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Nektar::ProtocolS1S2 Class Reference

Protocol base class. More...

#include <ProtocolS1S2.h>

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Public Member Functions

virtual ~ProtocolS1S2 ()
 
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

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

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 46 of file ProtocolS1S2.h.

Constructor & Destructor Documentation

virtual Nektar::ProtocolS1S2::~ProtocolS1S2 ( )
inlinevirtual

Definition at line 63 of file ProtocolS1S2.h.

63 {}
Nektar::ProtocolS1S2::ProtocolS1S2 ( const LibUtilities::SessionReaderSharedPtr pSession,
const TiXmlElement *  pXml 
)
private

Protocol base class constructor.

Definition at line 57 of file ProtocolS1S2.cpp.

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

58  : Protocol(pSession, pXml)
59  {
60  m_session = pSession;
61 
62  if (!pXml)
63  {
64  return;
65  }
66 
67  const TiXmlElement *pXmlparameter; //Declaring variable called pxml...
68  // See if we have parameters defined. They are optional so we go on if not.
69 
70  //member variables m_* defined in ProtocolS1S2.h
71 
72  pXmlparameter = pXml->FirstChildElement("START");
73  m_start = atof(pXmlparameter->GetText()); //text value within px1, convert to a floating pt and save in m_px1
74 
75  pXmlparameter = pXml->FirstChildElement("DURATION");
76  m_dur = atof(pXmlparameter->GetText());
77 
78  pXmlparameter = pXml->FirstChildElement("S1CYCLELENGTH");
79  m_s1cyclelength = atof(pXmlparameter->GetText());
80 
81  pXmlparameter = pXml->FirstChildElement("NUM_S1");
82  m_num_s1 = atof(pXmlparameter->GetText());
83 
84  pXmlparameter = pXml->FirstChildElement("S2CYCLELENGTH");
85  m_s2cyclelength = atof(pXmlparameter->GetText());
86 
88  }
NekDouble m_s2cyclelength
Definition: ProtocolS1S2.h:73
NekDouble m_s1cyclelength
Definition: ProtocolS1S2.h:71
Protocol(const LibUtilities::SessionReaderSharedPtr &pSession, const TiXmlElement *pXml)
Definition: Protocol.cpp:61
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: Protocol.h:82

Member Function Documentation

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

Creates an instance of this class.

Definition at line 50 of file ProtocolS1S2.h.

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

53  {
55  ::AllocateSharedPtr(pSession, pXml);
56  }
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
void Nektar::ProtocolS1S2::Initialise ( )

Initialise the protocol storage and set initial conditions.

Initialise the protocol. Allocate workspace and variable storage.

Definition at line 95 of file ProtocolS1S2.cpp.

96  {
97 
98  }
void Nektar::ProtocolS1S2::v_GenerateSummary ( SolverUtils::SummaryList s)
protectedvirtual

Implements Nektar::Protocol.

Definition at line 124 of file ProtocolS1S2.cpp.

125  {
126 
127  }
NekDouble Nektar::ProtocolS1S2::v_GetAmplitude ( const NekDouble  time)
protectedvirtual

Implements Nektar::Protocol.

Definition at line 101 of file ProtocolS1S2.cpp.

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

102  {
103  // Number of complete S1 intervals
104  NekDouble a = floor((time-m_start)/m_s1cyclelength);
105 
106  // Time since start of most recent S1 interval
107  NekDouble time1 = time - a * m_s1cyclelength - m_start;
108 
109  // S1
110  if( (time1 > 0) && (a < m_num_s1) && (time1 < m_dur))
111  {
112  return 1.0;
113  }
114 
115  // S2
116  if ((time > m_s2start) && (time < m_s2start + m_dur))
117  {
118  return 1.0;
119  }
120 
121  return 0.0;
122  }
NekDouble m_s1cyclelength
Definition: ProtocolS1S2.h:71
double NekDouble
void Nektar::ProtocolS1S2::v_SetInitialConditions ( )
protectedvirtual

Definition at line 129 of file ProtocolS1S2.cpp.

130  {
131 
132  }

Friends And Related Function Documentation

friend class MemoryManager< ProtocolS1S2 >
friend

Definition at line 61 of file ProtocolS1S2.h.

Member Data Documentation

std::string Nektar::ProtocolS1S2::className
static
Initial value:
"ProtocolS1S2",
"S1S2 stimulus protocol.")

Name of class.

Definition at line 59 of file ProtocolS1S2.h.

NekDouble Nektar::ProtocolS1S2::m_dur
protected

Definition at line 70 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

NekDouble Nektar::ProtocolS1S2::m_num_s1
protected

Definition at line 72 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

NekDouble Nektar::ProtocolS1S2::m_s1cyclelength
protected

Definition at line 71 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

NekDouble Nektar::ProtocolS1S2::m_s2cyclelength
protected

Definition at line 73 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2().

NekDouble Nektar::ProtocolS1S2::m_s2start
protected

Definition at line 74 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().

NekDouble Nektar::ProtocolS1S2::m_start
protected

Definition at line 69 of file ProtocolS1S2.h.

Referenced by ProtocolS1S2(), and v_GetAmplitude().