistanceConstraint (uint index, Real constraint_length)
void	ResetHarmonicPositionRestraint (uint index, const geom::Vec3 &ref_position, Real k, Real x_scale=1.0, Real y_scale=1.0, Real z_scale=1.0)
void	ResetHarmonicDistanceRestraint (uint index, Real length, Real force_constant)
void	ResetLJ (uint index, Real sigma, Real epsilon)
void	ResetGBSA (uint index, Real radius, Real scaling)
void	ResetCharge (uint index, Real charge)
void	ResetMass (uint index, Real mass)
void	AddPositionConstraint (uint index)
void	AddPositionConstraints (const std::vector< uint > &index)
void	ResetPositionConstraints ()
geom::Vec3	GetPeriodicBoxExtents ()
void	SetPeriodicBoxExtents (geom::Vec3 &vec)
Static Public Member Functions
static SimulationPtr	Load (const String &filename, SettingsPtr settings)

---

Detailed Description

Definition at line 55 of file simulation.hh.

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Constructor & Destructor Documentation

Simulation	(	const ost::mol::EntityHandle &	handle,
		const SettingsPtr	settings
	)

Simulation	(	const ost::mol::mm::TopologyPtr	top,
		const ost::mol::EntityHandle &	handle,
		const SettingsPtr	settings
	)

---

Member Function Documentation

void AddPositionConstraint

(

uint

index

)

void AddPositionConstraints

(

const std::vector< uint > &

index

)

void ApplyLBFGS	(	Real	tolerance = 1,
		int	max_iterations = 1000
	)

bool ApplySD	(	Real	tolerance = 100,
		int	max_iterations = 1000
	)

Real GetEnergy

(

)

ost::mol::EntityHandle GetEntity

(

)

[inline]

Definition at line 70 of file simulation.hh.

geom::Vec3List GetForces

(

)

Real GetKineticEnergy

(

)

geom::Vec3 GetPeriodicBoxExtents

(

)

geom::Vec3List GetPositions	(	bool	enforce_periodic_box = false,
		bool	in_angstrom = true
	)

Real GetPotentialEnergy

(

)

TopologyPtr GetTopology

(

)

[inline]

Definition at line 94 of file simulation.hh.

geom::Vec3List GetVelocities

(

)

static SimulationPtr Load	(	const String &	filename,
		SettingsPtr	settings
	)			[static]

void Register

(

ObserverPtr

o

)

void ResetCharge	(	uint	index,
		Real	charge
	)

void ResetDistanceConstraint	(	uint	index,
		Real	constraint_length
	)

void ResetGBSA	(	uint	index,
		Real	radius,
		Real	scaling
	)

void ResetHarmonicAngle	(	uint	index,
		Real	angle,
		Real	force_constant
	)

void ResetHarmonicBond	(	uint	index,
		Real	bond_length,
		Real	force_constant
	)

void ResetHarmonicDistanceRestraint	(	uint	index,
		Real	length,
		Real	force_constant
	)

void ResetHarmonicImproper	(	uint	index,
		Real	phase,
		Real	force_constant
	)

void ResetHarmonicPositionRestraint	(	uint	index,
		const geom::Vec3 &	ref_position,
		Real	k,
		Real	x_scale = 1.0,
		Real	y_scale = 1.0,
		Real	z_scale = 1.0
	)

void ResetLJ	(	uint	index,
		Real	sigma,
		Real	epsilon
	)

void ResetLJPair	(	uint	index,
		Real	sigma,
		Real	epsilon
	)

void ResetMass	(	uint	index,
		Real	mass
	)

void ResetPeriodicDihedral	(	uint	index,
		int	multiplicity,
		Real	phase,
		Real	force_constant
	)

void ResetPeriodicImproper	(	uint	index,
		int	multiplicity,
		Real	phase,
		Real	force_constant
	)

void ResetPositionConstraints

(

)

void ResetUreyBradleyAngle	(	uint	index,
		Real	angle,
		Real	angle_force_constant,
		Real	bond_length,
		Real	bond_force_constant
	)

void Save

(

const String &

filename

)

void SetPeriodicBoxExtents

(

geom::Vec3 &

vec

)

void SetPositions	(	const geom::Vec3List &	positions,
		bool	in_angstrom = true
	)

void SetVelocities

(

geom::Vec3List &

velocities

)

void Steps

(

int

steps

)

void UpdatePositions

(

bool

enforce_periodic_box = false

)

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

• stage/include/ost/mol/mm/simulation.hh