Basis Function Sampling Algorithm. More...

#include <BasisFunc.h>

Inheritance diagram for SSAGES::BFS:

Public Member Functions
	BFS (const MPI_Comm &world, const MPI_Comm &comm, Grid< unsigned int > h, Grid< std::vector< double >> f, Grid< double > b, const std::vector< BasisFunction > &functions, const std::vector< double > &restraint, const std::vector< double > &boundUp, const std::vector< double > &boundLow, unsigned int cyclefreq, unsigned int frequency, const std::string bnme, const double temperature, const double tol, const double weight, bool converge)
	Constructor. More...

void	PreSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call prior to simulation initiation. More...

void	PostIntegration (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call post integration. More...

void	PostSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call post simulation. More...

void	SetIteration (const int iter)
	Set the current iteration. More...

void	SetBasis (const std::vector< double > &coeff, std::vector< double > &unbias)
	Set the values for the basis. More...

	~BFS ()
	Destructor.

Public Member Functions inherited from SSAGES::Method
	Method (unsigned int frequency, const MPI_Comm &world, const MPI_Comm &comm)
	Constructor. More...

void	SetCVMask (const std::vector< unsigned int > &mask)
	Sets the collective variable mask. More...

virtual	~Method ()
	Destructor.

Public Member Functions inherited from SSAGES::EventListener
	EventListener (unsigned int frequency)
	Constructor. More...

unsigned int	GetFrequency () const
	Get frequency of event listener. More...

virtual	~EventListener ()
	Destructor.

Static Public Member Functions
static BFS *	Build (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
	Build a derived method from JSON node. More...

Static Public Member Functions inherited from SSAGES::Method
static Method *	BuildMethod (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
	Build a derived method from JSON node. More...

Static Public Member Functions inherited from SSAGES::EventListener
static unsigned int	GetWalkerID (const MPI_Comm &world, const MPI_Comm &comm)
	Get walker ID number of specified communicator. More...

static unsigned int	GetNumWalkers (const MPI_Comm &world, const MPI_Comm &comm)
	Get total number of walkers in the simulation. More...

static bool	IsMasterRank (const MPI_Comm &comm)
	Check if current processor is master. More...

Private Member Functions
void	ProjectBias (const CVList &cvs, const double beta)
	The functions which calculates the updated bias and coefficients and then stores them. More...

void	InBounds (const CVList &cvs)
	A function which checks to see if the CVs are still in bounds. More...

void	PrintBias (const CVList &cvs, const double beta)
	Prints the current bias to a defined file from the JSON. More...

Private Attributes
Grid< unsigned int > *	h_
	Grid of visited states. More...

Grid< double > *	b_
	Stored bias potential. More...

Grid< std::vector< double > > *	f_
	Stored gradients. More...

std::vector< double >	unbias_
	The biased histogram of states. More...

std::vector< double >	coeffArr_
	The coefficient array for restart runs.

BasisEvaluator	evaluator_
	The basis evaluator class. More...

std::vector< double >	restraint_
	Spring constants for restrained system. More...

std::vector< double >	boundUp_
	Upper position of the spring restraint.

std::vector< double >	boundLow_
	Lower position of the spring restraint.

unsigned int	cyclefreq_
	Frequency of coefficient updates.

unsigned int	cyclefreqTmp_
	Temporary cyclefrequency that ensures sweeps are of proper length for restrained simulations.

unsigned int	step_
	Step counter for the cyclefrequency.

unsigned int	mpiid_
	The node that the current system belongs to, primarily for printing and debugging.

double	weight_
	Weighting for potentially faster sampling. More...

double	temperature_
	Self-defined temperature. More...

double	tol_
	The tolerance criteria for the system .

bool	bounds_
	A variable to check to see if the simulation is in bounds or not.

bool	convergeExit_
	A check to see if you want the system to end when it reaches the convergence criteria.

std::string	bnme_

unsigned int	iteration_
	Iteration counter.

Additional Inherited Members
Protected Attributes inherited from SSAGES::Method
mxx::comm	world_
	Global MPI communicator.

mxx::comm	comm_
	Local MPI communicator.

std::vector< unsigned int >	cvmask_
	Mask which identifies which CVs to act on.

Detailed Description

Basis Function Sampling Algorithm.

Implementation of the Basis Function Sampling Method based on [5].

Definition at line 38 of file BasisFunc.h.

