Swarm of Trajectories String Method. More...

#include <Swarm.h>

Inheritance diagram for SSAGES::Swarm:

Public Member Functions
	Swarm (const MPI_Comm &world, const MPI_Comm &comm, const std::vector< double > &centers, unsigned int maxiterations, const std::vector< double > cvspring, unsigned int frequency, unsigned int InitialSteps, unsigned int HarvestLength, unsigned int NumberTrajectories, unsigned int SwarmLength)
	Constructor. More...

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

	~Swarm ()
	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 positions of the string.

bool	CVInitialized (const CVList &cvs)
	Helper function check if CVs are initialized correctly.

Private Attributes
std::vector< double >	cv_drift_
	Drift of CVs for one iteration.

unsigned int	initialize_steps_
	Total number of MD steps for initialization for one iteration.

unsigned int	harvest_length_
	Length to run before harvesting a trajectory for unrestrained sampling.

unsigned int	restrained_steps_
	Total number of restrained MD steps for one iteration.

unsigned int	number_trajectories_
	Number of trajectories per swarm.

unsigned int	swarm_length_
	Length of unrestrained trajectories.

unsigned int	unrestrained_steps_
	Total number of unrestrained MD steps for one iteration.

unsigned int	index_
	For indexing trajectory vectors.

std::vector< Label >	traj_atomids_
	Store atom IDs for starting trajecotires.

bool	sampling_started
	Flag for determing whether to perform initialization or not.

bool	snapshot_stored
	Flag for whether a snapshot was stored in the umbrella sampling.

int	initialized
	Flag for whether a system is initialized at a given iteration.

bool	original_initialized
	Flag for whether a system was initialized before it checked whether other systems were.

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

Swarm of Trajectories String Method.

Implementation of the swarm of trajectories string method.

Definition at line 32 of file Swarm.h.

Constructor & Destructor Documentation

SSAGES::Swarm::Swarm	(	const MPI_Comm &	world,
		const MPI_Comm &	comm,
		const std::vector< double > &	centers,
		unsigned int	maxiterations,
		const std::vector< double >	cvspring,
		unsigned int	frequency,
		unsigned int	InitialSteps,
		unsigned int	HarvestLength,
		unsigned int	NumberTrajectories,
		unsigned int	SwarmLength
	)

inline

Constructor.

Parameters

world	MPI global communicator.
comm	MPI local communicator.
centers	List of centers.
maxiterations	Maximum number of iterations.
cvspring	Spring constants for CVs.
frequency	Aplly method with this frequency.
InitialSteps	Number of initial steps.
HarvestLength	Length of trajectory before weighing.
NumberTrajectories	Number of trajectories.
SwarmLength	Lengt of the swarms.

Constructs an instance of the swarm of trajectories method.

Definition at line 98 of file Swarm.h.

References SSAGES::StringMethod::centers_, cv_drift_, harvest_length_, index_, SSAGES::StringMethod::iterator_, number_trajectories_, SSAGES::StringMethod::prev_IDs_, SSAGES::StringMethod::prev_positions_, SSAGES::StringMethod::prev_velocities_, restrained_steps_, sampling_started, snapshot_stored, swarm_length_, and unrestrained_steps_.

                                             : 
             StringMethod(world, comm, centers, maxiterations, cvspring, frequency),                 
             cv_drift_(), 
             initialize_steps_(InitialSteps), 
             harvest_length_(HarvestLength), 
             number_trajectories_(NumberTrajectories), 
             swarm_length_(SwarmLength)
             {
                 cv_drift_.resize(centers_.size(), 0);
                 prev_positions_.resize(number_trajectories_);
                 prev_velocities_.resize(number_trajectories_);
                 prev_IDs_.resize(number_trajectories_);
                 //Additional initializing
 
                 index_ = 0;  
                 restrained_steps_ = harvest_length_*number_trajectories_; 
                 unrestrained_steps_ = swarm_length_*number_trajectories_;
                 sampling_started = false;
                 snapshot_stored = false;
 
                 iterator_ = 0; //Override default StringMethod.h initializing
             }

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

/home/cody/SSAGES/src/Methods/Swarm.h
/home/cody/SSAGES/src/Methods/Swarm.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation