Abstract class for a collective variable. More...

#include <CollectiveVariable.h>

Inheritance diagram for SSAGES::CollectiveVariable:

[legend]

Public Member Functions
	CollectiveVariable ()
	Constructor.

virtual	~CollectiveVariable ()
	Destructor.

virtual void	Initialize (const class Snapshot &)
	Initialize CV. More...

virtual void	Evaluate (const class Snapshot &)=0
	Evaluate CV. More...

double	GetValue () const
	Get current value of the CV. More...

virtual double	GetMinimumImage (double) const
	Returns the minimum image of a CV based on the input location. More...

virtual double	GetPeriodicValue (double location) const
	Apply periodic boundaries to a given value. More...

const std::vector< Vector3 > &	GetGradient () const
	Get current gradient of the CV. More...

const Matrix3 &	GetBoxGradient () const
	Get gradient contribution to box. More...

const std::array< double, 2 > &	GetBoundaries ()
	Get CV boundaries. More...

virtual double	GetDifference (double location) const

Static Public Member Functions
static CollectiveVariable *	BuildCV (const Json::Value &json, const std::string &path)
	Set up collective variable. More...

Protected Attributes
std::vector< Vector3 >	grad_
	Gradient vector dCv/dxi.

Matrix3	boxgrad_
	Gradient w.r.t box vectors dCv/dHij.

double	val_
	Current value of CV.

std::array< double, 2 >	bounds_
	Bounds on CV.

Detailed Description

Abstract class for a collective variable.

Definition at line 40 of file CollectiveVariable.h.

Member Function Documentation

◆ BuildCV()

CollectiveVariable * SSAGES::CollectiveVariable::BuildCV	(	const Json::Value &	json,
		const std::string &	path
	)

static

Set up collective variable.

Parameters

json	JSON input value.
path	Path for JSON path specification.

Returns: Pointer to the CV built by this function. nullptr in case of unknown error.

Builds a CV from a JSON node. Returns a pointer to the built cv. If an unknown error is encountered, this function will return a nullptr, but generally it will throw a BuildException on failure.

Warning: Object lifetime is the caller's responsibility.

Definition at line 43 of file CollectiveVariable.cpp.

     {
         // Get CV type. 
         auto type = json.get("type", "none").asString();
  
         if(type == "Angle")
             return AngleCV::Build(json, path);
         else if (type == "ANNCV") 
             return ANNCV::Build(json, path);
         else if(type == "BoxVolume")
             return BoxVolumeCV::Build(json, path);
         else if(type == "GyrationTensor")
             return GyrationTensorCV::Build(json, path);
         else if(type == "Pairwise")
             return PairwiseCV::Build(json, path);
         else if(type == "ParticleCoordinate")
             return ParticleCoordinateCV::Build(json, path);
         else if(type == "ParticlePosition")
             return ParticlePositionCV::Build(json, path);
         else if(type == "ParticleSeparation")
             return ParticleSeparationCV::Build(json, path);
         else if(type == "RouseMode")
             return RouseModeCV::Build(json, path);
         else if(type == "Torsional")
             return TorsionalCV::Build(json, path);
         else if (type == "AlphaRMSD")
             return AlphaRMSDCV::Build(json, path);
         else if (type == "ParallelBetaRMSD")
             return ParallelBetaRMSDCV::Build(json, path);
         else if (type == "AntiBetaRMSD")
             return AntiBetaRMSDCV::Build(json, path);
         else if (type == "RMSD")
             return RMSDCV::Build(json, path);
         else
             throw std::invalid_argument(path + ": Unknown CV type specified.");
     }

References SSAGES::AlphaRMSDCV::Build(), SSAGES::AngleCV::Build(), SSAGES::ANNCV::Build(), SSAGES::AntiBetaRMSDCV::Build(), SSAGES::BoxVolumeCV::Build(), SSAGES::GyrationTensorCV::Build(), SSAGES::PairwiseCV::Build(), SSAGES::ParallelBetaRMSDCV::Build(), SSAGES::ParticleCoordinateCV::Build(), SSAGES::ParticlePositionCV::Build(), SSAGES::ParticleSeparationCV::Build(), SSAGES::RMSDCV::Build(), SSAGES::RouseModeCV::Build(), and SSAGES::TorsionalCV::Build().

Referenced by SSAGES::ResourceHandler::Build().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ Evaluate()

virtual void SSAGES::CollectiveVariable::Evaluate ( const class Snapshot & )

pure virtual

Evaluate CV.