Constructor & Destructor Documentation

◆ BFS()

SSAGES::BFS::BFS	(	const MPI_Comm &	world,
		const MPI_Comm &	comm,
		Grid< unsigned int > *	h,
		Grid< std::vector< double >> *	f,
		Grid< double > *	b,
		const std::vector< BasisFunction * > &	functions,
		const std::vector< double > &	restraint,
		const std::vector< double > &	boundUp,
		const std::vector< double > &	boundLow,
		unsigned int	cyclefreq,
		unsigned int	frequency,
		const std::string	bnme,
		const double	temperature,
		const double	tol,
		const double	weight,
		bool	converge
	)

inline

Constructor.

Parameters

world	MPI global communicator.
comm	MPI local communicator.
h	Grid containing histogram.
f	Grid containing histogram.
b	Grid containing histogram.
functions	Vector of basis functions.
restraint	Restraint spring constants.
boundUp	Upper bounds of restraint springs.
boundLow	Lower bounds of restraint springs.
cyclefreq	Cycle frequency.
frequency	Frequency with which this Method is applied.
bnme	Basis file name.
temperature	Automatically set temperature.
tol	Threshold for tolerance criterion.
weight	Weight for improved sampling.
converge	If `True` quit on convergence.

Constructs an instance of the Basis function sampling method. The coefficients describe the basis projection of the system. This is updated once every cyclefreq_. For now, only the Legendre polynomial is implemented. Others will be added later.

Definition at line 181 of file BasisFunc.h.

                            :
         Method(frequency, world, comm), 
         h_(h),  b_(b), f_(f), unbias_(), coeffArr_(), evaluator_(functions),
         restraint_(restraint), boundUp_(boundUp), boundLow_(boundLow),
         cyclefreq_(cyclefreq), mpiid_(0), weight_(weight),
         temperature_(temperature), tol_(tol),
         convergeExit_(converge), bnme_(bnme), iteration_(0)
         {
         }

Member Function Documentation

◆ Build()

BFS * SSAGES::BFS::Build	(	const Json::Value &	json,
		const MPI_Comm &	world,
		const MPI_Comm &	comm,
		const std::string &	path
	)

static

Build a derived method from JSON node.

Parameters

json	JSON Value containing all input information.
world	MPI global communicator.
comm	MPI local communicator.
path	Path for JSON path specification.

Returns: Pointer to the Method built. nullptr if an unknown error occurred.

This function builds a registered method from a JSON node. The difference between this function and "Build" is that this automatically determines the appropriate derived type based on the JSON node information.

Note: Object lifetime is the caller's responsibility.

Definition at line 308 of file BasisFunc.cpp.

     {
         ObjectRequirement validator;
         Value schema;
         CharReaderBuilder rbuilder;
         CharReader* reader = rbuilder.newCharReader();
  
         reader->parse(JsonSchema::BFSMethod.c_str(),
                       JsonSchema::BFSMethod.c_str() + JsonSchema::BFSMethod.size(),
                       &schema, nullptr);
         validator.Parse(schema, path);
  
         //Validate Inputs
         validator.Validate(json, path);
         if(validator.HasErrors())
             throw BuildException(validator.GetErrors());
  
         std::vector<double> restrCV(0);
         for(auto& restr : json["CV_restraint_spring_constants"])
             restrCV.push_back(restr.asDouble());
  
         std::vector<double> boundLow(0);
         for(auto& bndl : json["CV_restraint_minimums"])
             boundLow.push_back(bndl.asDouble());
     
         std::vector<double> boundUp(0);
         for(auto& bndu : json["CV_restraint_maximums"])
             boundUp.push_back(bndu.asDouble());
  
         auto cyclefreq = json.get("cycle_frequency", 100000).asInt();
         auto freq = json.get("frequency", 1).asInt();
         auto wght = json.get("weight", 1.0).asDouble();
         auto bnme = json.get("basis_filename", "").asString();
         auto temp = json.get("temperature", 0.0).asDouble();
         auto tol  = json.get("tolerance", 1e-6).asDouble();
         auto conv = json.get("convergence_exit", false).asBool();
  
         Grid<unsigned int> *h = Grid<unsigned int>::BuildGrid(
                                         json.get("grid", Json::Value()) );
  
         Grid<std::vector<double>> *f = Grid<std::vector<double>>::BuildGrid(
                                         json.get("grid", Json::Value()) );
  
         Grid<double> *b = Grid<double>::BuildGrid(
                                         json.get("grid", Json::Value()) );
  
         size_t ii = 0;
         std::vector<BasisFunction*> functions;
         for(auto& m : json["basis_functions"])
         {
             auto *bf = BasisFunction::Build(m, path, b->GetNumPoints(ii));
             functions.push_back(bf);
             ii++;
         }
  
