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)
	Constructor. More...
	ParticlePositionCV (const Label &atomids, const Vector3 &position, bool dimx, bool dimy, bool dimz)
	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.
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 ParticlePositionCV *	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_
	Vector of atom ids of interest.
Vector3	point_
	Target point in space.
Bool3	dim_
	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

ParticlePositionCV() [1/2]

SSAGES::ParticlePositionCV::ParticlePositionCV ( const Label &  atomids, const Vector3 &  position  )

inline

Constructor.

Parameters

atomids	Vector of atom ID's.
position	Point in (1,2,3)D space for the distance calculation.

Construct a particle position CV.

Todo:

Bounds needs to be an input.

Definition at line 61 of file ParticlePositionCV.h.

                                                                          :
        atomids_(atomids), point_(position), dim_{true, true, true}
        {
        }

Referenced by Build().

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ParticlePositionCV() [2/2]

SSAGES::ParticlePositionCV::ParticlePositionCV ( const Label &  atomids, const Vector3 &  position, bool  dimx, bool  dimy, bool  dimz  )

inline

Constructor.

Parameters

atomids	Vector of atom ID's.
position	Point in (1,2,3)D space for the distance calculation.
dimx	If True, include x dimension.
dimy	If True, include y dimension.
dimz	If True, include z dimension.

Construct a particle position CV.

Todo:

Bounds needs to be an input.

Definition at line 78 of file ParticlePositionCV.h.

                                                                                                           :
        atomids_(atomids), point_(position), dim_{dimx, dimy, dimz}
        {
        }

Member Function Documentation

Build()

static ParticlePositionCV* SSAGES::ParticlePositionCV::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 148 of file ParticlePositionCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::ParticlePositionCV.c_str(),
                          JsonSchema::ParticlePositionCV.c_str() + JsonSchema::ParticlePositionCV.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());
            
            Vector3 position;
            position[0] = json["position"][0].asDouble();
            position[1] = json["position"][1].asDouble();
            position[2] = json["position"][2].asDouble();
 
            ParticlePositionCV* c;
 
            if(json.isMember("dimension"))
            {
                auto dimx = json["dimension"][0].asBool();
                auto dimy = json["dimension"][1].asBool();
                auto dimz = json["dimension"][2].asBool();
                c = new ParticlePositionCV(atomids, position, dimx, dimy, dimz);
            }
            else
                c = new ParticlePositionCV(atomids, position);
 
            return c;
        }

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

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

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Evaluate()

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

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 116 of file ParticlePositionCV.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);
 
            // Compute difference between point and account for requested 
            // dimensions only.
            Vector3 dx = snapshot.ApplyMinimumImage(com - point_).cwiseProduct(dim_.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;
        }

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

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Initialize()

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 87 of file ParticlePositionCV.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({
                    "ParticlePositionCV: 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/ParticlePositionCV.h