SSAGES::BoxVolumeCV Class Reference

Collective variable on the volume of a box. More...

#include <BoxVolumeCV.h>

Inheritance diagram for SSAGES::BoxVolumeCV:

Public Member Functions
	BoxVolumeCV ()
	Constructor.
void	Initialize (const Snapshot &) override
	Initialize the CV.
void	Evaluate (const Snapshot &snapshot) override
	Evaluate the CV. More...
Public Member Functions inherited from SSAGES::CollectiveVariable
	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 BoxVolumeCV *	Build (const Json::Value &json, const std::string &path)
	Set up collective variable. More...
Static Public Member Functions inherited from SSAGES::CollectiveVariable
static CollectiveVariable *	BuildCV (const Json::Value &json, const std::string &path)
	Set up collective variable. More...

Additional Inherited Members
Protected Attributes inherited from SSAGES::CollectiveVariable
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

Collective variable on the volume of a box.

Collective variable on the volume of a box.

Definition at line 36 of file BoxVolumeCV.h.

Member Function Documentation

Build()

static BoxVolumeCV* SSAGES::BoxVolumeCV::Build ( const Json::Value &  json, const std::string &  path  )

inlinestatic

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 65 of file BoxVolumeCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::BoxVolumeCV.c_str(),
                          JsonSchema::BoxVolumeCV.c_str() + JsonSchema::BoxVolumeCV.size(),
                          &schema, nullptr);
            validator.Parse(schema, path);
 
            // Validate inputs.
            validator.Validate(json, path);
            if(validator.HasErrors())
                throw BuildException(validator.GetErrors());
 
            return new BoxVolumeCV();
        }

References BoxVolumeCV(), Json::Requirement::GetErrors(), Json::Requirement::HasErrors(), Json::ObjectRequirement::Parse(), and Json::ObjectRequirement::Validate().

Referenced by SSAGES::CollectiveVariable::BuildCV().

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Evaluate()

void SSAGES::BoxVolumeCV::Evaluate ( const Snapshot &  snapshot )

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 52 of file BoxVolumeCV.h.

        {
            // Fill empty gradient. 
            auto n = snapshot.GetNumAtoms();
            std::fill(grad_.begin(), grad_.end(), Vector3{0,0,0});
            grad_.resize(n, Vector3{0,0,0});
 
            val_ = snapshot.GetVolume();
            if(snapshot.GetCommunicator().rank() == 0)
                boxgrad_ = val_*Matrix3::Identity();
        }

References SSAGES::CollectiveVariable::boxgrad_, SSAGES::Snapshot::GetCommunicator(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::Snapshot::GetVolume(), SSAGES::CollectiveVariable::grad_, and SSAGES::CollectiveVariable::val_.

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

• /home/michael/development/SSAGES/src/CVs/BoxVolumeCV.h