         // If restraints were not specified then set them equal to zero
         if (restrCV.size() == 0) {
             // Choose simplest array that should have equivalent size
             for(size_t i = 0; i<functions.size(); i++)
                 restrCV.push_back(0); // Push back value of 0
         }
  
         // This also needs to be the same for upper bounds and lower bounds
         if (boundLow.size() == 0) {
             // Choose simplest array that should have equivalent size
             for(size_t i = 0; i<functions.size(); i++)
                 boundLow.push_back(0); // Push back value of 0
         }
  
         // This also needs to be the same for upper bounds and lower bounds
         if (boundUp.size() == 0) {
             // Choose simplest array that should have equivalent size
             for(size_t i = 0; i<functions.size(); i++)
                 boundUp.push_back(0); // Push back value of 0
         }
  
         // Check to make sure that the arrays for boundaries and restraints are of the same length
         if (boundUp.size() != boundLow.size() && boundLow.size() != restrCV.size()) {
             std::cerr<<"ERROR: Number of restraint boundaries do not match number of spring constants."<<std::endl;
             std::cerr<<"Boundary size is " << boundUp.size() << " boundary low size is " << boundLow.size() << " restraints size is" << restrCV.size() << std::endl;
             MPI_Abort(world, EXIT_FAILURE);
         }
  
         auto* m = new BFS(world, comm, h, f, b, functions, restrCV, boundUp, boundLow,
                             cyclefreq, freq, bnme, temp, tol, wght,
                             conv);
       
         if(json.isMember("iteration"))
             m->SetIteration(json.get("iteration",0).asInt());
  
         // Check if previously saved grids exist. If so, check that data match and load grids.
         std::ifstream restrFile;
         restrFile.open("restart"+bnme+".out");
         if(restrFile.is_open())
         {
             std::string line;
             std::vector<double> coeff;
             std::vector<double> unbias;
             bool coeffFlag = false;
             bool basisFlag = false;
             std::cout << "Attempting to load data from a previous run of BFS." << std::endl;
  
             while(!std::getline(restrFile,line).eof()) 
             {
                 if(line.find("COEFFICIENTS") != std::string::npos) {
                     std::getline(restrFile,line);
                     coeffFlag = true;
                 }
                 else if (line.find("HISTOGRAM") != std::string::npos) {
                     std::getline(restrFile,line);
                     basisFlag = true;
                     coeffFlag = false;
                 }
                 if(coeffFlag) {
                     coeff.push_back(std::stod(line));
                 }
                 else if (basisFlag) { 
                     unbias.push_back(std::stod(line));
                 }
             }
             m->SetBasis(coeff, unbias);
             restrFile.close();
         }
  
         return m;
     }

References Json::Requirement::GetErrors(), SSAGES::GridBase< T >::GetNumPoints(), Json::Requirement::HasErrors(), Json::ObjectRequirement::Parse(), and Json::ObjectRequirement::Validate().

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◆ InBounds()

void SSAGES::BFS::InBounds ( const CVList & cvs )

private

A function which checks to see if the CVs are still in bounds.

Parameters

cvs	List of CVs to check

Definition at line 272 of file BasisFunc.cpp.

     {   
         std::vector<double> x (cvs.size(),0);
         //This is calculating the derivatives for the bias force
         for (size_t j = 0; j < cvs.size(); ++j)
         {
             x[j] = cvs[j]->GetValue();
             double min = h_->GetLower(j);
             double max = h_->GetUpper(j);
  
             if(!h_->GetPeriodic(j))
             {
                 // In order to prevent the index for the histogram from going out of bounds a check is in place
                 if(x[j] > max && bounds_)
                 {
                     //std::cout<<"WARNING: CV is above the maximum boundary."<<std::endl;
                     //std::cout<<"Statistics will not be gathered during this interval"<<std::endl;
                     bounds_ = false;
                     break;
                 }
                 else if(x[j] < min && bounds_)
                 {
                     //std::cout<<"WARNING: CV is below the minimum boundary."<<std::endl;
                     //std::cout<<"Statistics will not be gathered during this interval"<<std::endl;
                     bounds_ = false;
                     break;
                 }
                 else if(x[j] < max && x[j] > min && !bounds_)
                 {
                     //std::cout<<"CV has returned in between bounds. Run is resuming"<<std::endl;
                     bounds_ = true;
                 }
             }
         }
     }

◆ PostIntegration()

void SSAGES::BFS::PostIntegration	(	Snapshot *	snapshot,
		const class CVManager &	cvmanager
	)

overridevirtual

Method call post integration.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called after each integration step.

