Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
CardiacElectroMechanicsProblem.cpp
1/*
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34*/
35
36#include "CardiacElectroMechanicsProblem.hpp"
37
38#include "OutputFileHandler.hpp"
39#include "ReplicatableVector.hpp"
40#include "HeartConfig.hpp"
41#include "LogFile.hpp"
42#include "ChastePoint.hpp"
43#include "Element.hpp"
44#include "BoundaryConditionsContainer.hpp"
45#include "AbstractDynamicLinearPdeSolver.hpp"
46#include "TimeStepper.hpp"
47#include "TrianglesMeshWriter.hpp"
48#include "Hdf5ToMeshalyzerConverter.hpp"
49#include "Hdf5ToCmguiConverter.hpp"
50#include "MeshalyzerMeshWriter.hpp"
51#include "PetscTools.hpp"
52#include "ImplicitCardiacMechanicsSolver.hpp"
53#include "ExplicitCardiacMechanicsSolver.hpp"
54#include "CmguiDeformedSolutionsWriter.hpp"
55#include "VoltageInterpolaterOntoMechanicsMesh.hpp"
56#include "BidomainProblem.hpp"
57
58
59template<unsigned DIM, unsigned ELEC_PROB_DIM>
61{
62 assert(mIsWatchedLocation);
63
64 // find the nearest electrics mesh node
65 double min_dist = DBL_MAX;
66 unsigned node_index = UNSIGNED_UNSET;
67 for (unsigned i=0; i<mpElectricsMesh->GetNumNodes(); i++)
68 {
69 double dist = norm_2(mWatchedLocation - mpElectricsMesh->GetNode(i)->rGetLocation());
70 if (dist < min_dist)
71 {
72 min_dist = dist;
73 node_index = i;
74 }
75 }
76
77 // set up watched node, if close enough
78 assert(node_index != UNSIGNED_UNSET); // should def have found something
79 c_vector<double,DIM> pos = mpElectricsMesh->GetNode(node_index)->rGetLocation();
80
81 if (min_dist > 1e-8)
82 {
83 // LCOV_EXCL_START
84 std::cout << "ERROR: Could not find an electrics node very close to requested watched location - "
85 << "min distance was " << min_dist << " for node " << node_index
86 << " at location " << pos << std::flush;;
87
89 //EXCEPTION("Could not find an electrics node very close to requested watched location");
91 // LCOV_EXCL_STOP
92 }
93 else
94 {
95 LOG(2,"Chosen electrics node "<<node_index<<" at location " << pos << " to be watched");
96 mWatchedElectricsNodeIndex = node_index;
97 }
98
99 // find nearest mechanics mesh
100 min_dist = DBL_MAX;
101 node_index = UNSIGNED_UNSET;
102 c_vector<double,DIM> pos_at_min;
103
104 for (unsigned i=0; i<mpMechanicsMesh->GetNumNodes(); i++)
105 {
106 c_vector<double,DIM> position = mpMechanicsMesh->GetNode(i)->rGetLocation();
107
108 double dist = norm_2(position-mWatchedLocation);
109
110 if (dist < min_dist)
111 {
112 min_dist = dist;
113 node_index = i;
114 pos_at_min = position;
115 }
116 }
117
118 // set up watched node, if close enough
119 assert(node_index != UNSIGNED_UNSET); // should def have found something
120
121 if (min_dist > 1e-8)
122 {
123 // LCOV_EXCL_START
124 std::cout << "ERROR: Could not find a mechanics node very close to requested watched location - "
125 << "min distance was " << min_dist << " for node " << node_index
126 << " at location " << pos_at_min;
127
129 //EXCEPTION("Could not find a mechanics node very close to requested watched location");
131 // LCOV_EXCL_STOP
132 }
133 else
134 {
135 LOG(2,"Chosen mechanics node "<<node_index<<" at location " << pos << " to be watched");
136 mWatchedMechanicsNodeIndex = node_index;
137 }
138
139 OutputFileHandler handler(mOutputDirectory,false);
140 mpWatchedLocationFile = handler.OpenOutputFile("watched.txt");
141}
142
143template<unsigned DIM, unsigned ELEC_PROB_DIM>
145{
146 assert(mIsWatchedLocation);
147
148 std::vector<c_vector<double,DIM> >& deformed_position = mpMechanicsSolver->rGetDeformedPosition();
149
151 ReplicatableVector voltage_replicated(voltage);
152 double V = voltage_replicated[mWatchedElectricsNodeIndex];
153
156 // // Metadata is currently being added to CellML models and then this will be avoided by asking for Calcium.
