SSAGES::ParticleCoordinateCV Class Reference

Collective variable on a particle coordinate. More...

#include <ParticleCoordinateCV.h>

Inheritance diagram for SSAGES::ParticleCoordinateCV:

Public Member Functions
	ParticleCoordinateCV (const Label &atomids, Dimension dim)
	Constructor. More...
void	Initialize (const Snapshot &snapshot) override
	Initialize necessary variables. More...
void	Evaluate (const Snapshot &snapshot) override
	Evaluate the CV. More...
double	GetPeriodicValue (double Location) const override
	Return value taking periodic boundary conditions into account. More...
double	GetDifference (const double Location) const override
	Return difference considering periodic boundaries. 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...
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...

Static Public Member Functions
static ParticleCoordinateCV *	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...

Private Attributes
Label	atomids_
	IDs of atoms of interest.
Dimension	dim_
	Index of dimension.

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 a particle coordinate.

This will return the value of either the x, y, or z coordinate, depending on the user specification for a defined particle, which is a collection of one or more atoms.

Definition at line 40 of file ParticleCoordinateCV.h.

Constructor & Destructor Documentation

ParticleCoordinateCV()

SSAGES::ParticleCoordinateCV::ParticleCoordinateCV ( const Label &  atomids, Dimension  dim  )

inline

Constructor.

Parameters

atomids	Atom ID's of interest.
dim	Index of dimension.

Construct a particle coordinate CV. The atomids specify a vector of the atom ID's of interest, and index specifies the dimension to report (x,y,z).

Todo:

Bounds needs to be an input.

Definition at line 60 of file ParticleCoordinateCV.h.

                                                                  : 
        atomids_(atomids), dim_(dim)
        {}

Member Function Documentation

Build()

static ParticleCoordinateCV* SSAGES::ParticleCoordinateCV::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 168 of file ParticleCoordinateCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::ParticleCoordinateCV.c_str(),
                          JsonSchema::ParticleCoordinateCV.c_str() + JsonSchema::ParticleCoordinateCV.size(),
                          &schema, nullptr);
            validator.Parse(schema, path);
 
            // Validate inputs.
            validator.Validate(json, path);
            if(validator.HasErrors())
                throw BuildException(validator.GetErrors());
 
            Label atomids;
            for(auto& id : json["atom_ids"])
                atomids.push_back(id.asInt());
 
            auto indextype = json.get("dimension","x").asString();
 
            Dimension index;
            if(indextype == "x")
                index = Dimension::x;
            else if(indextype == "y")
                index = Dimension::y;
            else if(indextype == "z")
                index = Dimension::z;
            else
                throw BuildException({"Could not obtain ParticleCoordinate dimension specified."});
 
            return new ParticleCoordinateCV(atomids, index);
        }

References 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::ParticleCoordinateCV::Evaluate ( const Snapshot &  snapshot )

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 97 of file ParticleCoordinateCV.h.

        {
            // Get local atom indices and compute COM. 
            std::vector<int> idx;
            snapshot.GetLocalIndices(atomids_, &idx);
 
            // Get data from snapshot. 
            auto n = snapshot.GetNumAtoms();
            const auto& masses = snapshot.GetMasses();
 
            // Initialize gradient.
            std::fill(grad_.begin(), grad_.end(), Vector3{0,0,0});
            grad_.resize(n, Vector3{0,0,0});
            
            // Compute total and center of mass.
            auto masstot = snapshot.TotalMass(idx);
            Vector3 com = snapshot.CenterOfMass(idx);
 
            // Assign CV value. 
            switch(dim_)
            {
                case Dimension::x:
                    val_ = com[0];
                    break;
                case Dimension::y:
                    val_ = com[1];
                    break;
                case Dimension::z:
                    val_ = com[2];
                    break;
            }
 
            // Assign gradient to appropriate atoms.
            for(auto& id : idx)
            {
                grad_[id][0] = (dim_ == Dimension::x) ? masses[id]/masstot : 0;
                grad_[id][1] = (dim_ == Dimension::y) ? masses[id]/masstot : 0;
                grad_[id][2] = (dim_ == Dimension::z) ? masses[id]/masstot : 0;
            }
        }

References atomids_, SSAGES::Snapshot::CenterOfMass(), dim_, SSAGES::Snapshot::GetLocalIndices(), SSAGES::Snapshot::GetMasses(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::CollectiveVariable::grad_, and SSAGES::Snapshot::TotalMass().

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GetDifference()

double SSAGES::ParticleCoordinateCV::GetDifference ( const double  Location ) const

inlineoverridevirtual

Return difference considering periodic boundaries.

Parameters

Location

Calculate difference of CV value to this location.

Returns

Direct difference.

As the AtomCoordinate CV does not consider periodic boundary conditions, the difference between the current value of the CV and another value is always the direct difference.

Reimplemented from SSAGES::CollectiveVariable.

Definition at line 162 of file ParticleCoordinateCV.h.

        {
            return val_ - Location;
        }

References SSAGES::CollectiveVariable::val_.

GetPeriodicValue()

double SSAGES::ParticleCoordinateCV::GetPeriodicValue ( double  Location ) const

inlineoverridevirtual

Return value taking periodic boundary conditions into account.

Parameters

Location

Get wrapped value of this location.

Returns

Input value

The AtomCoordinate CV does not consider periodic boundary conditions. Thus, this function always returns the input value.

Reimplemented from SSAGES::CollectiveVariable.

Definition at line 147 of file ParticleCoordinateCV.h.

        {
            return Location;
        }

Initialize()

void SSAGES::ParticleCoordinateCV::Initialize ( const Snapshot &  snapshot )

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 68 of file ParticleCoordinateCV.h.

        {
            using std::to_string;
 
            auto n = atomids_.size();
 
            // Make sure atom ID's are on at least one processor. 
            std::vector<int> found(n, 0);
            for(size_t i = 0; i < n; ++i)
            {
                if(snapshot.GetLocalIndex(atomids_[i]) != -1)
                    found[i] = 1;
            }
 
            MPI_Allreduce(MPI_IN_PLACE, found.data(), n, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
            unsigned ntot = std::accumulate(found.begin(), found.end(), 0, std::plus<int>());
            if(ntot != n)
                throw BuildException({
                    "ParticleCoordinateCV: Expected to find " + 
                    to_string(n) + 
                    " atoms, but only found " + 
                    to_string(ntot) + "."
                });         
        }

References atomids_, SSAGES::Snapshot::GetCommunicator(), and SSAGES::Snapshot::GetLocalIndex().

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

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