Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
ElectrodesStimulusFactory.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
17 this list of conditions and the following disclaimer in the documentation
18 and/or other materials provided with the distribution.
19 * Neither the name of the University of Oxford nor the names of its
20 contributors may be used to endorse or promote products derived from this
21 software without specific prior written permission.
22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
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)