157 // double Ca = mpElectricsProblem->GetMonodomainTissue()->GetCardiacCell(mWatchedElectricsNodeIndex)->GetIntracellularCalciumConcentration();
158
159 *mpWatchedLocationFile << time << " ";
160 for (unsigned i=0; i<DIM; i++)
161 {
162 *mpWatchedLocationFile << deformed_position[mWatchedMechanicsNodeIndex](i) << " ";
163 }
164 *mpWatchedLocationFile << V << "\n";
165 mpWatchedLocationFile->flush();
166}
167
168template<unsigned DIM, unsigned ELEC_PROB_DIM>
169c_matrix<double,DIM,DIM>& CardiacElectroMechanicsProblem<DIM,ELEC_PROB_DIM>::rCalculateModifiedConductivityTensor(unsigned elementIndex, const c_matrix<double,DIM,DIM>& rOriginalConductivity, unsigned domainIndex)
170{
171
172 // first get the deformation gradient for this electrics element
173 unsigned containing_mechanics_elem = mpMeshPair->rGetCoarseElementsForFineElementCentroids()[elementIndex];
174 c_matrix<double,DIM,DIM>& r_deformation_gradient = mDeformationGradientsForEachMechanicsElement[containing_mechanics_elem];
175
176 // compute sigma_def = F^{-1} sigma_undef F^{-T}
177 c_matrix<double,DIM,DIM> inv_F = Inverse(r_deformation_gradient);
178 mModifiedConductivityTensor = prod(inv_F, rOriginalConductivity);
179 mModifiedConductivityTensor = prod(mModifiedConductivityTensor, trans(inv_F));
180
181 return mModifiedConductivityTensor;
182}
183
184
188template<unsigned DIM, unsigned PROBLEM_DIM>
190{
191public:
198 static AbstractCardiacProblem<DIM, DIM, PROBLEM_DIM>* Create(ElectricsProblemType problemType,
199 AbstractCardiacCellFactory<DIM>* pCellFactory);
200};
201
205template<unsigned DIM>
207{
208public:
215 static AbstractCardiacProblem<DIM, DIM, 1u>* Create(ElectricsProblemType problemType,
217 {
218 if (problemType == MONODOMAIN)
219 {
220 return new MonodomainProblem<DIM>(pCellFactory);
221 }
222 EXCEPTION("The second template parameter should be 2 when a bidomain problem is chosen");
223 }
224};
225
229template<unsigned DIM>
231{
232public:
239 static AbstractCardiacProblem<DIM, DIM, 2u>* Create(ElectricsProblemType problemType,
241 {
242 if (problemType == BIDOMAIN)
243 {
244 return new BidomainProblem<DIM>(pCellFactory, false);//false-> no bath
245 }
246 if (problemType == BIDOMAIN_WITH_BATH)
247 {
248 return new BidomainProblem<DIM>(pCellFactory, true);// true-> bath
249 }
250 EXCEPTION("The second template parameter should be 1 when a monodomain problem is chosen");
251 }
252};
253
254
255template<unsigned DIM, unsigned ELEC_PROB_DIM>
257 CompressibilityType compressibilityType,
258 ElectricsProblemType electricsProblemType,
259 TetrahedralMesh<DIM,DIM>* pElectricsMesh,
260 QuadraticMesh<DIM>* pMechanicsMesh,
262 ElectroMechanicsProblemDefinition<DIM>* pProblemDefinition,
263 std::string outputDirectory)
264 : mCompressibilityType(compressibilityType),
265 mpCardiacMechSolver(NULL),
266 mpMechanicsSolver(NULL),
267 mpElectricsMesh(pElectricsMesh),
268 mpMechanicsMesh(pMechanicsMesh),
269 mpProblemDefinition(pProblemDefinition),
270 mHasBath(false),
271 mpMeshPair(NULL),
272 mNoElectricsOutput(false),
273 mIsWatchedLocation(false),
274 mWatchedElectricsNodeIndex(UNSIGNED_UNSET),
275 mWatchedMechanicsNodeIndex(UNSIGNED_UNSET),
276 mNumTimestepsToOutputDeformationGradientsAndStress(UNSIGNED_UNSET)
277{
278 // Do some initial set up...
279 // However, NOTE, we don't use either the passed in meshes or the problem_definition.
280 // These pointers are allowed to be NULL, in case a child constructor wants to set
281 // them up (eg CardiacElectroMechProbRegularGeom).
282 // The meshes and problem_defn are used for the first time in Initialise().
283
284
285 // Start-up mechanics event handler..
287 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ALL);
288 // disable the electric event handler, because we use a problem class but
289 // don't call Solve, so we would have to worry about starting and ending any
290 // events in AbstractCardiacProblem::Solve() (esp. calling EndEvent(EVERYTHING))
291 // if we didn't disable it.
