SSAGES::AngleCV Class Reference

Collective variable to calculate angle. More...

#include <AngleCV.h>

Inheritance diagram for SSAGES::AngleCV:

Public Member Functions
	AngleCV (int atomid1, int atomid2, int atomid3)
	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 AngleCV *	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 3 atom ID's of interest.

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 to calculate angle.

Definition at line 35 of file AngleCV.h.

Constructor & Destructor Documentation

AngleCV()

SSAGES::AngleCV::AngleCV ( int  atomid1, int  atomid2, int  atomid3  )

inline

Constructor.

Parameters

atomid1	ID of the first atom defining the angle.
atomid2	ID of the second atom defining the angle.
atomid3	ID of the third atom defining the angle.

Construct an dihedral CV.

Todo:

Bounds needs to be an input and periodic boundary conditions

Definition at line 53 of file AngleCV.h.

                                                       :
        atomids_({atomid1, atomid2, atomid3})
        {
            bounds_ = {{0,M_PI}};
        }

Referenced by Build().

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Member Function Documentation

Build()

static AngleCV* SSAGES::AngleCV::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 137 of file AngleCV.h.

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

References AngleCV(), 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::AngleCV::Evaluate ( const Snapshot &  snapshot )

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 85 of file AngleCV.h.

        {
            // Get data from snapshot. 
            auto n = snapshot.GetNumAtoms();
            const auto& pos = snapshot.GetPositions();
            auto& comm = snapshot.GetCommunicator();
 
            // Initialize gradient.
            std::fill(grad_.begin(), grad_.end(), Vector3{0,0,0});
            grad_.resize(n, Vector3{0,0,0});
 
            Vector3 xi{0, 0, 0}, xj{0, 0, 0}, xk{0, 0, 0};
 
            auto iindex = snapshot.GetLocalIndex(atomids_[0]);
            auto jindex = snapshot.GetLocalIndex(atomids_[1]);
            auto kindex = snapshot.GetLocalIndex(atomids_[2]);
 
            if(iindex != -1) xi = pos[iindex];
            if(jindex != -1) xj = pos[jindex];
            if(kindex != -1) xk = pos[kindex];
 
            // By performing a reduce, we actually collect all. This can 
            // be converted to a more intelligent allgater on rank then bcast. 
            MPI_Allreduce(MPI_IN_PLACE, xi.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            MPI_Allreduce(MPI_IN_PLACE, xj.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            MPI_Allreduce(MPI_IN_PLACE, xk.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
 
            // Two vectors
            auto rij = snapshot.ApplyMinimumImage(xi - xj);
            auto rkj = snapshot.ApplyMinimumImage(xk - xj);
 
            auto dotP = rij.dot(rkj);
            auto nrij = rij.norm();
            auto nrkj = rkj.norm();
            auto dotPnn = dotP/(nrij*nrkj);
 
            val_ = acos(dotPnn);
 
            // Calculate gradients
            auto prefactor = -1.0/(sqrt(1. - dotPnn*dotPnn)*nrij*nrkj);
 
            Vector3 gradi{0, 0, 0}, gradk{0, 0, 0};
            if(iindex != -1) gradi = prefactor*(rkj - dotP*rij/(nrij*nrij));
            if(kindex != -1) gradk = prefactor*(rij - dotP*rkj/(nrkj*nrkj));
            MPI_Allreduce(MPI_IN_PLACE, gradi.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            MPI_Allreduce(MPI_IN_PLACE, gradk.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            if(iindex != -1) grad_[iindex] = gradi;
            if(kindex != -1) grad_[kindex] = gradk;
            if(jindex != -1) grad_[jindex] = -gradi - gradk;
        }

References SSAGES::Snapshot::ApplyMinimumImage(), atomids_, SSAGES::Snapshot::GetCommunicator(), SSAGES::Snapshot::GetLocalIndex(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::Snapshot::GetPositions(), SSAGES::CollectiveVariable::grad_, and SSAGES::CollectiveVariable::val_.

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Initialize()

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 63 of file AngleCV.h.

        {
            using std::to_string;
            
            std::vector<int> found;
            snapshot.GetLocalIndices(atomids_, &found);
            int nfound = found.size();
            MPI_Allreduce(MPI_IN_PLACE, &nfound, 1, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
            
            if(nfound != 3)
                throw BuildException({
                    "TorsionalCV: Expected to find " + 
                    to_string(3) + 
                    " atoms, but only found " + 
                    to_string(nfound) + "."
                }); 
        }

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

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

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