SSAGES::ParticleSeparationCV Class Reference

Collective variable on the distance between two particles' centers of mass. More...

#include <ParticleSeparationCV.h>

Inheritance diagram for SSAGES::ParticleSeparationCV:

Public Member Functions
	ParticleSeparationCV (const Label &group1, const Label &group2)
	Constructor. More...
	ParticleSeparationCV (const Label &group1, const Label &group2, 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 ParticleSeparationCV *	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	group1_
	Atom ID's of group 1.
Label	group2_
	Atom ID's of group 2.
Bool3	dim_
	Each dimension determines if it 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 the distance between two particles' centers of mass.

Collective variable on two particle positions. This CV will return the distance between two specific atom groups of the simulation.

Definition at line 39 of file ParticleSeparationCV.h.

Constructor & Destructor Documentation

ParticleSeparationCV() [1/2]

SSAGES::ParticleSeparationCV::ParticleSeparationCV ( const Label &  group1, const Label &  group2  )

inline

Constructor.

Parameters

group1	Vector of atom ID's of the first particle.
group2	Vector of atom ID's of the second particle.

Construct a paarticle separation CV.

Todo:

bounds needs to be an input.

Definition at line 58 of file ParticleSeparationCV.h.

                                                                       :
        group1_(group1), group2_(group2), dim_{true, true, true}
        {}

Referenced by Build().

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ParticleSeparationCV() [2/2]

SSAGES::ParticleSeparationCV::ParticleSeparationCV ( const Label &  group1, const Label &  group2, bool  dimx, bool  dimy, bool  dimz  )

inline

Constructor.

Parameters

group1	Vector of atom ID's of the first particle.
group2	Vector of atom ID's of the second particle.
dimx	If True, include x dimension.
dimy	If True, include y dimension.
dimz	If True, include z dimension.

Construct a particle separation CV.

Todo:

Bounds needs to be an input.

Definition at line 74 of file ParticleSeparationCV.h.

                                                                                                        :
        group1_(group1), group2_(group2), dim_{dimx, dimy, dimz}
        {}

Member Function Documentation

Build()

static ParticleSeparationCV* SSAGES::ParticleSeparationCV::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 167 of file ParticleSeparationCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::ParticleSeparationCV.c_str(),
                          JsonSchema::ParticleSeparationCV.c_str() + JsonSchema::ParticleSeparationCV.size(),
                          &schema, nullptr);
            validator.Parse(schema, path);
 
            // Validate inputs.
            validator.Validate(json, path);
            if(validator.HasErrors())
                throw BuildException(validator.GetErrors());
            
            std::vector<int> group1, group2;
            
            for(auto& s : json["group1"])
                group1.push_back(s.asInt());
 
            for(auto& s : json["group2"])
                group2.push_back(s.asInt());
 
            ParticleSeparationCV* c;
            if(json.isMember("dimension"))
            {
                auto fixx = json["dimension"][0].asBool();
                auto fixy = json["dimension"][1].asBool();
                auto fixz = json["dimension"][2].asBool();
                c = new ParticleSeparationCV(group1, group2, fixx, fixy, fixz);
            }
            else
                c = new ParticleSeparationCV(group1, group2);
            
            return c;
        }

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

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

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Evaluate()

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

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 128 of file ParticleSeparationCV.h.

        {
            // Get local atom indices.
            std::vector<int> idx1, idx2;
            snapshot.GetLocalIndices(group1_, &idx1);
            snapshot.GetLocalIndices(group2_, &idx2);
 
            // 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});
            boxgrad_ = Matrix3::Zero();
 
            // Get centers of mass.
            auto mtot1 = snapshot.TotalMass(idx1);
            auto mtot2 = snapshot.TotalMass(idx2);
            Vector3 com1 = snapshot.CenterOfMass(idx1);
            Vector3 com2 = snapshot.CenterOfMass(idx2);
 
            // Account for pbc. 
            Vector3 rij = snapshot.ApplyMinimumImage(com1 - com2).cwiseProduct(dim_.cast<double>());
 
            // Compute gradient.
            val_ = rij.norm();
 
            for(auto& id : idx1)
            {
                grad_[id] = rij/val_*masses[id]/mtot1;
                boxgrad_ += grad_[id]*rij.transpose();
            }
            
            for(auto& id : idx2)
                grad_[id] = -rij/val_*masses[id]/mtot2;
        }

References SSAGES::Snapshot::ApplyMinimumImage(), SSAGES::CollectiveVariable::boxgrad_, SSAGES::Snapshot::CenterOfMass(), dim_, SSAGES::Snapshot::GetLocalIndices(), SSAGES::Snapshot::GetMasses(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::CollectiveVariable::grad_, group1_, group2_, SSAGES::Snapshot::TotalMass(), and SSAGES::CollectiveVariable::val_.

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Initialize()

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 82 of file ParticleSeparationCV.h.

        {
            using std::to_string;
 
            auto n1 = group1_.size(), n2 = group2_.size();
 
            // Make sure atom ID's are on at least one processor. 
            std::vector<int> found1(n1, 0), found2(n2, 0);
            for(size_t i = 0; i < n1; ++i)
            {
                if(snapshot.GetLocalIndex(group1_[i]) != -1)
                    found1[i] = 1;
            }
            
            for(size_t i = 0; i < n2; ++i)
            {
                if(snapshot.GetLocalIndex(group2_[i]) != -1)
                    found2[i] = 1;
            }
 
            MPI_Allreduce(MPI_IN_PLACE, found1.data(), n1, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
            MPI_Allreduce(MPI_IN_PLACE, found2.data(), n2, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
    
            unsigned ntot1 = std::accumulate(found1.begin(), found1.end(), 0, std::plus<int>());
            unsigned ntot2 = std::accumulate(found2.begin(), found2.end(), 0, std::plus<int>());
            if(ntot1 != n1)
                throw BuildException({
                    "ParticleSeparationCV: Expected to find " + 
                    to_string(n1) + 
                    " atoms in particle 1, but only found " + 
                    to_string(ntot1) + "."
                });         
 
            if(ntot2 != n2)
                throw BuildException({
                    "ParticleSeparationCV: Expected to find " + 
                    to_string(n2) + 
                    " atoms in particle 2, but only found " + 
                    to_string(ntot2) + "."
                });         
        }

References SSAGES::Snapshot::GetCommunicator(), SSAGES::Snapshot::GetLocalIndex(), group1_, and group2_.

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

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