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StimulusCircle.cpp
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2 //
3 // File StimulusCircle.cpp
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9 // Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10 // Department of Aeronautics, Imperial College London (UK), and Scientific
11 // Computing and Imaging Institute, University of Utah (USA).
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31 //
32 // Description: Circular stimulus file.
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 #include <iostream>
36 #include <tinyxml.h>
39 
40 namespace Nektar
41 {
42  std::string StimulusCirc::className
44  "StimulusCirc",
46  "Circular stimulus.");
47 
48  /**
49  * @class StimulusCirc
50  *
51  * The Stimulus class and derived classes implement a range of stimuli.
52  * The stimulus contains input stimuli that can be applied throughout the
53  * domain, on specified regions determined by the derived classes of
54  * Stimulus, at specified frequencies determined by the derived classes of
55  * Protocol.
56  */
57 
58  /**
59  * Stimulus base class constructor.
60  */
63  const MultiRegions::ExpListSharedPtr& pField,
64  const TiXmlElement* pXml)
65  : Stimulus(pSession, pField, pXml)
66  {
67  m_session = pSession;
68  m_field = pField;
69  m_nq = pField->GetTotPoints();
70  m_chiCapMembrane = m_session->GetParameter("chi")
71  * m_session->GetParameter("Cm");
72 
73  if (!pXml)
74  {
75  return;
76  }
77 
78  const TiXmlElement *pXmlparameter;
79 
80  pXmlparameter = pXml->FirstChildElement("p_x1");
81  m_px1 = atof(pXmlparameter->GetText());
82 
83  pXmlparameter = pXml->FirstChildElement("p_y1");
84  m_py1 = atof(pXmlparameter->GetText());
85 
86  pXmlparameter = pXml->FirstChildElement("p_z1");
87  m_pz1 = atof(pXmlparameter->GetText());
88 
89  pXmlparameter = pXml->FirstChildElement("p_r1");
90  m_pr1 = atof(pXmlparameter->GetText());
91 
92  pXmlparameter = pXml->FirstChildElement("p_is");
93  m_pis = atof(pXmlparameter->GetText());
94 
95  pXmlparameter = pXml->FirstChildElement("p_strength");
96  m_strength = atof(pXmlparameter->GetText());
97  }
98 
99 
100  /**
101  * Initialise the stimulus. Allocate workspace and variable storage.
102  */
104  {
105  }
106 
107 
108  /**
109  *
110  */
112  const NekDouble time)
113  {
114  // Get the dimension of the expansion
115  int dim = m_field->GetCoordim(0);
116 
117  //Retrieve coodrinates of quadrature points
118  int nq = m_field->GetNpoints();
119  Array<OneD,NekDouble> x0(nq);
120  Array<OneD,NekDouble> x1(nq);
121  Array<OneD,NekDouble> x2(nq);
122 
123  // Get the protocol amplitude
124  NekDouble v_amp = m_Protocol->GetAmplitude(time) * m_strength;
125 
126  // get the coordinates
127  m_field->GetCoords(x0,x1,x2);
128 
129  switch (dim)
130  {
131  case 1:
132  for(int j=0; j<nq; j++)
133  {
134  outarray[0][j] += v_amp
135  * ( -tanh( (m_pis * x0[j] - m_px1 + m_pr1)
136  * (m_pis * x0[j] - m_px1 - m_pr1)
137  ) / 2.0 + 0.5 );
138  }
139  break;
140  case 2:
141  for(int j=0; j<nq; j++)
142  {
143  outarray[0][j] += v_amp
144  * ( -tanh( (m_pis * x0[j] - m_px1+m_pr1)
145  * (m_pis * x0[j] - m_px1-m_pr1)
146  + (m_pis * x1[j] - m_py1+m_pr1)
147  * (m_pis * x1[j] - m_py1-m_pr1)
148  ) / 2.0 + 0.5 );
149  }
150  break;
151  case 3:
152  for(int j=0; j<nq; j++)
153  {
154  outarray[0][j] += v_amp
155  * ( -tanh( (m_pis * x0[j] - m_px1+m_pr1)
156  * (m_pis * x0[j] - m_px1-m_pr1)
157  + (m_pis * x1[j] - m_py1+m_pr1)
158  * (m_pis * x1[j] - m_py1-m_pr1)
159  + (m_pis * x2[j] - m_pz1+m_pr1)
160  * (m_pis * x2[j] - m_pz1-m_pr1)
161  ) / 2.0 + 0.5 );
162  }
163  break;
164  }
165  }
166 
167 
168  /**
169  *
170  */
172  {
173  }
174 }
void Initialise()
Initialise the protocol storage and set initial conditions.
virtual void v_Update(Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
NekDouble m_chiCapMembrane
std::vector< std::pair< std::string, std::string > > SummaryList
Definition: Misc.h:47
ProtocolSharedPtr m_Protocol
Stimulus protocol to apply.
Definition: Stimulus.h:99
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: Stimulus.h:93
boost::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: MeshPartition.h:51
StimulusCirc(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
int m_nq
Number of physical points.
Definition: Stimulus.h:97
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
virtual void v_GenerateSummary(SolverUtils::SummaryList &s)
Stimulus base class.
Definition: Stimulus.h:66
double NekDouble
static std::string className
Name of class.
MultiRegions::ExpListSharedPtr m_field
Transmembrane potential field from PDE system.
Definition: Stimulus.h:95
StimulusFactory & GetStimulusFactory()
Definition: Stimulus.cpp:45
static StimulusSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
Creates an instance of this class.
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, tDescription pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:215