Evaluation of the CV. This function is called by the Hook in the post-integration phase every iteration. The CV should compute its value and gradient, storing them in a local private variable.

◆ GetBoundaries()

const std::array<double, 2>& SSAGES::CollectiveVariable::GetBoundaries ( )

inline

Get CV boundaries.

Returns: List of lower and upper boundaries of the CV.

Returns the boundaries of the CV. These represent the bounds within which the CV is expected to be constrained. There is no requirement on the method to respect the values returned here.

Definition at line 151 of file CollectiveVariable.h.

         {
             return bounds_;
         }

◆ GetBoxGradient()

const Matrix3& SSAGES::CollectiveVariable::GetBoxGradient ( ) const

inline

Get gradient contribution to box.

Returns: Gradient of CV with respect to box.

Returns the gradient of the CV with respect to the box.

Definition at line 138 of file CollectiveVariable.h.

         {
             return boxgrad_;
         }

◆ GetDifference()

virtual double SSAGES::CollectiveVariable::GetDifference ( double location ) const

inlinevirtual

Get difference between current CV value and a given value, taking periodic boundaries into account.

Parameters

location Value whose distance from the current CV value should be calculated.

Returns: Difference taking periodic boundaries into account.

Returns the difference betwen the current cv value and Location: (value_ - Location) respecting periodic boundary conditions of the CV, if the CV has periodic boundary conditions. For example Torsional angle has boundaries at pi and -pi, in which the difference beteen the angles is 0 not 2pi

Reimplemented in SSAGES::TorsionalCV, and SSAGES::ParticleCoordinateCV.

Definition at line 168 of file CollectiveVariable.h.

         {
             return val_ - location;
         }

◆ GetGradient()

const std::vector<Vector3>& SSAGES::CollectiveVariable::GetGradient ( ) const

inline

Get current gradient of the CV.

Returns: Per-atom gradient of the CV.

Returns the current value of the CV gradient. This should be an n length vector, where n is the number of atoms in the snapshot. Each element in the vector is the derivative of the CV with respect to the atom's coordinate (dCV/dxi).

Definition at line 127 of file CollectiveVariable.h.

         {
             return grad_;
         }

◆ GetMinimumImage()

virtual double SSAGES::CollectiveVariable::GetMinimumImage ( double ) const

inlinevirtual

Returns the minimum image of a CV based on the input location.

Returns: Minimum image of the CV

Takes the input location and applies the periodic boundary conditions to return a minimum image of the CV.

Reimplemented in SSAGES::TorsionalCV.

Definition at line 98 of file CollectiveVariable.h.

         {
             return val_;
         }

◆ GetPeriodicValue()

virtual double SSAGES::CollectiveVariable::GetPeriodicValue ( double location ) const

inlinevirtual

Apply periodic boundaries to a given value.

Parameters

location Value to which the periodic boundaries should be applied.

Returns: Correct value.

Takes location and applies periodic boundaries of the CV on it and returns a correct value. Example would be torsional angle which has bounds at pi and -pi. If location = 2pi, GetPeriodicValue(location) would return 0.

Reimplemented in SSAGES::TorsionalCV, and SSAGES::ParticleCoordinateCV.

Definition at line 113 of file CollectiveVariable.h.

         {
             return location;
         }

◆ GetValue()

double SSAGES::CollectiveVariable::GetValue ( ) const

inline

Get current value of the CV.

Returns: Current value of the CV.

Returns the current value of the CV which has been computed before via the call to CollectiveVariable::Evaluate().

Definition at line 86 of file CollectiveVariable.h.

         {
             return val_;
         }

◆ Initialize()

virtual void SSAGES::CollectiveVariable::Initialize ( const class Snapshot & )

inlinevirtual

Initialize CV.

Initialization of the CV. This is an optional method and is called during the pre-simulation phase of the hook. It is typically used to allocate/reserve memory.

Definition at line 69 of file CollectiveVariable.h.

69 {}

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

/home/michael/development/SSAGES/src/CVs/CollectiveVariable.h
/home/michael/development/SSAGES/src/CVs/CollectiveVariable.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ BuildCV()

◆ Evaluate()

◆ GetBoundaries()

◆ GetBoxGradient()

◆ GetDifference()

◆ GetGradient()

◆ GetMinimumImage()

◆ GetPeriodicValue()

◆ GetValue()

◆ Initialize()