Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ElectrodesStimulusFactory.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35
36#include "ElectrodesStimulusFactory.hpp"
37#include "DistributedTetrahedralMesh.hpp"
38#include "HeartConfig.hpp"
39#include "GaussianQuadratureRule.hpp"
40#include "RegularStimulus.hpp"
41
42#include <cmath>
43
44template<unsigned DIM>
46 std::vector<double>& rStimulusMagnitudes,
47 std::vector<double>& rDurations,
48 std::vector<double>& rPeriods,
49 std::vector<double>& rStarts,
50 std::vector<double>& rEnds)
51 : mrElectrodePairs(rElectrodePairs),
52 mrMagnitudes(rStimulusMagnitudes),
53 mrDurations(rDurations),
54 mrPeriods(rPeriods),
55 mrStarts(rStarts),
56 mrEnds(rEnds),
57 mGroundSecondElectrode(false)
58{
59 if ((rElectrodePairs.size() != rStimulusMagnitudes.size()) ||
60 (rElectrodePairs.size() != rDurations.size()) ||
61 (rElectrodePairs.size() != rPeriods.size()) ||
62 (rElectrodePairs.size() != rStarts.size()) ||
63 (rElectrodePairs.size() != rEnds.size()))
64 {
65 EXCEPTION ("Vector of electrode pairs and vector of stimulation parameters must have the same size");
66 }
67
70}
71
72template<unsigned DIM>
76
77template<unsigned DIM>
79{
80 std::vector<unsigned> nodes_in_all_electrodes;
81 for (unsigned global_node_index = 0; global_node_index < this->mpMesh->GetNumNodes(); global_node_index++)
82 {
83 if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(global_node_index))
84 {
85 for (unsigned pair_index = 0; pair_index <mrElectrodePairs.size(); pair_index++)
86 {
87 if (mrElectrodePairs[pair_index].first->DoesContain( this->mpMesh->GetNode(global_node_index)->GetPoint()))
88 {
89 nodes_in_all_electrodes.push_back( this->mpMesh->GetNode(global_node_index)->GetIndex() );
90 }
91 if (mrElectrodePairs[pair_index].second->DoesContain( this->mpMesh->GetNode(global_node_index)->GetPoint()))
92 {
93 nodes_in_all_electrodes.push_back( this->mpMesh->GetNode(global_node_index)->GetIndex() );
94 }
95 }
96 }
97 }
99 for (unsigned node_index = 0; node_index < nodes_in_all_electrodes.size(); node_index++)
100 {
101 unsigned number_of_hits = 0;
102 for (unsigned node_to_check = 0; node_to_check < nodes_in_all_electrodes.size(); node_to_check++)
103 {
104 if (nodes_in_all_electrodes[node_index] == nodes_in_all_electrodes[node_to_check] )
105 {
106 number_of_hits++;
107 }
108 }
109 if (number_of_hits>1)
110 {
111 EXCEPTION("Two or more electrodes intersect with each other");
112 }
113 }
114}
115
116template<unsigned DIM>
118{
119 mGroundSecondElectrode = grounded;
120}
121
122template<unsigned DIM>
124{
125 assert(this->mpMesh!=NULL);
126 try
127 {
128 CheckForElectrodesIntersection();
129 }
130 catch (Exception &e)
131 {
132 PetscTools::ReplicateException(true); //Electrodes intersect
133 throw e;
134 }
136
137 for (unsigned pair_index = 0; pair_index < mrElectrodePairs.size(); pair_index++)
138 {
139
140 if (!mGroundSecondElectrode)//no grounding of second electrode
141 {
142 //compute the two fluxes for this pair
143 double flux_electrode_1 = ComputeElectrodeTotalFlux(mrElectrodePairs[pair_index].first, mMagnitudesElectrode1[pair_index]);
144 double flux_electrode_2 = ComputeElectrodeTotalFlux(mrElectrodePairs[pair_index].second, mMagnitudesElectrode2[pair_index]);
145
146 //Scale the magnitude of the second electrode for this pair
147 mMagnitudesElectrode2[pair_index] = -mMagnitudesElectrode1[pair_index]*flux_electrode_1/flux_electrode_2;
148
149 // Paranoia.
