Nektar::ProtocolS1S2 Class Reference

Protocol base class. More...

#include <ProtocolS1S2.h>

Inheritance diagram for Nektar::ProtocolS1S2:

Public Member Functions
	~ProtocolS1S2 () override
void	Initialise ()
	Initialise the protocol storage and set initial conditions. More...
Public Member Functions inherited from Nektar::Protocol
virtual	~Protocol ()
void	Initialise ()
	Initialise the protocol storage and set initial conditions. More...
NekDouble	GetAmplitude (const NekDouble time)
	Returns amplitude of stimulus (1 or 0) at given time. More...
void	GenerateSummary (SolverUtils::SummaryList &s)
	Print a summary of the cell model. More...

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

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

Protected Member Functions
NekDouble	v_GetAmplitude (const NekDouble time) override
void	v_GenerateSummary (SolverUtils::SummaryList &s) override
virtual void	v_SetInitialConditions ()
Protected Member Functions inherited from Nektar::Protocol
	Protocol (const LibUtilities::SessionReaderSharedPtr &pSession, const TiXmlElement *pXml)
virtual NekDouble	v_GetAmplitude (const NekDouble time)=0
virtual void	v_GenerateSummary (SolverUtils::SummaryList &s)=0

Protected Attributes
NekDouble	m_start
NekDouble	m_dur
NekDouble	m_s1cyclelength
NekDouble	m_num_s1
NekDouble	m_s2cyclelength
NekDouble	m_s2start
Protected Attributes inherited from Nektar::Protocol
LibUtilities::SessionReaderSharedPtr	m_session
	Session. More...

Private Member Functions
	ProtocolS1S2 (const LibUtilities::SessionReaderSharedPtr &pSession, const TiXmlElement *pXml)

Friends
class	MemoryManager< ProtocolS1S2 >

Detailed Description

Protocol base class.

The Stimuli 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 45 of file ProtocolS1S2.h.

Constructor & Destructor Documentation

~ProtocolS1S2()

Nektar::ProtocolS1S2::~ProtocolS1S2 ( )

inlineoverride

Definition at line 61 of file ProtocolS1S2.h.

    {
    }

ProtocolS1S2()

Nektar::ProtocolS1S2::ProtocolS1S2 ( const LibUtilities::SessionReaderSharedPtr &  pSession, const TiXmlElement *  pXml  )

private

Protocol base class constructor.

Definition at line 55 of file ProtocolS1S2.cpp.

    : Protocol(pSession, pXml)
{
    m_session = pSession;
 
    if (!pXml)
    {
        return;
    }
 
    const TiXmlElement *pXmlparameter; // Declaring variable called pxml...
    // See if we have parameters defined.  They are optional so we go on if not.
 
    // member variables m_* defined in ProtocolS1S2.h
 
    pXmlparameter = pXml->FirstChildElement("START");
    m_start =
        atof(pXmlparameter->GetText()); // text value within px1, convert to a
                                        // floating pt and save in m_px1
 
    pXmlparameter = pXml->FirstChildElement("DURATION");
    m_dur         = atof(pXmlparameter->GetText());
 
    pXmlparameter   = pXml->FirstChildElement("S1CYCLELENGTH");
    m_s1cyclelength = atof(pXmlparameter->GetText());
 
    pXmlparameter = pXml->FirstChildElement("NUM_S1");
    m_num_s1      = atof(pXmlparameter->GetText());
 
    pXmlparameter   = pXml->FirstChildElement("S2CYCLELENGTH");
    m_s2cyclelength = atof(pXmlparameter->GetText());
 
    m_s2start = m_s1cyclelength * (m_num_s1 - 1) + m_s2cyclelength + m_start;
}

References m_dur, m_num_s1, m_s1cyclelength, m_s2cyclelength, m_s2start, Nektar::Protocol::m_session, and m_start.

Member Function Documentation

create()

static ProtocolSharedPtr Nektar::ProtocolS1S2::create ( const LibUtilities::SessionReaderSharedPtr &  pSession, const TiXmlElement *  pXml  )

inlinestatic

Creates an instance of this class.

Definition at line 49 of file ProtocolS1S2.h.

    {
        return MemoryManager<ProtocolS1S2>::AllocateSharedPtr(pSession, pXml);
    }

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

Initialise()

void Nektar::ProtocolS1S2::Initialise

(

)

Initialise the protocol storage and set initial conditions.

Initialise the protocol. Allocate workspace and variable storage.

Definition at line 94 of file ProtocolS1S2.cpp.

{
}

v_GenerateSummary()

void Nektar::ProtocolS1S2::v_GenerateSummary ( SolverUtils::SummaryList &  s )

overrideprotectedvirtual

Implements Nektar::Protocol.

Definition at line 121 of file ProtocolS1S2.cpp.

{
}

v_GetAmplitude()

NekDouble Nektar::ProtocolS1S2::v_GetAmplitude ( const NekDouble  time )

overrideprotectedvirtual

Implements Nektar::Protocol.

Definition at line 98 of file ProtocolS1S2.cpp.

{
    // Number of complete S1 intervals
    NekDouble a = floor((time - m_start) / m_s1cyclelength);
 
    // Time since start of most recent S1 interval
    NekDouble time1 = time - a * m_s1cyclelength - m_start;
 
    // S1
    if ((time1 > 0) && (a < m_num_s1) && (time1 < m_dur))
    {
        return 1.0;
    }
 
    // S2
    if ((time > m_s2start) && (time < m_s2start + m_dur))
    {
        return 1.0;
    }
 
    return 0.0;
}

References m_dur, m_num_s1, m_s1cyclelength, m_s2start, and m_start.

v_SetInitialConditions()

void Nektar::ProtocolS1S2::v_SetInitialConditions ( )

protectedvirtual

Definition at line 126 of file ProtocolS1S2.cpp.

{
}

Friends And Related Function Documentation

MemoryManager< ProtocolS1S2 >

friend class MemoryManager< ProtocolS1S2 >

friend

Definition at line 57 of file ProtocolS1S2.h.

Member Data Documentation

className

std::string Nektar::ProtocolS1S2::className

static

Initial value:

=
    GetProtocolFactory().RegisterCreatorFunction(
        "ProtocolS1S2", ProtocolS1S2::create, "S1S2 stimulus protocol.")

Name of class.

Definition at line 57 of file ProtocolS1S2.h.

m_dur

NekDouble Nektar::ProtocolS1S2::m_dur

protected

Definition at line 70 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

m_num_s1

NekDouble Nektar::ProtocolS1S2::m_num_s1

protected

Definition at line 72 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

m_s1cyclelength

NekDouble Nektar::ProtocolS1S2::m_s1cyclelength

protected

Definition at line 71 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

m_s2cyclelength

NekDouble Nektar::ProtocolS1S2::m_s2cyclelength

protected

Definition at line 73 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2().

m_s2start

NekDouble Nektar::ProtocolS1S2::m_s2start

protected

Definition at line 74 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

m_start

NekDouble Nektar::ProtocolS1S2::m_start

protected

Definition at line 69 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().