293
294 assert(HeartConfig::Instance()->GetSimulationDuration()>0.0);
295 assert(HeartConfig::Instance()->GetPdeTimeStep()>0.0);
296
297 // Create the monodomain problem.
298 // **NOTE** WE ONLY USE THIS TO: set up the cells, get an initial condition
299 // (voltage) vector, and get a solver. We won't ever call Solve on the cardiac problem class
300 assert(pCellFactory != NULL);
301 mpElectricsProblem = CreateElectricsProblem<DIM,ELEC_PROB_DIM>::Create(electricsProblemType, pCellFactory);
302
303 if (electricsProblemType == BIDOMAIN_WITH_BATH)
304 {
305 mHasBath = true;
306 }
307 // check whether output is required
308 mWriteOutput = (outputDirectory!="");
309 if (mWriteOutput)
310 {
311 mOutputDirectory = outputDirectory;
312 // create the directory
317 }
318 else
319 {
321 }
322
323// mpImpactRegion=NULL;
324}
325
326template<unsigned DIM, unsigned ELEC_PROB_DIM>
328{
329 // NOTE if SetWatchedLocation but not Initialise has been called, mpWatchedLocationFile
330 // will be uninitialised and using it will cause a seg fault. Hence the mpMechanicsMesh!=NULL
331 // it is true if Initialise has been called.
332 if (mIsWatchedLocation && mpMechanicsMesh)
333 {
334 mpWatchedLocationFile->close();
335 }
336
337 delete mpElectricsProblem;
338 delete mpCardiacMechSolver;
339 delete mpMeshPair;
340
342}
343
344template<unsigned DIM, unsigned ELEC_PROB_DIM>
346{
347 assert(mpElectricsMesh!=NULL);
348 assert(mpMechanicsMesh!=NULL);
349 assert(mpProblemDefinition!=NULL);
350 assert(mpCardiacMechSolver==NULL);
351
354 mNumElecTimestepsPerMechTimestep = (unsigned) floor((mpProblemDefinition->GetMechanicsSolveTimestep()/HeartConfig::Instance()->GetPdeTimeStep())+0.5);
355 if (fabs(mNumElecTimestepsPerMechTimestep*HeartConfig::Instance()->GetPdeTimeStep() - mpProblemDefinition->GetMechanicsSolveTimestep()) > 1e-6)
356 {
357 EXCEPTION("Electrics PDE timestep does not divide mechanics solve timestep");
358 }
359
360 // Create the Logfile (note we have to do this after the output dir has been
361 // created, else the log file might get cleaned away
362 std::string log_dir = mOutputDirectory; // just the TESTOUTPUT dir if mOutputDir="";
363 LogFile::Instance()->Set(2, mOutputDirectory);
364 LogFile::Instance()->WriteHeader("Electromechanics");
365 LOG(2, DIM << "d Implicit CardiacElectroMechanics Simulation:");
366 LOG(2, "End time = " << HeartConfig::Instance()->GetSimulationDuration() << ", electrics time step = " << HeartConfig::Instance()->GetPdeTimeStep() << ", mechanics timestep = " << mpProblemDefinition->GetMechanicsSolveTimestep() << "\n");
367 LOG(2, "Contraction model ode timestep " << mpProblemDefinition->GetContractionModelOdeTimestep());
368 LOG(2, "Output is written to " << mOutputDirectory << "/[deformation/electrics]");
369
370 LOG(2, "Electrics mesh has " << mpElectricsMesh->GetNumNodes() << " nodes");
371 LOG(2, "Mechanics mesh has " << mpMechanicsMesh->GetNumNodes() << " nodes");
372
373 LOG(2, "Initialising..");
374
375
376 if (mIsWatchedLocation)
377 {
378 DetermineWatchedNodes();
379 }
380
381 // initialise electrics problem
382 mpElectricsProblem->SetMesh(mpElectricsMesh);
383 mpElectricsProblem->Initialise();
384
385 if (mCompressibilityType==INCOMPRESSIBLE)
386 {
387 switch(mpProblemDefinition->GetSolverType())
388 {
389 case EXPLICIT:
391 *mpMechanicsMesh,*mpProblemDefinition,mDeformationOutputDirectory);
392 break;
393 case IMPLICIT:
395 *mpMechanicsMesh,*mpProblemDefinition,mDeformationOutputDirectory);
396 break;
397 default:
399 }
400 }
401 else
402 {
403 // repeat above with Compressible solver rather than incompressible -
404 // not the neatest but avoids having to template this class.
