SSAGES::Method Class Reference

Interface for Method implementations. More...

#include <Method.h>

Inheritance diagram for SSAGES::Method:

Public Member Functions
	Method (unsigned int frequency, const MPI_Comm &world, const MPI_Comm &comm)
	Constructor. More...
virtual void	PreSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override=0
	Method call prior to simulation initiation. More...
virtual void	PostIntegration (Snapshot *snapshot, const class CVManager &cvmanager) override=0
	Method call post integration. More...
virtual void	PostSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override=0
	Method call post simulation. 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 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...

Protected Attributes
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

Interface for Method implementations.

The base method class from which advanced sampling routines derive. A method is allowed to manipulate a simulation at three points: before the simulation begins (usually initialization), after each integration step by the simulation engine, and after the integration steps are complete (usually cleanup).

Definition at line 43 of file Method.h.

Constructor & Destructor Documentation

Method()

SSAGES::Method::Method ( unsigned int  frequency, const MPI_Comm &  world, const MPI_Comm &  comm  )

inline

Constructor.

Parameters

frequency	Frequency of sampling.
world	Global MPI communicator.
comm	MPI communicator of walker.

Frequency of sampling must be specified by all methods.

Definition at line 61 of file Method.h.

                                                                                    :
        EventListener(frequency), world_(world), comm_(comm), cvmask_()
        {}

Member Function Documentation

BuildMethod()

Method * SSAGES::Method::BuildMethod ( 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 40 of file Method.cpp.

    {
        ObjectRequirement validator;
        Value schema;
        CharReaderBuilder rbuilder;
        CharReader* reader = rbuilder.newCharReader();
 
        reader->parse(JsonSchema::Method.c_str(),
                      JsonSchema::Method.c_str() + JsonSchema::Method.size(),
                      &schema, nullptr);
        validator.Parse(schema, path);
        validator.Validate(json, path);
        if(validator.HasErrors())
            throw BuildException(validator.GetErrors());
 
        Method* method = nullptr;
 
        if(json["type"] == "ABF")
            method = ABF::Build(json, world, comm, path);
        else if(json["type"] == "ANN")
            method = ANN::Build(json, world, comm, path);
        else if(json["type"] == "BFSMethod")
            method = BFS::Build(json, world, comm, path);
        else if(json["type"] == "CFF")
            method = CFF::Build(json, world, comm, path);
        else if(json["type"] == "ForwardFlux")
            method = ForwardFlux::Build(json, world, comm, path);
        else if(json["type"] == "Metadynamics")
            method = Meta::Build(json, world, comm, path);
        else if(json["type"] == "Umbrella")
            method = Umbrella::Build(json, world, comm, path);
        else if(json["type"] == "String")
            method = StringMethod::Build(json, world, comm, path);
        else
            throw std::invalid_argument(path + ": Unknown method type specified.");
 
        // Load cv mask.
        std::vector<unsigned int> cvmask;
        for(auto& cv : json["cvs"])
        {
            cvmask.push_back(CVManager::LookupCV(cv, path));
        }
 
        method->SetCVMask(cvmask);
        return method;
    }

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

Referenced by SSAGES::ResourceHandler::Build().

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PostIntegration()

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

overridepure virtual

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::EventListener.

Implemented in SSAGES::StringMethod, SSAGES::ForwardFlux, SSAGES::Umbrella, SSAGES::Swarm, SSAGES::Meta, SSAGES::FiniteTempString, SSAGES::ElasticBand, SSAGES::DirectForwardFlux, SSAGES::CFF, SSAGES::BFS, SSAGES::ANN, and SSAGES::ABF.

PostSimulation()

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

overridepure virtual

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::EventListener.

Implemented in SSAGES::Umbrella, SSAGES::StringMethod, SSAGES::Meta, SSAGES::ForwardFlux, SSAGES::CFF, SSAGES::BFS, SSAGES::ANN, and SSAGES::ABF.

PreSimulation()

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

overridepure virtual

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::EventListener.

Implemented in SSAGES::Umbrella, SSAGES::StringMethod, SSAGES::Meta, SSAGES::ForwardFlux, SSAGES::CFF, SSAGES::BFS, SSAGES::ANN, and SSAGES::ABF.

SetCVMask()

void SSAGES::Method::SetCVMask ( const std::vector< unsigned int > &  mask )

inline

Sets the collective variable mask.

Parameters

mask	Vector mask which contains the indices of which CV to include in the container.

This function sets the Snapshot's CV mask.

Definition at line 99 of file Method.h.

        {
            cvmask_ = mask;
        }

References cvmask_.

Referenced by BuildMethod().

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

• /home/michael/development/SSAGES/src/Methods/Method.h
• /home/michael/development/SSAGES/src/Methods/Method.cpp