Nektar::StimulusRect Class Reference

Protocol base class. More...

#include <StimulusRect.h>

Inheritance diagram for Nektar::StimulusRect:

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

Static Public Member Functions
static StimulusSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
	Creates an instance of this class. More...
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. More...

Protected Member Functions
virtual void	v_Update (Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time) override
virtual void	v_GenerateSummary (SolverUtils::SummaryList &s) override
Protected Member Functions inherited from Nektar::Stimulus
	Stimulus (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)

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
NekDouble	m_chiCapMembrane
Protected Attributes inherited from Nektar::Stimulus
LibUtilities::SessionReaderSharedPtr	m_session
	Session. More...
MultiRegions::ExpListSharedPtr	m_field
	Transmembrane potential field from PDE system. More...
int	m_nq
	Number of physical points. More...
ProtocolSharedPtr	m_Protocol
	Stimulus protocol to apply. More...

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

Friends
class	MemoryManager< StimulusRect >

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 49 of file StimulusRect.h.

Constructor & Destructor Documentation

~StimulusRect()

virtual Nektar::StimulusRect::~StimulusRect ( )

inlinevirtual

Definition at line 66 of file StimulusRect.h.

    {
    }

StimulusRect()

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

private

Stimulus base class constructor.

Definition at line 59 of file StimulusRect.cpp.

    : Stimulus(pSession, pField, pXml)
{
    m_session = pSession;
    m_field   = pField;
    m_nq      = pField->GetTotPoints();
    m_chiCapMembrane =
        m_session->GetParameter("chi") * m_session->GetParameter("Cm");
 
    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());
}

References m_chiCapMembrane, 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.

Member Function Documentation

create()

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 53 of file StimulusRect.h.

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

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

Initialise()

void Nektar::StimulusRect::Initialise

(

)

Initialise the stimulus storage and set initial conditions.

Initialise the stimulus. Allocate workspace and variable storage.

Definition at line 105 of file StimulusRect.cpp.

{
}

v_GenerateSummary()

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

overrideprotectedvirtual

Implements Nektar::Stimulus.

Definition at line 172 of file StimulusRect.cpp.

{
    boost::ignore_unused(s);
}

v_Update()

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

overrideprotectedvirtual

Implements Nektar::Stimulus.

Definition at line 112 of file StimulusRect.cpp.

{
    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 / m_chiCapMembrane;
 
    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;
    }
}

References m_chiCapMembrane, 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.

Friends And Related Function Documentation

MemoryManager< StimulusRect >

friend class MemoryManager< StimulusRect >

friend

Definition at line 62 of file StimulusRect.h.

Member Data Documentation

className

std::string Nektar::StimulusRect::className

static

Initial value:

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

Name of class.

Definition at line 62 of file StimulusRect.h.

m_chiCapMembrane

NekDouble Nektar::StimulusRect::m_chiCapMembrane

protected

Definition at line 82 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_pis

NekDouble Nektar::StimulusRect::m_pis

protected

Definition at line 80 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_px1

NekDouble Nektar::StimulusRect::m_px1

protected

Definition at line 74 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_px2

NekDouble Nektar::StimulusRect::m_px2

protected

Definition at line 77 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_py1

NekDouble Nektar::StimulusRect::m_py1

protected

Definition at line 75 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_py2

NekDouble Nektar::StimulusRect::m_py2

protected

Definition at line 78 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_pz1

NekDouble Nektar::StimulusRect::m_pz1

protected

Definition at line 76 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_pz2

NekDouble Nektar::StimulusRect::m_pz2

protected

Definition at line 79 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().

m_strength

NekDouble Nektar::StimulusRect::m_strength

protected

Definition at line 81 of file StimulusRect.h.

Referenced by StimulusRect(), and v_Update().