405 switch(mpProblemDefinition->GetSolverType())
406 {
407 case EXPLICIT:
409 *mpMechanicsMesh,*mpProblemDefinition,mDeformationOutputDirectory);
410 break;
411 case IMPLICIT:
413 *mpMechanicsMesh,*mpProblemDefinition,mDeformationOutputDirectory);
414 break;
415 default:
417 }
418 }
419
420
421 mpMechanicsSolver = dynamic_cast<AbstractNonlinearElasticitySolver<DIM>*>(mpCardiacMechSolver);
422 assert(mpMechanicsSolver);
423
424 // set up mesh pair and determine the fine mesh elements and corresponding weights for each
425 // quadrature point in the coarse mesh
426 mpMeshPair = new FineCoarseMeshPair<DIM>(*mpElectricsMesh, *mpMechanicsMesh);
427 mpMeshPair->SetUpBoxesOnFineMesh();
428 mpMeshPair->ComputeFineElementsAndWeightsForCoarseQuadPoints(*(mpCardiacMechSolver->GetQuadratureRule()), false);
429 mpMeshPair->DeleteFineBoxCollection();
430
431 mpCardiacMechSolver->SetFineCoarseMeshPair(mpMeshPair);
432 mpCardiacMechSolver->Initialise();
433
434 unsigned num_quad_points = mpCardiacMechSolver->GetTotalNumQuadPoints();
435 mInterpolatedCalciumConcs.assign(num_quad_points, 0.0);
436 mInterpolatedVoltages.assign(num_quad_points, 0.0);
437
438 if (mpProblemDefinition->ReadFibreSheetDirectionsFromFile())
439 {
440 mpCardiacMechSolver->SetVariableFibreSheetDirections(mpProblemDefinition->GetFibreSheetDirectionsFile(),
441 mpProblemDefinition->GetFibreSheetDirectionsDefinedPerQuadraturePoint());
442 }
443
444
445 if (mpProblemDefinition->GetDeformationAffectsConductivity() || mpProblemDefinition->GetDeformationAffectsCellModels())
446 {
447 mpMeshPair->SetUpBoxesOnCoarseMesh();
448 }
449
450
451 if (mpProblemDefinition->GetDeformationAffectsCellModels() || mpProblemDefinition->GetDeformationAffectsConductivity())
452 {
453 // initialise the stretches saved for each mechanics element
454 mStretchesForEachMechanicsElement.resize(mpMechanicsMesh->GetNumElements(), 1.0);
455
456 // initialise the store of the F in each mechanics element (one constant value of F) in each
457 mDeformationGradientsForEachMechanicsElement.resize(mpMechanicsMesh->GetNumElements(),identity_matrix<double>(DIM));
458 }
459
460
461 if (mpProblemDefinition->GetDeformationAffectsCellModels())
462 {
463 // compute the coarse elements which contain each fine node -- for transferring stretch from
464 // mechanics solve electrics cell models
465 mpMeshPair->ComputeCoarseElementsForFineNodes(false);
466
467 }
468
469 if (mpProblemDefinition->GetDeformationAffectsConductivity())
470 {
471 // compute the coarse elements which contain each fine element centroid -- for transferring F from
472 // mechanics solve to electrics mesh elements
473 mpMeshPair->ComputeCoarseElementsForFineElementCentroids(false);
474
475 // tell the abstract tissue class that the conductivities need to be modified, passing in this class
476 // (which is of type AbstractConductivityModifier)
477 mpElectricsProblem->GetTissue()->SetConductivityModifier(this);
478 }
479
480 if (mWriteOutput)
481 {
482 TrianglesMeshWriter<DIM,DIM> mesh_writer(mOutputDirectory,"electrics_mesh",false);
483 mesh_writer.WriteFilesUsingMesh(*mpElectricsMesh);
484 }
485}
486
487template<unsigned DIM, unsigned ELEC_PROB_DIM>
489{
490 // initialise the meshes and mechanics solver
491 if (mpCardiacMechSolver==NULL)
492 {
493 Initialise();
494 }
495
496 bool verbose_during_solve = ( mpProblemDefinition->GetVerboseDuringSolve()
497 || CommandLineArguments::Instance()->OptionExists("-mech_verbose")
498 || CommandLineArguments::Instance()->OptionExists("-mech_very_verbose"));
499
500
501 mpProblemDefinition->Validate();
502
503 boost::shared_ptr<BoundaryConditionsContainer<DIM,DIM,ELEC_PROB_DIM> > p_bcc(new BoundaryConditionsContainer<DIM,DIM,ELEC_PROB_DIM>);
504 p_bcc->DefineZeroNeumannOnMeshBoundary(mpElectricsMesh, 0);
505 mpElectricsProblem->SetBoundaryConditionsContainer(p_bcc);
506
507 // get an electrics solver from the problem. Note that we don't call
508 // Solve() on the CardiacProblem class, we do the looping here.
