SSAGES::ParticlePositionCV Class Reference

Collective variable on an particle position. More...

#include <ParticlePositionCV.h>

Inheritance diagram for SSAGES::ParticlePositionCV:

Public Member Functions
	ParticlePositionCV (const Label &atomids, const Vector3 &position, bool fixx, bool fixy, bool fixz)
	Constructor. More...
void	Initialize (const Snapshot &snapshot) override
	Initialize necessary variables. More...
void	Evaluate (const Snapshot &snapshot) override
	Evaluate the CV. More...
Public Member Functions inherited from SSAGES::CollectiveVariable
	CollectiveVariable ()
	Constructor.
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.
const std::array< double, 2 > &	GetBoundaries ()
	Get CV boundaries. More...
virtual double	GetDifference (double location) const

Static Public Member Functions
static ParticlePositionCV *	Build (const Json::Value &json, const std::string &path)
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_
	Vector of atom ids of interest.
Vector3	point_
	Target point in space.
Bool3	fix_
	Each dimension determines if a constraint is applied by the CV.

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 an particle position.

This CV will return the distance of a particle (collection of atoms) from a particular point in (1,2,3)-dimensional space.

Definition at line 39 of file ParticlePositionCV.h.

Constructor & Destructor Documentation

SSAGES::ParticlePositionCV::ParticlePositionCV ( const Label &  atomids, const Vector3 &  position, bool  fixx, bool  fixy, bool  fixz  )

inline

Constructor.

Parameters

atomids	Vector of atom ID's.
position	Point in (1,2,3)D space for the distance calculation.
fixx	If False, constrain x dimension.
fixy	If False, constrain y dimension.
fixz	If False, constrain z dimension.

Construct a particle position CV. If a dimension is constrained, this dimension does not contribute to the distance calculation. For example, if the y- and z-dimension are constrained, the CV calculates only the distance in x-direction.

Todo:

Bounds needs to be an input.

Definition at line 67 of file ParticlePositionCV.h.

                                                                                                           : 
        atomids_(atomids), point_(position), fix_{fixx, fixy, fixz}
        {
        }

Member Function Documentation

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

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 105 of file ParticlePositionCV.h.

References SSAGES::Snapshot::ApplyMinimumImage(), atomids_, SSAGES::Snapshot::CenterOfMass(), fix_, SSAGES::Snapshot::GetLocalIndices(), SSAGES::Snapshot::GetMasses(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::CollectiveVariable::grad_, point_, SSAGES::Snapshot::TotalMass(), and SSAGES::CollectiveVariable::val_.

        {
            // 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, masstot);

            // Compute difference between point and account for requested 
            // dimensions only.
            Vector3 dx = snapshot.ApplyMinimumImage(com - point_).cwiseProduct(fix_.cast<double>());
            val_ = dx.norm();

            // If distance is zero, we have nothing to do.
            if(val_ == 0)
                return;

            for(auto& id : idx)
                grad_[id] = dx/val_*masses[id]/masstot;
        }

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 76 of file ParticlePositionCV.h.

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

        {
            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({
                    "ParticlePositionCV: Expected to find " + 
                    to_string(n) + 
                    " atoms, but only found " + 
                    to_string(ntot) + "."
                });         
        }

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

• /home/cody/SSAGES/src/CVs/ParticlePositionCV.h