Multi-walker Elastic Band. More...

#include <ElasticBand.h>

Inheritance diagram for SSAGES::ElasticBand:

Public Member Functions
	ElasticBand (const MPI_Comm &world, const MPI_Comm &comm, const std::vector< double > &centers, unsigned int maxiterations, unsigned int nsamples, double tau, const std::vector< double > cvspring, unsigned int equilibrate, unsigned int evolution, double stringspring, unsigned int frequency)
	Constructor. More...

void	PostIntegration (Snapshot *snapshot, const class CVManager &cvmanager) override
	Post-integration hook. More...

	~ElasticBand ()
	Destructor.

Public Member Functions inherited from SSAGES::StringMethod
	StringMethod (const MPI_Comm &world, const MPI_Comm &comm, const std::vector< double > &centers, unsigned int maxiterations, const std::vector< double > cvspring, unsigned int frequency)
	Constructor. More...

void	PreSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
	Pre-simulation hook.

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

void	SetTolerance (std::vector< double > tol)
	Set the tolerance for quitting method. More...

void	SetSendRecvNeighbors ()
	Communicate neighbor lists over MPI.

virtual	~StringMethod ()
	Destructor.

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

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

virtual	~Method ()
	Destructor.

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

uint	GetFrequency () const
	Get frequency of event listener. More...

virtual	~EventListener ()
	Destructor.

Private Member Functions
void	StringUpdate ()
	Updates the nudged elastic band string.

Private Attributes
unsigned int	equilibrate_

unsigned int	evolution_

unsigned int	nsamples_
	Block iterations.

unsigned int	nsampled_
	Number samples actually sampled.

double	tau_
	Time step of string change.

double	stringspring_
	String spring constant.

Additional Inherited Members
Static Public Member Functions inherited from SSAGES::StringMethod
static StringMethod *	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...

Protected Member Functions inherited from SSAGES::StringMethod
double	distance (const std::vector< double > &x, const std::vector< double > &y) const
	Helper function for calculating distances. More...

void	PrintString (const CVList &CV)
	Prints the CV positions to file.

void	GatherNeighbors (std::vector< double > lcv0, std::vector< double > ucv0)
	Gather neighbors over MPI. More...

void	StringReparam (double alpha_star)
	Reparameterize the string. More...

void	UpdateWorldString (const CVList &cvs)
	Update the world string over MPI. More...

bool	TolCheck () const
	Check whether tolerance criteria has been met.

bool	CheckEnd (const CVList &CV)
	Check if method reached one of the exit criteria. More...

Protected Attributes inherited from SSAGES::StringMethod
std::vector< double >	centers_
	CV starting location values.

std::vector< double >	newcenters_
	CV starting location values.

std::vector< std::vector < double > >	worldstring_
	The world's strings centers for each CV. More...

int	mpiid_
	The node this belongs to.

std::vector< double >	tol_
	Tolerance criteria for determining when to stop string (default 0 if no tolerance criteria)

int	numnodes_
	Number of nodes on a string.

unsigned int	maxiterator_
	Maximum cap on number of string method iterations performed.

std::vector< double >	cvspring_
	Vector of spring constants.

unsigned int	iterator_
	The local method iterator.

uint	iteration_
	The global method iteration.

std::ofstream	stringout_
	Output stream for string data.

int	sendneigh_
	Neighbor to send info to.

int	recneigh_
	Neighbor to gain info from.

std::vector< std::vector < double > >	prev_positions_
	Store positions for starting trajectories.

std::vector< std::vector < double > >	prev_velocities_
	Store velocities for starting trajectories.

std::vector< std::vector< int > >	prev_IDs_
	Store atom IDs for starting trajectories.

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

mxx::comm	comm_
	Local MPI communicator.

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

Detailed Description

Multi-walker Elastic Band.

Implementation of a multi-walker Elastic Band method with no bells and whistles.

Definition at line 34 of file ElasticBand.h.

Constructor & Destructor Documentation

SSAGES::ElasticBand::ElasticBand	(	const MPI_Comm &	world,
		const MPI_Comm &	comm,
		const std::vector< double > &	centers,
		unsigned int	maxiterations,
		unsigned int	nsamples,
		double	tau,
		const std::vector< double >	cvspring,
		unsigned int	equilibrate,
		unsigned int	evolution,
		double	stringspring,
		unsigned int	frequency
	)

inline

Constructor.

Parameters

world	MPI global communicator.
comm	MPI local communicator.
centers	List of centers.
maxiterations	Maximum number of iterations.
nsamples	Number of samples to collect before updating string.
tau	Value of tau (default: 0.1).
cvspring	Spring constants for cvs.
equilibrate	Number of MD steps to allow the system to reequilibrate after updating string.
evolution	Number of MD steps to allow the system to evolve before gathering statistics.
stringspring	Spring constant used between nodes.
frequency	Frequency with which this method is invoked.

Constructs an instance of Elastic Band method.

Definition at line 77 of file ElasticBand.h.

                                             : 
         StringMethod(world, comm, centers, maxiterations,
         cvspring, frequency), equilibrate_(equilibrate),
         evolution_(evolution), nsamples_(nsamples),
         nsampled_(0), tau_(tau), stringspring_(stringspring)
         {
         }

Member Function Documentation

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

overridevirtual

Post-integration hook.

Parameters

snapshot	Current simulation snapshot.
cvmanager	Collective variable manager.

Implements SSAGES::StringMethod.

Definition at line 30 of file ElasticBand.cpp.

References SSAGES::StringMethod::centers_, SSAGES::StringMethod::CheckEnd(), SSAGES::Method::cvmask_, SSAGES::StringMethod::cvspring_, equilibrate_, evolution_, SSAGES::CVManager::GetCVs(), SSAGES::Snapshot::GetForces(), SSAGES::StringMethod::iteration_, SSAGES::StringMethod::iterator_, SSAGES::StringMethod::newcenters_, nsampled_, nsamples_, SSAGES::StringMethod::PrintString(), StringUpdate(), and SSAGES::StringMethod::UpdateWorldString().

     {
         auto& forces = snapshot->GetForces();
         auto cvs = cvmanager.GetCVs(cvmask_);
 
         // Apply umbrella to cvs
         for(size_t i = 0; i < cvs.size(); ++i)
         {
             // Get current CV and gradient.
             auto& cv = cvs[i];
             auto& grad = cv->GetGradient();
 
             // Compute dV/dCV.
             auto diff = cv->GetDifference(centers_[i]);
             auto D = cvspring_[i] * diff;
 
             // Update forces.
             for(size_t j = 0; j < forces.size(); ++j)
                 for(int k = 0; k < forces[j].size(); ++k)
                     forces[j][k] -= D*grad[j][k];
 
             // If not equilibrating and has evolved enough steps,
             // generate the gradient
             if(iterator_ >= equilibrate_ && iterator_ % evolution_ == 0)
             {
                 newcenters_[i] += diff;
                 nsampled_++;
             }
         }
 
         // Restart iteration and zero gradients when moving onto
         // next elastic band iteration
         if(iterator_ > (equilibrate_ + evolution_ * nsamples_))
         {   
             StringUpdate();
             CheckEnd(cvs);
             UpdateWorldString(cvs); 
             PrintString(cvs); 
 
             iterator_ = 0;
 
             for(size_t ii = 0; ii < newcenters_.size(); ii++)
                 newcenters_[ii] = 0;
 
             nsampled_ = 0;
             iteration_++;
         }
 
         iterator_++;
     }