510 = mpElectricsProblem->CreateSolver();
511
512 // set up initial voltage etc
513 Vec electrics_solution=NULL; //This will be set and used later
514 Vec calcium_data= mpElectricsMesh->GetDistributedVectorFactory()->CreateVec();
515 Vec initial_voltage = mpElectricsProblem->CreateInitialCondition();
516
517 // write the initial position
518 unsigned counter = 0;
519
520 TimeStepper stepper(0.0, HeartConfig::Instance()->GetSimulationDuration(), mpProblemDefinition->GetMechanicsSolveTimestep());
521
522 CmguiDeformedSolutionsWriter<DIM>* p_cmgui_writer = NULL;
523
524 std::vector<std::string> variable_names;
525
526 if (mWriteOutput)
527 {
528 mpMechanicsSolver->SetWriteOutput();
529 mpMechanicsSolver->WriteCurrentSpatialSolution("undeformed","nodes");
530
531 p_cmgui_writer = new CmguiDeformedSolutionsWriter<DIM>(mOutputDirectory+"/deformation/cmgui",
532 "solution",
533 *(this->mpMechanicsMesh),
534 WRITE_QUADRATIC_MESH);
535 variable_names.push_back("V");
536 if (ELEC_PROB_DIM==2)
537 {
538 variable_names.push_back("Phi_e");
539 if (mHasBath==true)
540 {
541 std::vector<std::string> regions;
542 regions.push_back("tissue");
543 regions.push_back("bath");
544 p_cmgui_writer->SetRegionNames(regions);
545 }
546 }
547 p_cmgui_writer->SetAdditionalFieldNames(variable_names);
548 p_cmgui_writer->WriteInitialMesh("undeformed");
549 }
550
557
558 LOG(2, "\nSolving for initial deformation");
559 // LCOV_EXCL_START
560 if (verbose_during_solve)
561 {
562 std::cout << "\n\n ** Solving for initial deformation\n";
563 }
564 // LCOV_EXCL_STOP
565
566 mpMechanicsSolver->SetWriteOutput(false);
567
568 mpMechanicsSolver->SetCurrentTime(0.0);
569 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ALL_MECH);
570
571 mpMechanicsSolver->SetIncludeActiveTension(false);
572 if (mNumTimestepsToOutputDeformationGradientsAndStress!=UNSIGNED_UNSET)
573 {
574 mpMechanicsSolver->SetComputeAverageStressPerElementDuringSolve(true);
575 }
576
577 unsigned total_newton_iters = 0;
578 for (unsigned index=1; index<=mpProblemDefinition->GetNumIncrementsForInitialDeformation(); index++)
579 {
580 // LCOV_EXCL_START
581 if (verbose_during_solve)
582 {
583 std::cout << " Increment " << index << " of " << mpProblemDefinition->GetNumIncrementsForInitialDeformation() << "\n";
584 }
585 // LCOV_EXCL_STOP
586
587 if (mpProblemDefinition->GetTractionBoundaryConditionType()==PRESSURE_ON_DEFORMED)
588 {
589 mpProblemDefinition->SetPressureScaling(((double)index)/mpProblemDefinition->GetNumIncrementsForInitialDeformation());
590 }
591 mpMechanicsSolver->Solve();
592
593 total_newton_iters += mpMechanicsSolver->GetNumNewtonIterations();
594 }
595
596 mpMechanicsSolver->SetIncludeActiveTension(true);
597 MechanicsEventHandler::EndEvent(MechanicsEventHandler::ALL_MECH);
598 LOG(2, " Number of newton iterations = " << total_newton_iters);
599
600
601 unsigned mech_writer_counter = 0;
602
603 if (mWriteOutput)
604 {
605 LOG(2, " Writing output");
606 mpMechanicsSolver->SetWriteOutput();
607 mpMechanicsSolver->WriteCurrentSpatialSolution("solution","nodes",mech_writer_counter);
608 p_cmgui_writer->WriteDeformationPositions(rGetDeformedPosition(), mech_writer_counter);
609
610 if (!mNoElectricsOutput)
611 {
612 // the writer inside monodomain problem uses the printing timestep
613 // inside HeartConfig to estimate total number of timesteps, so make
614 // sure this is set to what we will use.
615 HeartConfig::Instance()->SetPrintingTimeStep(mpProblemDefinition->GetMechanicsSolveTimestep());
616
617 // When we consider archiving these simulations we will need to get a bool back from the following
618 // command to decide whether or not the file is being extended, and hence whether to write the
619 // initial conditions into the .h5 file.
