SSAGES::PairwiseCV Class Reference

Generalized collective variable based on pairwise properties of atoms. More...

#include <PairwiseCV.h>

Inheritance diagram for SSAGES::PairwiseCV:

Public Member Functions
	PairwiseCV (const Label &group1, const Label &group2, PairwiseKernel *pk)
	Constructor. More...
void	Initialize (const Snapshot &snapshot) override
	Initialize necessary variables. More...
void	Evaluate (const Snapshot &snapshot) override
	Evaluate the CV. More...
	~PairwiseCV ()
	Destructor.
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 PairwiseCV *	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_
	IDs of the first group of atoms.
Label	group2_
	IDs of the second group of atoms.
PairwiseKernel *	pk_
	Pairwise kernel function used for 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

Generalized collective variable based on pairwise properties of atoms.

Collective variable on pairwise properties between two groups of atoms. To ensure generality of usage, there are various pairwise kernel functions from which to choose.

Definition at line 40 of file PairwiseCV.h.

Constructor & Destructor Documentation

PairwiseCV()

SSAGES::PairwiseCV::PairwiseCV ( const Label &  group1, const Label &  group2, PairwiseKernel *  pk  )

inline

Constructor.

Parameters

group1	IDs of the first group of atoms.
group2	IDs of the second group of atoms.
pk	pairwise kernel (function) to use.

Construct a PairwiseCV.

Definition at line 57 of file PairwiseCV.h.

                                                                                 : 
        group1_(group1), group2_(group2), pk_(pk)
        {
        }

Referenced by Build().

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Member Function Documentation

Build()

static PairwiseCV* SSAGES::PairwiseCV::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 200 of file PairwiseCV.h.

        {
            Json::ObjectRequirement validator;
            Json::Value schema;
            Json::CharReaderBuilder rbuilder;
            Json::CharReader* reader = rbuilder.newCharReader();
 
            reader->parse(JsonSchema::PairwiseCV.c_str(),
                          JsonSchema::PairwiseCV.c_str() + JsonSchema::PairwiseCV.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());
            
            return new PairwiseCV(group1, group2, PairwiseKernel::Build(json["kernel"], path));
        }

References SSAGES::PairwiseKernel::Build(), Json::Requirement::GetErrors(), Json::Requirement::HasErrors(), PairwiseCV(), Json::ObjectRequirement::Parse(), and Json::ObjectRequirement::Validate().

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

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Evaluate()

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

inlineoverride

Evaluate the CV.

Parameters

snapshot

Current simulation snapshot.

Definition at line 112 of file PairwiseCV.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();
            auto& atomids = snapshot.GetAtomIDs();
            auto& positions = 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});
            boxgrad_ = Matrix3::Zero();
 
            // Fill eigen matrix with coordinate data. 
            std::vector<double> pos1(3*idx1.size()), pos2(3*idx2.size());
            std::vector<int> id1(idx1.size()), id2(idx2.size()); 
            for(size_t i = 0; i < idx1.size(); ++i)
            {
                pos1[3*i+0] = positions[idx1[i]][0]; 
                pos1[3*i+1] = positions[idx1[i]][1]; 
                pos1[3*i+2] = positions[idx1[i]][2];
 
                id1[i] = atomids[idx1[i]];
            }
 
            for(size_t i = 0; i < idx2.size(); ++i)
            {
                pos2[3*i+0] = positions[idx2[i]][0]; 
                pos2[3*i+1] = positions[idx2[i]][1]; 
                pos2[3*i+2] = positions[idx2[i]][2];
 
                id2[i] = atomids[idx2[i]];
            }
 
            // Gather across all procs. 
            pos1 = mxx::allgatherv(pos1.data(), pos1.size(), comm);
            pos2 = mxx::allgatherv(pos2.data(), pos2.size(), comm);
            id1 = mxx::allgatherv(id1.data(), id1.size(), comm);
            id2 = mxx::allgatherv(id2.data(), id2.size(), comm);
 
            // Create Eigen map for ease of use.
            using Map = Eigen::Map<Eigen::Matrix<double, Eigen::Dynamic, 3, Eigen::RowMajor>>;
            Map gpos1(pos1.data(), group1_.size(), 3), gpos2(pos2.data(), group2_.size(), 3);
 
            val_ = 0;
            double df = 0.;
            // Compute gradient and value.
            for(size_t i = 0; i < group1_.size(); ++i)
            {
                auto t1 = id1[i];
                const auto& pi = gpos1.row(i);
                for(size_t j = 0; j < group2_.size(); ++j)
                {
                    auto t2 = id2[j];
                    const auto& pj = gpos2.row(j);
 
                    // Skip identical pairs. 
                    if(t1 == t2)
                        continue;
                    
                    // Compute distance and pairwise function. 
                    Vector3 rij = pi - pj;
                    snapshot.ApplyMinimumImage(&rij);
                    auto r = rij.norm();
                    val_ +=  pk_->Evaluate(r, df);
 
                    // Get local indices and sum gradients.
                    auto lid1 = snapshot.GetLocalIndex(t1);
                    if(lid1 != -1)
                        grad_[lid1] += df*rij/r;
                    
                    auto lid2 = snapshot.GetLocalIndex(t2);
                    if(lid2 != -1)
                        grad_[lid2] -= df*rij/r;
 
                    // Only sum box gradient on a single proc.
                    if(comm.rank() == 0)
                        boxgrad_ += df*rij/r*rij.transpose();
                }
            }
        }

References SSAGES::Snapshot::ApplyMinimumImage(), SSAGES::CollectiveVariable::boxgrad_, SSAGES::PairwiseKernel::Evaluate(), SSAGES::Snapshot::GetAtomIDs(), SSAGES::Snapshot::GetCommunicator(), SSAGES::Snapshot::GetLocalIndex(), SSAGES::Snapshot::GetLocalIndices(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::Snapshot::GetPositions(), SSAGES::CollectiveVariable::grad_, group1_, group2_, pk_, and SSAGES::CollectiveVariable::val_.

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Initialize()

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

inlineoverride

Initialize necessary variables.

Parameters

snapshot

Current simulation snapshot.

Definition at line 66 of file PairwiseCV.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({
                    "Pairwise: Expected to find " + 
                    to_string(n1) + 
                    " atoms in group 1, but only found " + 
                    to_string(ntot1) + "."
                });         
 
            if(ntot2 != n2)
                throw BuildException({
                    "Pairwise: Expected to find " + 
                    to_string(n2) + 
                    " atoms in group 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/PairwiseCV.h