Implements SSAGES::Method.

Definition at line 81 of file BasisFunc.cpp.

     {
         auto cvs = cvmanager.GetCVs(cvmask_);        
         std::vector<double> x(cvs.size(),0);
  
         /*The binned cv space is updated at every step
          *After a certain number of steps has been passed, the system updates a
          *bias projection based on the visited histogram states
          */
         for(size_t i = 0; i < cvs.size(); ++i)
         {
             x[i] = cvs[i]->GetValue();
         }
        
         // The histogram is updated based on the index
         InBounds(cvs);
         if (bounds_) {h_->at(x) += 1;}
         else {cyclefreq_++;}
     
         // Update the basis projection after the requisite number of steps
         int steps = snapshot->GetIteration()-step_;
         if(steps  % cyclefreq_ == 0) {
             step_ = snapshot->GetIteration();
             cyclefreq_ = cyclefreqTmp_;
             double beta;
             beta = 1.0 / (temperature_ * snapshot->GetKb());
  
             // For systems with poorly defined temperature (ie: 1 particle) the
             // user needs to define their own temperature. This is a hack that
             // will be removed in future versions.
  
             iteration_+= 1;
             ProjectBias(cvs,beta);
             std::cout<<"Node: ["<<mpiid_<<"]"<<std::setw(10)<<"\tSweep: "<<iteration_<<std::endl;
         }
  
         // This gets the bias force from the grid
         std::vector<double> bias_grad(cvs.size(),0);
  
         if (bounds_) 
         {
             auto& bias = f_->at(x); 
             for (size_t ii = 0; ii<bias.size(); ii++)
                 bias_grad[ii] = bias[ii];
         }
         else 
         {
             // This is where the wall potentials are going to be thrown into the method if the system is not a periodic CV
             for(size_t j = 0; j < cvs.size(); ++j)
             {
                 if(!h_->GetPeriodic(j))
                 {
                     if(x[j] > boundUp_[j])
                         bias_grad[j] = -restraint_[j] * (x[j] - boundUp_[j]);
                     else if(x[j] < boundLow_[j])
                         bias_grad[j] = restraint_[j] * (x[j] - boundLow_[j]);
                 }
             }
         }
  
         // Take each CV and add its biased forces to the atoms using the chain rule
         auto& forces = snapshot->GetForces();
         auto& virial = snapshot->GetVirial();
         for(size_t i = 0; i < cvs.size(); ++i)
         {
             auto& grad = cvs[i]->GetGradient();
             auto& boxgrad = cvs[i]->GetBoxGradient();
  
             /* Update the forces in snapshot by adding in the force bias from each
              *CV to each atom based on the gradient of the CV.
              */
             for (size_t j = 0; j < forces.size(); ++j) 
                 forces[j] += bias_grad[i]*grad[j];
             
             virial -= bias_grad[i]*boxgrad;
         }
     }

References SSAGES::CVManager::GetCVs(), SSAGES::Snapshot::GetForces(), SSAGES::Snapshot::GetIteration(), SSAGES::Snapshot::GetKb(), and SSAGES::Snapshot::GetVirial().

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◆ PostSimulation()

void SSAGES::BFS::PostSimulation	(	Snapshot *	snapshot,
		const class CVManager &	cvmanager
	)

overridevirtual

Method call post simulation.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called after the end of the simulation run.

Implements SSAGES::Method.

Definition at line 160 of file BasisFunc.cpp.

     {
         std::cout<<"Run has finished"<<std::endl;   
     }

◆ PreSimulation()

void SSAGES::BFS::PreSimulation	(	Snapshot *	snapshot,
		const class CVManager &	cvmanager
	)

overridevirtual

Method call prior to simulation initiation.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called before the simulation is started.

Implements SSAGES::Method.

Definition at line 36 of file BasisFunc.cpp.