620 mpElectricsProblem->InitialiseWriter();
621 mpElectricsProblem->WriteOneStep(stepper.GetTime(), initial_voltage);
622 }
623
624 if (mIsWatchedLocation)
625 {
626 WriteWatchedLocationData(stepper.GetTime(), initial_voltage);
627 }
628
629 if (mNumTimestepsToOutputDeformationGradientsAndStress!=UNSIGNED_UNSET)
630 {
631 mpMechanicsSolver->WriteCurrentStrains(DEFORMATION_GRADIENT_F,"deformation_gradient",mech_writer_counter);
632 mpMechanicsSolver->WriteCurrentAverageElementStresses("second_PK",mech_writer_counter);
633 }
634 }
635
636
637 PrepareForSolve();
638
642// std::vector<double> current_solution_previous_time_step = mpMechanicsSolver->rGetCurrentSolution();
643// std::vector<double> current_solution_second_last_time_step = mpMechanicsSolver->rGetCurrentSolution();
644// bool first_step = true;
645
646
647 // reset this to false, may be reset again below
648 mpMechanicsSolver->SetComputeAverageStressPerElementDuringSolve(false);
649
650 while (!stepper.IsTimeAtEnd())
651 {
652 LOG(2, "\nCurrent time = " << stepper.GetTime());
653 // LCOV_EXCL_START
654 if (verbose_during_solve)
655 {
656 // also output time to screen as newton solve information will be output
657 std::cout << "\n\n ** Current time = " << stepper.GetTime() << "\n";
658 }
659 // LCOV_EXCL_STOP
660
667 if (mpProblemDefinition->GetDeformationAffectsCellModels() || mpProblemDefinition->GetDeformationAffectsConductivity())
668 {
669 // Determine the stretch and deformation gradient on each element.
670 //
671 // If mpProblemDefinition->GetDeformationAffectsCellModels()==true:
672 // Stretch will be passed to the cell models.
673 //
674 // If mpProblemDefinition->GetDeformationAffectsConductivity()==true:
675 // The deformation gradient needs to be set up but does not need to be passed to the tissue
676 // so that F is used to compute the conductivity. Instead this is
677 // done through the line "mpElectricsProblem->GetMonodomainTissue()->SetConductivityModifier(this);" line above, which means
678 // rCalculateModifiedConductivityTensor() will be called on this class by the tissue, which then uses the F
679
680 mpCardiacMechSolver->ComputeDeformationGradientAndStretchInEachElement(mDeformationGradientsForEachMechanicsElement, mStretchesForEachMechanicsElement);
681 }
682
683 if (mpProblemDefinition->GetDeformationAffectsCellModels())
684 {
685 // Set the stretches on each of the cell models
686 for (unsigned global_index = mpElectricsMesh->GetDistributedVectorFactory()->GetLow();
687 global_index < mpElectricsMesh->GetDistributedVectorFactory()->GetHigh();
688 global_index++)
689 {
690 unsigned containing_elem = mpMeshPair->rGetCoarseElementsForFineNodes()[global_index];
691 double stretch = mStretchesForEachMechanicsElement[containing_elem];
692 mpElectricsProblem->GetTissue()->GetCardiacCell(global_index)->SetStretch(stretch);
693 }
694 }
695
696 p_electrics_solver->SetTimeStep(HeartConfig::Instance()->GetPdeTimeStep());
697
703 LOG(2, " Solving electrics");
704 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::NON_MECH);
705 for (unsigned i=0; i<mNumElecTimestepsPerMechTimestep; i++)
706 {
707 double current_time = stepper.GetTime() + i*HeartConfig::Instance()->GetPdeTimeStep();
708 double next_time = stepper.GetTime() + (i+1)*HeartConfig::Instance()->GetPdeTimeStep();
709
710 // solve the electrics
711 p_electrics_solver->SetTimes(current_time, next_time);
712 p_electrics_solver->SetInitialCondition( initial_voltage );
713
