Interface for Method implementations. More...

#include <Method.h>

Inheritance diagram for SSAGES::Method:

Public Member Functions
	Method (uint 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< 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.

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...

Protected Attributes
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

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

SSAGES::Method::Method	(	uint	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

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 38 of file Method.cpp.

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

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

     {
         ObjectRequirement validator;
         Value schema;
         Reader reader;
         
         reader.parse(JsonSchema::Method, schema);
         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"] == "Basis")
             method = Basis::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<uint> cvmask; 
         for(auto& v : json["cvs"])
         {
             if(v.isString())
             {
                 auto id = CVManager::LookupCV(v.asString());
                 if(id == -1)
                     throw std::invalid_argument(path + ": CV mask name \"" + v.asString() + "\" does not exist.");
                 
                 cvmask.push_back(CVManager::LookupCV(v.asString()));
             }
             else if(v.isIntegral() && v.asInt() >= 0)
                 cvmask.push_back(v.asUInt());
             else
                 throw std::invalid_argument(path + ": CV mask must contain strings or unsigned integers.");
 
         }
         
         method->SetCVMask(cvmask);
         return method;
     }

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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::ForwardFlux, SSAGES::Basis, SSAGES::ABF, SSAGES::StringMethod, SSAGES::Meta, SSAGES::Umbrella, SSAGES::Swarm, SSAGES::FiniteTempString, SSAGES::ElasticBand, and SSAGES::DirectForwardFlux.

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::ForwardFlux, SSAGES::Basis, SSAGES::ABF, SSAGES::StringMethod, SSAGES::Meta, and SSAGES::Umbrella.

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::ForwardFlux, SSAGES::Basis, SSAGES::ABF, SSAGES::StringMethod, SSAGES::Meta, and SSAGES::Umbrella.

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

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation