#include <StimulusRect.h>

Inheritance diagram for Nektar::StimulusRect:

Collaboration diagram for Nektar::StimulusRect:

Public Member Functions
	StimulusRect (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
virtual	~StimulusRect ()
void	Initialise ()
	Initialise the stimulus storage and set initial conditions.
Public Member Functions inherited from Nektar::Stimulus
	Stimulus (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
virtual	~Stimulus ()
void	Update (Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
	Updates RHS of outarray by adding a stimulus to it.
void	GenerateSummary (SolverUtils::SummaryList &s)
	Print a summary of the outarray.

Static Public Member Functions
static StimulusSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
	Creates an instance of this class.
Static Public Member Functions inherited from Nektar::Stimulus
static std::vector < StimulusSharedPtr >	LoadStimuli (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)

Static Public Attributes
static std::string	className
	Name of class.

Protected Member Functions
virtual void	v_Update (Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
virtual void	v_GenerateSummary (SolverUtils::SummaryList &s)

Protected Attributes
NekDouble	m_px1
NekDouble	m_py1
NekDouble	m_pz1
NekDouble	m_px2
NekDouble	m_py2
NekDouble	m_pz2
NekDouble	m_pis
NekDouble	m_strength
Protected Attributes inherited from Nektar::Stimulus
LibUtilities::SessionReaderSharedPtr	m_session
	Session.
MultiRegions::ExpListSharedPtr	m_field
	Transmembrane potential field from PDE system.
int	m_nq
	Number of physical points.
ProtocolSharedPtr	m_Protocol

Detailed Description

Protocol base class.

The Stimulus class and derived classes implement a range of stimuli. The stimulus contains input stimuli that can be applied throughout the domain, on specified regions determined by the derived classes of Stimulus, at specified frequencies determined by the derived classes of Protocol.

Definition at line 50 of file StimulusRect.h.

Constructor & Destructor Documentation

Nektar::StimulusRect::StimulusRect	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const MultiRegions::ExpListSharedPtr &	pField,
		const TiXmlElement *	pXml
	)

Stimulus base class constructor.

Definition at line 62 of file StimulusRect.cpp.

References Nektar::Stimulus::m_field, Nektar::Stimulus::m_nq, m_pis, m_px1, m_px2, m_py1, m_py2, m_pz1, m_pz2, Nektar::Stimulus::m_session, and m_strength.

            : Stimulus(pSession, pField, pXml)
    {
        m_session = pSession;
        m_field = pField;
        m_nq = pField->GetTotPoints();
        
        if (!pXml)
        {
            return;
        }
        
        const TiXmlElement *pXmlparameter; 
        
        pXmlparameter = pXml->FirstChildElement("p_x1");
        m_px1 = atof(pXmlparameter->GetText());
        
        pXmlparameter = pXml->FirstChildElement("p_y1");
        m_py1 = atof(pXmlparameter->GetText());
    
        pXmlparameter = pXml->FirstChildElement("p_z1");
        m_pz1 = atof(pXmlparameter->GetText());
    
        pXmlparameter = pXml->FirstChildElement("p_x2");
        m_px2 = atof(pXmlparameter->GetText());
        pXmlparameter = pXml->FirstChildElement("p_y2");
        m_py2 = atof(pXmlparameter->GetText());
    
        pXmlparameter = pXml->FirstChildElement("p_z2");
        m_pz2 = atof(pXmlparameter->GetText());
        
        pXmlparameter = pXml->FirstChildElement("p_is");
        m_pis = atof(pXmlparameter->GetText());
        
        pXmlparameter = pXml->FirstChildElement("p_strength");
        m_strength = atof(pXmlparameter->GetText());
    }

virtual Nektar::StimulusRect::~StimulusRect ( )

inlinevirtual

Definition at line 70 of file StimulusRect.h.

{}

Member Function Documentation

static StimulusSharedPtr Nektar::StimulusRect::create	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const MultiRegions::ExpListSharedPtr &	pField,
		const TiXmlElement *	pXml
	)

inlinestatic

Creates an instance of this class.

Definition at line 54 of file StimulusRect.h.

        {
            return MemoryManager<StimulusRect>
                    ::AllocateSharedPtr(pSession, pField, pXml);
        }

void Nektar::StimulusRect::Initialise ( )

Initialise the stimulus storage and set initial conditions.

Initialise the stimulus. Allocate workspace and variable storage.

Reimplemented from Nektar::Stimulus.

Definition at line 109 of file StimulusRect.cpp.

    {
        
    }

void Nektar::StimulusRect::v_GenerateSummary ( SolverUtils::SummaryList & s )

protectedvirtual

Implements Nektar::Stimulus.

Definition at line 179 of file StimulusRect.cpp.

    {
    }

void Nektar::StimulusRect::v_Update	(	Array< OneD, Array< OneD, NekDouble > > &	outarray,
		const NekDouble	time
	)

protectedvirtual

Implements Nektar::Stimulus.

Definition at line 118 of file StimulusRect.cpp.

References Nektar::Stimulus::m_field, m_pis, Nektar::Stimulus::m_Protocol, m_px1, m_px2, m_py1, m_py2, m_pz1, m_pz2, and m_strength.

    {
        if (m_field->GetNumElmts() == 0)
        {
            return;
        }
        // Get the dimension of the expansion
        int dim = m_field->GetCoordim(0);
        // Retrieve coordinates of quadrature points
        int nq = m_field->GetNpoints();
        Array<OneD,NekDouble> x0(nq);
        Array<OneD,NekDouble> x1(nq);
        Array<OneD,NekDouble> x2(nq);
        m_field->GetCoords(x0,x1,x2);
        // Get the protocol amplitude
        NekDouble v_amp = m_Protocol->GetAmplitude(time) * m_strength;
        
        switch (dim)
        {
        case 1:
            for(int j=0; j<nq; j++)
            {
                outarray[0][j] += v_amp * ( ( tanh(m_pis*(x0[j] - m_px1)) 
                                              - tanh(m_pis*(x0[j] - m_px2)) 
                                            ) / 2.0 );
            }
            break;
        case 2:
            for(int j=0; j<nq; j++)
            {
                outarray[0][j] += v_amp * ( ( (tanh(m_pis*(x0[j] - m_px1))
                                               - tanh(m_pis*(x0[j] - m_px2)))
                                            * (tanh(m_pis*(x1[j] - m_py1))
                                               - tanh(m_pis*(x1[j] - m_py2)))
                                            ) / 2.0 );
            }
            break;
        case 3:
            for(int j=0; j<nq; j++)
            {   
                outarray[0][j] += v_amp * ( ( (tanh(m_pis*(x0[j] - m_px1)) 
                                               - tanh(m_pis*(x0[j] - m_px2)))
                                            * (tanh(m_pis*(x1[j] - m_py1)) 
                                               - tanh(m_pis*(x1[j] - m_py2)))
                                            * (tanh(m_pis*(x2[j] - m_pz1)) 
                                               - tanh(m_pis*(x2[j] - m_pz2)))
                                            ) / 2.0 );
            }
            break;
        }
    }

Member Data Documentation

std::string Nektar::StimulusRect::className

static

Initial value:

 GetStimulusFactory().RegisterCreatorFunction(
                    "StimulusRect",
                    StimulusRect::create,
                     "Rectangular stimulus.")

Name of class.

Definition at line 64 of file StimulusRect.h.

NekDouble Nektar::StimulusRect::m_pis

protected

Definition at line 82 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

NekDouble Nektar::StimulusRect::m_px1

protected

Definition at line 76 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

NekDouble Nektar::StimulusRect::m_px2

protected