714 electrics_solution = p_electrics_solver->Solve();
715
716 PetscReal min_voltage, max_voltage;
717 VecMax(electrics_solution,CHASTE_PETSC_NULLPTR,&max_voltage); //the second param is where the index would be returned
718 VecMin(electrics_solution,CHASTE_PETSC_NULLPTR,&min_voltage);
719 if (i==0)
720 {
721 LOG(2, " minimum and maximum voltage is " << min_voltage <<", "<<max_voltage);
722 }
723 else if (i==1)
724 {
725 LOG(2, " ..");
726 }
727
728 PetscTools::Destroy(initial_voltage);
729 initial_voltage = electrics_solution;
730 }
731
732 if (mpProblemDefinition->GetDeformationAffectsConductivity())
733 {
734 p_electrics_solver->SetMatrixIsNotAssembled();
735 }
736
737
743
744 // compute Ca_I at each quad point (by interpolation, using the info on which
745 // electrics element the quad point is in. Then set Ca_I on the mechanics solver
746 LOG(2, " Interpolating Ca_I and voltage");
747
748 //Collect the distributed calcium data into one Vec to be later replicated
749 for (unsigned node_index = 0; node_index<mpElectricsMesh->GetNumNodes(); node_index++)
750 {
751 if (mpElectricsMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(node_index))
752 {
753 double calcium_value = mpElectricsProblem->GetTissue()->GetCardiacCell(node_index)->GetIntracellularCalciumConcentration();
754 VecSetValue(calcium_data, node_index ,calcium_value, INSERT_VALUES);
755 }
756 }
757 PetscTools::Barrier();//not sure this is needed
758
759 //Replicate electrics solution and calcium (replication is inside this constructor of ReplicatableVector)
760 ReplicatableVector electrics_solution_repl(electrics_solution);//size=(number of electrics nodes)*ELEC_PROB_DIM
761 ReplicatableVector calcium_repl(calcium_data);//size = number of electrics nodes
762
763 //interpolate values onto mechanics mesh
764 for (unsigned i=0; i<mpMeshPair->rGetElementsAndWeights().size(); i++)
765 {
766 double interpolated_CaI = 0;
767 double interpolated_voltage = 0;
768
769 Element<DIM,DIM>& element = *(mpElectricsMesh->GetElement(mpMeshPair->rGetElementsAndWeights()[i].ElementNum));
770
771 for (unsigned node_index = 0; node_index<element.GetNumNodes(); node_index++)
772 {
773 unsigned global_index = element.GetNodeGlobalIndex(node_index);
774 double CaI_at_node = calcium_repl[global_index];
775 interpolated_CaI += CaI_at_node*mpMeshPair->rGetElementsAndWeights()[i].Weights(node_index);
776 //the following line assumes interleaved solution for ELEC_PROB_DIM>1 (e.g, [Vm_0, phi_e_0, Vm1, phi_e_1...])
777 interpolated_voltage += electrics_solution_repl[global_index*ELEC_PROB_DIM]*mpMeshPair->rGetElementsAndWeights()[i].Weights(node_index);
778 }
779
780 assert(i<mInterpolatedCalciumConcs.size());
781 assert(i<mInterpolatedVoltages.size());
782 mInterpolatedCalciumConcs[i] = interpolated_CaI;
783 mInterpolatedVoltages[i] = interpolated_voltage;
784 }
785
786 LOG(2, " Setting Ca_I. max value = " << Max(mInterpolatedCalciumConcs));
787
788 // NOTE IF NHS: HERE WE SHOULD PERHAPS CHECK WHETHER THE CELL MODELS HAVE Ca_Trop
789 // AND UPDATE FROM NHS TO CELL_MODEL, BUT NOT SURE HOW TO DO THIS.. (esp for implicit)
790
791 // set [Ca], V, t
792 mpCardiacMechSolver->SetCalciumAndVoltage(mInterpolatedCalciumConcs, mInterpolatedVoltages);
793 MechanicsEventHandler::EndEvent(MechanicsEventHandler::NON_MECH);
794
795
801 LOG(2, " Solving mechanics ");
802 mpMechanicsSolver->SetWriteOutput(false);
803
804 // make sure the mechanics solver knows the current time (in case
805 // the traction say is time-dependent).
