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StimulusRect.cpp
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2 //
3 // File StimulusRect.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
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31 //
32 // Description: Rectangular stimulus class
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 #include <iostream>
36 #include <tinyxml.h>
38 
40 
41 namespace Nektar
42 {
43  std::string StimulusRect::className
45  "StimulusRect",
47  "Rectangular stimulus.");
48 
49  /**
50  * @class StimulusRect
51  *
52  * The Stimulus class and derived classes implement a range of stimuli.
53  * The stimulus contains input stimuli that can be applied throughout the
54  * domain, on specified regions determined by the derived classes of
55  * Stimulus, at specified frequencies determined by the derived classes of
56  * Protocol.
57  */
58 
59  /**
60  * Stimulus base class constructor.
61  */
64  const MultiRegions::ExpListSharedPtr& pField,
65  const TiXmlElement* pXml)
66  : Stimulus(pSession, pField, pXml)
67  {
68  m_session = pSession;
69  m_field = pField;
70  m_nq = pField->GetTotPoints();
71  m_chiCapMembrane = m_session->GetParameter("chi")
72  * m_session->GetParameter("Cm");
73 
74  if (!pXml)
75  {
76  return;
77  }
78 
79 
80  const TiXmlElement *pXmlparameter;
81 
82  pXmlparameter = pXml->FirstChildElement("p_x1");
83  m_px1 = atof(pXmlparameter->GetText());
84 
85  pXmlparameter = pXml->FirstChildElement("p_y1");
86  m_py1 = atof(pXmlparameter->GetText());
87 
88  pXmlparameter = pXml->FirstChildElement("p_z1");
89  m_pz1 = atof(pXmlparameter->GetText());
90 
91  pXmlparameter = pXml->FirstChildElement("p_x2");
92  m_px2 = atof(pXmlparameter->GetText());
93 
94  pXmlparameter = pXml->FirstChildElement("p_y2");
95  m_py2 = atof(pXmlparameter->GetText());
96 
97  pXmlparameter = pXml->FirstChildElement("p_z2");
98  m_pz2 = atof(pXmlparameter->GetText());
99 
100  pXmlparameter = pXml->FirstChildElement("p_is");
101  m_pis = atof(pXmlparameter->GetText());
102 
103  pXmlparameter = pXml->FirstChildElement("p_strength");
104  m_strength = atof(pXmlparameter->GetText());
105  }
106 
107 
108  /**
109  * Initialise the stimulus. Allocate workspace and variable storage.
110  */
112  {
113  }
114 
115  /**
116  *
117  */
119  Array<OneD, Array<OneD, NekDouble> >&outarray,
120  const NekDouble time)
121  {
122  if (m_field->GetNumElmts() == 0)
123  {
124  return;
125  }
126 
127  // Get the dimension of the expansion
128  int dim = m_field->GetCoordim(0);
129 
130  // Retrieve coordinates of quadrature points
131  int nq = m_field->GetNpoints();
132  Array<OneD,NekDouble> x0(nq);
133  Array<OneD,NekDouble> x1(nq);
134  Array<OneD,NekDouble> x2(nq);
135  m_field->GetCoords(x0,x1,x2);
136 
137  // Get the protocol amplitude
138  NekDouble v_amp = m_Protocol->GetAmplitude(time) * m_strength
140 
141  switch (dim)
142  {
143  case 1:
144  for(int j=0; j<nq; j++)
145  {
146  outarray[0][j] += v_amp * ( ( tanh(m_pis*(x0[j] - m_px1))
147  - tanh(m_pis*(x0[j] - m_px2))
148  ) / 2.0 );
149  }
150  break;
151  case 2:
152  for(int j=0; j<nq; j++)
153  {
154  outarray[0][j] += v_amp * ( ( (tanh(m_pis*(x0[j] - m_px1))
155  - tanh(m_pis*(x0[j] - m_px2)))
156  * (tanh(m_pis*(x1[j] - m_py1))
157  - tanh(m_pis*(x1[j] - m_py2)))
158  ) / 2.0 );
159  }
160  break;
161  case 3:
162  for(int j=0; j<nq; j++)
163  {
164  outarray[0][j] += v_amp * ( ( (tanh(m_pis*(x0[j] - m_px1))
165  - tanh(m_pis*(x0[j] - m_px2)))
166  * (tanh(m_pis*(x1[j] - m_py1))
167  - tanh(m_pis*(x1[j] - m_py2)))
168  * (tanh(m_pis*(x2[j] - m_pz1))
169  - tanh(m_pis*(x2[j] - m_pz2)))
170  ) / 2.0 );
171  }
172  break;
173  }
174  }
175 
176 
177  /**
178  *
179  */
181  {
182  }
183 }
virtual void v_Update(Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
std::vector< std::pair< std::string, std::string > > SummaryList
Definition: Misc.h:47
ProtocolSharedPtr m_Protocol
Stimulus protocol to apply.
Definition: Stimulus.h:99
void Initialise()
Initialise the stimulus storage and set initial conditions.
LibUtilities::SessionReaderSharedPtr m_session
Session.
Definition: Stimulus.h:93
boost::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: MeshPartition.h:51
int m_nq
Number of physical points.
Definition: Stimulus.h:97
StimulusRect(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField, const TiXmlElement *pXml)
boost::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Stimulus base class.
Definition: Stimulus.h:66
double NekDouble
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.
Definition: StimulusRect.h:54
static std::string className
Name of class.
Definition: StimulusRect.h:64
virtual void v_GenerateSummary(SolverUtils::SummaryList &s)
NekDouble m_chiCapMembrane
Definition: StimulusRect.h:82
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, tDescription pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:215