Stimulus.h

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///////////////////////////////////////////////////////////////////////////////
//
// File: Stimulus.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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// DEALINGS IN THE SOFTWARE.
//
// Description: Stimulus base class header.
//
///////////////////////////////////////////////////////////////////////////////
 
#ifndef NEKTAR_SOLVERS_CARDIACEPSOLVER_STIMULI_STIMULUS
#define NEKTAR_SOLVERS_CARDIACEPSOLVER_STIMULI_STIMULUS
 
#include <CardiacEPSolver/Stimuli/Protocol.h>
#include <LibUtilities/BasicUtils/NekFactory.hpp>
#include <LibUtilities/BasicUtils/SessionReader.h>
#include <LibUtilities/BasicUtils/SharedArray.hpp>
#include <MultiRegions/ExpList.h>
#include <SolverUtils/Core/Misc.h>
 
namespace Nektar
{
// Forward declaration
class Stimulus;
 
/// A shared pointer to an EquationSystem object
typedef std::shared_ptr<Stimulus> StimulusSharedPtr;
 
/// Datatype of the NekFactory used to instantiate classes derived from
/// the EquationSystem class.
typedef LibUtilities::NekFactory<
    std::string, Stimulus, const LibUtilities::SessionReaderSharedPtr &,
    const MultiRegions::ExpListSharedPtr &, const TiXmlElement *>
    StimulusFactory;
 
StimulusFactory &GetStimulusFactory();
 
/// Stimulus base class.
class Stimulus
{
public:
    virtual ~Stimulus()
    {
    }
 
    /// Initialise the stimulus storage and set initial conditions
    void Initialise();
 
    /// Updates RHS of outarray by adding a stimulus to it
    void Update(Array<OneD, Array<OneD, NekDouble>> &outarray,
                const NekDouble time)
    {
        v_Update(outarray, time);
    }
 
    /// Print a summary of the outarray
    void GenerateSummary(SolverUtils::SummaryList &s)
    {
        v_GenerateSummary(s);
    }
 
    static std::vector<StimulusSharedPtr> LoadStimuli(
        const LibUtilities::SessionReaderSharedPtr &pSession,
        const MultiRegions::ExpListSharedPtr &pField);
 
protected:
    /// Session
    LibUtilities::SessionReaderSharedPtr m_session;
    /// Transmembrane potential field from PDE system
    MultiRegions::ExpListSharedPtr m_field;
    /// Number of physical points.
    int m_nq;
    /// Stimulus protocol to apply
    ProtocolSharedPtr m_Protocol;
 
    Stimulus(const LibUtilities::SessionReaderSharedPtr &pSession,
             const MultiRegions::ExpListSharedPtr &pField,
             const TiXmlElement *pXml);
 
    virtual void v_Update(Array<OneD, Array<OneD, NekDouble>> &outarray,
                          const NekDouble time) = 0;
 
    virtual void v_GenerateSummary(SolverUtils::SummaryList &s) = 0;
};
} // namespace Nektar
 
#endif