     {
         auto cvs = cvmanager.GetCVs(cvmask_);
         // For print statements and file I/O, the walker IDs are used
         mpiid_ = snapshot->GetWalkerID();
  
         // Make sure the iteration index is set correctly
         iteration_ = 0;
         step_ = 0;
  
         // Set the temporary sweep frequency to the same as the input
         cyclefreqTmp_ = cyclefreq_;
  
         // There are a few error messages / checks that are in place with
         // defining CVs and grids
         if(h_->GetDimension() != cvs.size())
         {
             std::cerr<<"ERROR: Grid dimensions doesn't match number of CVS."<<std::endl;
             MPI_Abort(world_, EXIT_FAILURE);
         }
  
         // This is to check for non-periodic bounds. It comes into play in the update bias function
         bounds_ = true;        
         unbias_.resize(h_->size(),0);
         std::fill(unbias_.begin(),unbias_.end(),1.0);
  
         // Initialize the mapping for the hist function
         for (auto &val : *h_) {
             val = 0;
         }
  
         // Reset the values in the force grid
         for (auto &val : *f_) {
             for (size_t i = 0; i <val.size(); i++) {
                 val[i] = 0;
             }
         }
  
         // Reset the values in the bias potential grid
         for (auto &val : *b_) {
             val = 0;
         }
     }

References SSAGES::CVManager::GetCVs(), and SSAGES::Snapshot::GetWalkerID().

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◆ PrintBias()

void SSAGES::BFS::PrintBias	(	const CVList &	cvs,
		const double	beta
	)

private

Prints the current bias to a defined file from the JSON.

Parameters

cvs	List of collective variables.
beta	Scale parameter.

Definition at line 227 of file BasisFunc.cpp.

     {
         // The filenames will have a standard name, with a user-defined suffix
         std::string filename1 = "basis"+bnme_+".out"; 
         std::string filename2 = "restart"+bnme_+".out";
         std::ofstream basisout;
         std::ofstream coeffout;
         basisout.precision(5);
         coeffout.precision(5);
         basisout.open(filename1.c_str());
         coeffout.open(filename2.c_str());
  
         // The CV values, PMF projection, PMF, and biased histogram are output for the user
         basisout << "The information stored in this file is the output of a Basis Function Sampling run" << std::endl;
         basisout << "CV Values" << std::setw(15*cvs.size()) << "Basis Set Bias" << std::setw(15) << "PMF Estimate" << std::endl;
         coeffout << "The information stored in this file is for the purpose of restarting simulations with BFS" << std::endl;
         coeffout << "***COEFFICIENTS***" << std::endl;
         
         size_t j = 0;
         for(Grid<double>::iterator it = b_->begin(); it != b_->end(); ++it, ++j)
         {
             for(size_t k = 0; k < cvs.size(); ++k)
             {
                 // Evaluate the CV values for printing purposes
                 basisout << it.coordinate(k) << std::setw(15);
             }
             basisout << -(*it) << std::setw(15) <<
                         -1.0/beta*log(unbias_[j]) << 
                         std::endl;
         }
  
         std::vector<double> coeff = evaluator_.GetCoeff();
         for (auto& val : coeff) {
             coeffout << val << std::endl;
         }
         coeffout << "***HISTOGRAM***" << std::endl;
         for (auto& val : unbias_) {
             coeffout << val << std::endl;
         }
  
         basisout.close();
         coeffout.close();
     }

References SSAGES::Grid< T >::begin().

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◆ ProjectBias()

void SSAGES::BFS::ProjectBias	(	const CVList &	cvs,
		const double	beta
	)

private

The functions which calculates the updated bias and coefficients and then stores them.

Parameters

cvs	List of CVs onto which the bias is projected
beta	Thermodynamic beta (1/kT)

Definition at line 166 of file BasisFunc.cpp.

     {
         double sum  = 0.0;
  
         // For multiple walkers, the struct is unpacked
         Grid<unsigned int> histlocal(*h_);
  
         // Summed between all walkers
         MPI_Allreduce(histlocal.data(), h_->data(), h_->size(), MPI_INT, MPI_SUM, world_);
  
         h_->syncGrid();
  
         // Construct the biased histogram
         size_t i = 0;
         for (Grid<unsigned int>::iterator it2 = h_->begin(); it2 != h_->end(); ++it2, ++i)
         {
             /* The evaluation of the biased histogram which projects the histogram to the
              * current bias of CV space.
              */
             unbias_[i] += (*it2) * exp(beta * b_->at(it2.coordinates()));
         }
  
         // Reset histogram
         for (auto &val : *h_) {
             val = 0;
         }
  
         // Create the log array and send that to the integrator
         std::vector<double> z (unbias_.size(),0);
         for (i = 0; i < unbias_.size(); i++)
             // Make sure the log of the biased histogram is a number
             z[i] = 1.0/beta*log(unbias_[i] * weight_);
  
