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.


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  ) 

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