SSAGES::TorsionalCV Class Reference

Collective variable on the torsion angles. More...

#include <TorsionalCV.h>

Inheritance diagram for SSAGES::TorsionalCV:

Public Member Functions
	TorsionalCV (int atomid1, int atomid2, int atomid3, int atomid4, bool periodic)
	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
	Get difference taking periodic boundary conditions into account. More...
double	GetMinimumImage (const double Location) const override
	Returns the minimum image of a CV based on the input location. 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...
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 TorsionalCV *	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 4 atom ID's of interest.
bool	periodic_
	If True, use periodic boundary conditions.

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 torsion angles.

Collective variable on an proper dihedral. This will return the angle between two planes as defined in [4]. Singularities are avoided as described in [1].

Definition at line 42 of file TorsionalCV.h.

Constructor & Destructor Documentation

TorsionalCV()

SSAGES::TorsionalCV::TorsionalCV ( int  atomid1, int  atomid2, int  atomid3, int  atomid4, bool  periodic  )

inline

Constructor.

Parameters

atomid1	ID of the first atom defining the dihedral angle.
atomid2	ID of the second atom defining the dihedral angle.
atomid3	ID of the third atom defining the dihedral angle.
atomid4	ID of the forth atom defining the dihedral angle.
periodic	If True consider periodic boundary conditions.

Construct an dihedral CV.

Todo:

Bounds needs to be an input and periodic boundary conditions

Definition at line 64 of file TorsionalCV.h.

                                                                                       : 
        atomids_({atomid1, atomid2, atomid3, atomid4}), periodic_(periodic)
        {
        }

Referenced by Build().

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Member Function Documentation

Build()

static TorsionalCV* SSAGES::TorsionalCV::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 229 of file TorsionalCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::TorsionalCV.c_str(),
                          JsonSchema::TorsionalCV.c_str() + JsonSchema::TorsionalCV.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());
 
            auto periodic = json.get("periodic", true).asBool();
            return new TorsionalCV(atomids[0], atomids[1], atomids[2], atomids[3], periodic);
        }

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

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

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Evaluate()

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

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 95 of file TorsionalCV.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}, xl{0, 0, 0};
 
            auto iindex = snapshot.GetLocalIndex(atomids_[0]);
            auto jindex = snapshot.GetLocalIndex(atomids_[1]);
            auto kindex = snapshot.GetLocalIndex(atomids_[2]);
            auto lindex = snapshot.GetLocalIndex(atomids_[3]);
 
            if(iindex != -1) xi = pos[iindex];
            if(jindex != -1) xj = pos[jindex];
            if(kindex != -1) xk = pos[kindex];
            if(lindex != -1) xl = pos[lindex];
 
            // 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);
            MPI_Allreduce(MPI_IN_PLACE, xl.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            
            //Calculate pertinent vectors
            auto F = snapshot.ApplyMinimumImage(xi - xj);
            auto G = snapshot.ApplyMinimumImage(xj - xk);
            auto H = snapshot.ApplyMinimumImage(xl - xk);
            auto A = F.cross(G);
            auto B = H.cross(G);
            
            auto y = B.cross(A).dot(G.normalized());
            auto x = A.dot(B);
 
            val_ = atan2(y, x);
 
            auto Zed = F.dot(G.normalized())/A.dot(A); 
            auto Ned = H.dot(G.normalized())/B.dot(B);
 
            Vector3 gradi{0,0,0}, gradl{0,0,0}; 
            if(iindex != -1) gradi = -G.norm()*A/A.dot(A);
            if(lindex != -1) gradl = G.norm()*B/B.dot(B);
            MPI_Allreduce(MPI_IN_PLACE, gradi.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            MPI_Allreduce(MPI_IN_PLACE, gradl.data(), 3, MPI_DOUBLE, MPI_SUM, comm);
            if(iindex != -1) grad_[iindex] = gradi;
            if(lindex != -1) grad_[lindex] = gradl;
            if(jindex != -1) grad_[jindex] = Zed*A - Ned*B - gradi;
            if(kindex != -1) grad_[kindex] = Ned*B  - Zed*A - gradl;
        }

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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GetDifference()

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

inlineoverridevirtual

Get difference taking periodic boundary conditions into account.

Parameters

Location

Input value

Returns

Wrapped or unwrapped difference depending on whether periodic boundaries are used.

If periodic boundaries are used, this function calculates the difference and wraps the result into the range (-pi, pi). Otherwise, the simple difference is returned.

Reimplemented from SSAGES::CollectiveVariable.

Definition at line 188 of file TorsionalCV.h.

        {
            double PeriodicDiff = val_ - Location;
 
            if(!periodic_)
                return PeriodicDiff;
 
            PeriodicDiff = GetPeriodicValue(PeriodicDiff);
 
            if(PeriodicDiff > M_PI)
                PeriodicDiff -= 2.0*M_PI;
            else if(PeriodicDiff < -M_PI)
                PeriodicDiff += 2.0*M_PI;
 
            return PeriodicDiff;
        }

References GetPeriodicValue(), periodic_, and SSAGES::CollectiveVariable::val_.

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GetMinimumImage()

double SSAGES::TorsionalCV::GetMinimumImage ( const double  Location ) const

inlineoverridevirtual

Returns the minimum image of a CV based on the input location.

Parameters

Location

Value against which the minimum image is calculated.

Returns

Minimum image of the CV

Takes the input location and applies the periodic boundary conditions to return a minimum image of the CV.

Reimplemented from SSAGES::CollectiveVariable.

Definition at line 213 of file TorsionalCV.h.

        {
            double PeriodicDiff = val_ - Location;
 
            if(!periodic_)
                return val_;    
 
            if(PeriodicDiff > M_PI)
                return (val_ - 2.0*M_PI);
            else if(PeriodicDiff < -M_PI)
                return (val_ + 2.0*M_PI);   
 
            return val_;
        }

References periodic_, and SSAGES::CollectiveVariable::val_.

GetPeriodicValue()

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

inlineoverridevirtual

Return value taking periodic boundary conditions into account.

Parameters

Location

Input value.

Returns

Wrapped or unwrapped input value depending on whether periodic boundaries are used.

If periodic boundaries are used, this function wraps the input value into the range (-pi, pi). Otherwise the input value is returned unmodified.

Reimplemented from SSAGES::CollectiveVariable.

Definition at line 161 of file TorsionalCV.h.

        {
            if(!periodic_)
                return Location;
 
            int n = (int)(Location/(2.0*M_PI));
            double PeriodicLocation;
 
            PeriodicLocation = Location - n*M_PI;
            if(PeriodicLocation < -M_PI)
                PeriodicLocation += 2.0*M_PI;
            else if (PeriodicLocation > M_PI)
                PeriodicLocation -= 2.0*M_PI;
 
            return PeriodicLocation;
        }

References periodic_.

Referenced by GetDifference().

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Initialize()

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 73 of file TorsionalCV.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 != 4)
                throw BuildException({
                    "TorsionalCV: Expected to find " + 
                    to_string(4) + 
                    " 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/TorsionalCV.h