         //Update the coefficients and determine the difference from the previous iteration
         sum = evaluator_.UpdateCoeff(z,h_);
         coeffArr_ = evaluator_.GetCoeff();
         //Update both the gradient and the bias on the grids
         evaluator_.UpdateBias(b_,f_);
  
         if(IsMasterRank(world_)) {
             // Write coeff at this step, but only one walker
             std::cout<<"Coefficient difference is: " <<sum<<std::endl;
             PrintBias(cvs,beta);
         }
  
         // The convergence tolerance and whether the user wants to exit are incorporated here
         if(sum < tol_)
         {
             std::cout<<"System has converged"<<std::endl;
             if(convergeExit_)
             {
                 std::cout<<"User has elected to exit. System is now exiting"<<std::endl;
                 exit(EXIT_SUCCESS);
             }
         }
     }

References SSAGES::Grid< T >::begin(), and SSAGES::GridBase< T >::data().

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◆ SetBasis()

void SSAGES::BFS::SetBasis	(	const std::vector< double > &	coeff,
		std::vector< double > &	unbias
	)

inline

Set the values for the basis.

Parameters

coeff	List of coefficients.
unbias	List of unbiased values.

This function is used to set starting values at the beginning of a run. For example when continuing from a restart value.

Definition at line 235 of file BasisFunc.h.

         {
             evaluator_.SetCoeff(coeff);
             unbias_ = unbias;
         }

References evaluator_, SSAGES::BasisEvaluator::SetCoeff(), and unbias_.

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◆ SetIteration()

void SSAGES::BFS::SetIteration ( const int iter )

inline

Set the current iteration.

Parameters

iter	New value for the current iteration.

This function is used to set the current iteration, for example when continuing from a restart.

Definition at line 222 of file BasisFunc.h.

         {
             iteration_ = iter;
         }

References iteration_.

Member Data Documentation

◆ b_

Grid<double>* SSAGES::BFS::b_

private

Stored bias potential.

The sum of basis functions that adds up to the bias potential of the surface

Definition at line 52 of file BasisFunc.h.

◆ bnme_

std::string SSAGES::BFS::bnme_

private

The option to name both the basis and coefficient files will be given Basis filename

Definition at line 151 of file BasisFunc.h.

◆ evaluator_

BasisEvaluator SSAGES::BFS::evaluator_

private

The basis evaluator class.

A class which holds the basis functions and updates the coefficients at each cycle

Definition at line 76 of file BasisFunc.h.

Referenced by SetBasis().

◆ f_

Grid<std::vector<double> >* SSAGES::BFS::f_

private

Stored gradients.

The gradients corresponding to each point on the grid

Definition at line 58 of file BasisFunc.h.

◆ h_

Grid<unsigned int>* SSAGES::BFS::h_

private

Grid of visited states.

Grid is stored locally.

Definition at line 46 of file BasisFunc.h.

◆ restraint_

std::vector<double> SSAGES::BFS::restraint_

private

Spring constants for restrained system.

The system uses this to determine if the system is to be restrained on the defined interval. The user inputs the spring constants if the system is not periodic.

Definition at line 84 of file BasisFunc.h.

◆ temperature_

double SSAGES::BFS::temperature_

private

Self-defined temperature.

In the case of the MD engine using a poorly defined temperature, the option to throw it into the method is available. If not provided it takes the value from the engine.

Definition at line 118 of file BasisFunc.h.

◆ unbias_

std::vector<double> SSAGES::BFS::unbias_

private

The biased histogram of states.

The biased histogram of states has the form hist_*exp(phi*beta), where phi is the bias potential and beta is the inverse of the temperature. It is defined globally.

Definition at line 66 of file BasisFunc.h.

Referenced by SetBasis().

◆ weight_

double SSAGES::BFS::weight_

private

Weighting for potentially faster sampling.

Weighting can be used to potentially sample faster, however it can cause the simulation to explode. By default this value will be set to 1.0

Definition at line 110 of file BasisFunc.h.

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

/home/michael/development/SSAGES/src/Methods/BasisFunc.h
/home/michael/development/SSAGES/src/Methods/BasisFunc.cpp

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BFS()

Member Function Documentation

◆ Build()

◆ InBounds()

◆ PostIntegration()

◆ PostSimulation()

◆ PreSimulation()

◆ PrintBias()

◆ ProjectBias()

◆ SetBasis()

◆ SetIteration()

Member Data Documentation

◆ b_

◆ bnme_

◆ evaluator_

◆ f_

◆ h_

◆ restraint_

◆ temperature_

◆ unbias_

◆ weight_