150 assert( flux_electrode_2 != 0.0);
151 assert( ! std::isnan(mMagnitudesElectrode2[pair_index]));
152
153 }
154 else//second electrode is grounded
155 {
156 this->mGroundedRegions.push_back( mrElectrodePairs[pair_index].second );
157 }
158 }
159}
160
161template<unsigned DIM>
162boost::shared_ptr<AbstractStimulusFunction> ElectrodesStimulusFactory<DIM>::CreateStimulusForNode(Node<DIM>* pNode)
163{
164 boost::shared_ptr<RegularStimulus> p_stimulus;
165 for (unsigned pair_index = 0; pair_index < mrElectrodePairs.size(); pair_index++)
166 {
167 if (mrElectrodePairs[pair_index].first->DoesContain(pNode->GetPoint()) )
168 {
169 p_stimulus.reset( new RegularStimulus(mMagnitudesElectrode1[pair_index], mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));
170
171 }
172 else if (mrElectrodePairs[pair_index].second->DoesContain(pNode->GetPoint()) )
173 {
174 p_stimulus.reset ( new RegularStimulus(mMagnitudesElectrode2[pair_index], mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));
175
176 }
177 else//no stimulus here
178 {
179 p_stimulus.reset ( new RegularStimulus(0.0, mrDurations[pair_index], mrPeriods[pair_index], mrStarts[pair_index], mrEnds[pair_index]));
180 }
181 }
182 return p_stimulus;
183}
184
185template<unsigned DIM>
187{
189
190 //the basis functions
191 c_vector<double, DIM+1> phi;
192
193 double total_electrode_flux = 0.0;
194 double ret;
195
196 for (typename AbstractTetrahedralMesh<DIM,DIM>::NodeIterator node_iter=this->mpMesh->GetNodeIteratorBegin();
197 node_iter != this->mpMesh->GetNodeIteratorEnd();
198 ++node_iter)
199 {
200 if (pRegion->DoesContain((*node_iter).GetPoint()))
201 {
202 unsigned node_index = node_iter->GetIndex();
203 assert(node_index < this->mpMesh->GetNumNodes());
204 double contribution_of_this_node = 0.0;
205 // Loop over the elements where this node is contained
206 for (std::set<unsigned>::iterator iter = this->mpMesh->GetNode(node_index)->rGetContainingElementIndices().begin();
207 iter != this->mpMesh->GetNode(node_index)->rGetContainingElementIndices().end();
208 ++iter)
209 {
210 Element<DIM,DIM>* p_element = this->mpMesh->GetElement(*iter);
211
212 /*Determine jacobian for this element*/
213 c_matrix<double, DIM, DIM> jacobian;
214 c_matrix<double, DIM, DIM> inverse_jacobian;//unused here, but needed for the function below
215 double jacobian_determinant;
216 this->mpMesh->GetInverseJacobianForElement(p_element->GetIndex(), jacobian, jacobian_determinant, inverse_jacobian);
217
218 double contribution_of_this_element = 0.0;//...to this node
219 // loop over Gauss points
220 for (unsigned quad_index=0; quad_index < pQuadRule->GetNumQuadPoints(); quad_index++)
221 {
222 const ChastePoint<DIM>& quad_point = pQuadRule->rGetQuadPoint(quad_index);
223 BasisFunction::ComputeBasisFunctions(quad_point, phi);
224
225 double interpolated_stimulus = 0.0;
226 //loop over nodes in this element
227 for (unsigned node_index_in_element = 0; node_index_in_element < p_element->GetNumNodes(); node_index_in_element++)
228 {
229 //const Node<DIM>* p_node = p_element->GetNode(node_index_in_element);
230 assert(p_element->GetNumNodes() == DIM+1);
231 interpolated_stimulus += stimulusMagnitude*phi(node_index_in_element);
232 contribution_of_this_element += interpolated_stimulus * phi(node_index_in_element) * jacobian_determinant * pQuadRule->GetWeight(quad_index);
233 }
234
235 }/*end of loop over gauss points*/
236 contribution_of_this_node += contribution_of_this_element;
237
238 }/*end of loop over elements where the node is contained*/
239 total_electrode_flux += contribution_of_this_node;
240 }/* end of if that checks if node is in the electrode*/
241 }/* end of loop over nodes in the mesh*/
242#ifndef NDEBUG
243 int mpi_ret = MPI_Allreduce(&total_electrode_flux, &ret, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
244 assert(mpi_ret == MPI_SUCCESS);
245#else
246 MPI_Allreduce(&total_electrode_flux, &ret, 1, MPI_DOUBLE, MPI_SUM, PETSC_COMM_WORLD);
247#endif
248
249 //clear up memory
250 delete pQuadRule;
251
252 assert(ret < DBL_MAX);
253 return ret;
254}
255
256// Explicit instantiation
257template class ElectrodesStimulusFactory<1>;
258template class ElectrodesStimulusFactory<2>;
259template class ElectrodesStimulusFactory<3>;
#define EXCEPTION(message)
virtual bool DoesContain(const ChastePoint< SPACE_DIM > &rPointToCheck) const =0
unsigned GetNumNodes() const
unsigned GetIndex() const
boost::shared_ptr< AbstractStimulusFunction > CreateStimulusForNode(Node< DIM > *pNode)
std::vector< double > mMagnitudesElectrode1
std::vector< double > mMagnitudesElectrode2
ElectrodesStimulusFactory(std::vector< std::pair< AbstractChasteRegion< DIM > *, AbstractChasteRegion< DIM > * > > &rElectrodePairs, std::vector< double > &rStimulusMagnitudes, std::vector< double > &rDurations, std::vector< double > &rPeriods, std::vector< double > &rStarts, std::vector< double > &rEnds)
double ComputeElectrodeTotalFlux(AbstractChasteRegion< DIM > *pRegion, double stimulusMagnitude)
const ChastePoint< ELEMENT_DIM > & rGetQuadPoint(unsigned index) const
double GetWeight(unsigned index) const
Definition Node.hpp:59
ChastePoint< SPACE_DIM > GetPoint() const
Definition Node.cpp:133
static void Barrier(const std::string callerId="")
static void ReplicateException(bool flag)