806 mpMechanicsSolver->SetCurrentTime(stepper.GetTime());
807
808 // see if we will need to output stresses at the end of this timestep
809 if (mNumTimestepsToOutputDeformationGradientsAndStress!=UNSIGNED_UNSET
810 && (counter+1)%mNumTimestepsToOutputDeformationGradientsAndStress == 0)
811 {
812 mpMechanicsSolver->SetComputeAverageStressPerElementDuringSolve(true);
813 }
814
817// for (unsigned i=0; i<mpMechanicsSolver->rGetCurrentSolution().size(); i++)
818// {
819// double current = mpMechanicsSolver->rGetCurrentSolution()[i];
820// double previous = current_solution_previous_time_step[i];
821// double second_last = current_solution_second_last_time_step[i];
822// //double guess = 2*current - previous;
823// double guess = 3*current - 3*previous + second_last;
824//
825// if (!first_step)
826// {
827// current_solution_second_last_time_step[i] = current_solution_previous_time_step[i];
828// }
829// current_solution_previous_time_step[i] = mpMechanicsSolver->rGetCurrentSolution()[i];
830// mpMechanicsSolver->rGetCurrentSolution()[i] = guess;
831// }
832// first_step = false;
833
834 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::ALL_MECH);
835 mpCardiacMechSolver->Solve(stepper.GetTime(), stepper.GetNextTime(), mpProblemDefinition->GetContractionModelOdeTimestep());
836 MechanicsEventHandler::EndEvent(MechanicsEventHandler::ALL_MECH);
837
838 LOG(2, " Number of newton iterations = " << mpMechanicsSolver->GetNumNewtonIterations());
839
840 // update the current time
841 stepper.AdvanceOneTimeStep();
842 counter++;
843
844
850 MechanicsEventHandler::BeginEvent(MechanicsEventHandler::OUTPUT);
851 if (mWriteOutput && (counter%WRITE_EVERY_NTH_TIME==0))
852 {
853 LOG(2, " Writing output");
854 // write deformed position
855 mech_writer_counter++;
856 mpMechanicsSolver->SetWriteOutput();
857 mpMechanicsSolver->WriteCurrentSpatialSolution("solution","nodes",mech_writer_counter);
858
859 p_cmgui_writer->WriteDeformationPositions(rGetDeformedPosition(), counter);
860
861 if (!mNoElectricsOutput)
862 {
863 mpElectricsProblem->mpWriter->AdvanceAlongUnlimitedDimension();
864 mpElectricsProblem->WriteOneStep(stepper.GetTime(), electrics_solution);
865 }
866
867 if (mIsWatchedLocation)
868 {
869 WriteWatchedLocationData(stepper.GetTime(), electrics_solution);
870 }
871 OnEndOfTimeStep(counter);
872
873 if (mNumTimestepsToOutputDeformationGradientsAndStress!=UNSIGNED_UNSET && counter%mNumTimestepsToOutputDeformationGradientsAndStress==0)
874 {
875 mpMechanicsSolver->WriteCurrentStrains(DEFORMATION_GRADIENT_F,"deformation_gradient",mech_writer_counter);
876 mpMechanicsSolver->WriteCurrentAverageElementStresses("second_PK",mech_writer_counter);
877 }
878 mpMechanicsSolver->SetComputeAverageStressPerElementDuringSolve(false);
879 }
880 MechanicsEventHandler::EndEvent(MechanicsEventHandler::OUTPUT);
881
882 // write the total elapsed time..
884 }
885
886 if ((mWriteOutput) && (!mNoElectricsOutput))
887 {
889 mpElectricsProblem->mpWriter->Close();
890 delete mpElectricsProblem->mpWriter;
891
892 std::string input_dir = mOutputDirectory+"/electrics";
893
894 // Convert simulation data to meshalyzer format - commented
895 std::string config_directory = HeartConfig::Instance()->GetOutputDirectory();
897
898// Hdf5ToMeshalyzerConverter<DIM,DIM> meshalyzer_converter(FileFinder(input_dir, RelativeTo::ChasteTestOutput),
899// "voltage", mpElectricsMesh,
900// HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering(),
901// HeartConfig::Instance()->GetVisualizerOutputPrecision() );
902
903 // convert output to CMGUI format
905 "voltage", mpElectricsMesh, mHasBath,
906 HeartConfig::Instance()->GetVisualizerOutputPrecision());
907
908 // Write mesh in a suitable form for meshalyzer
909 //std::string output_directory = mOutputDirectory + "/electrics/output";
910 // Write the mesh
911 //MeshalyzerMeshWriter<DIM,DIM> mesh_writer(output_directory, "mesh", false);
912 //mesh_writer.WriteFilesUsingMesh(*mpElectricsMesh);
913 // Write the parameters out
914 //HeartConfig::Instance()->Write();
915
916 // interpolate the electrical data onto the mechanics mesh nodes and write CMGUI...
917 // Note: this calculates the data on ALL nodes of the mechanics mesh (incl internal,
918 // non-vertex ones), which won't be used if linear CMGUI visualisation
919 // of the mechanics solution is used.
920 VoltageInterpolaterOntoMechanicsMesh<DIM> converter(*mpElectricsMesh,*mpMechanicsMesh,variable_names,input_dir,"voltage");
921
922 // reset to the default value
923 HeartConfig::Instance()->SetOutputDirectory(config_directory);
924 }
925
926 if (p_cmgui_writer)
927 {
928 if (mNoElectricsOutput)
929 {
930 p_cmgui_writer->WriteCmguiScript("","undeformed");
931 }
932 else
933 {
934 p_cmgui_writer->WriteCmguiScript("../../electrics/cmgui_output/voltage_mechanics_mesh","undeformed");
935 }
936 delete p_cmgui_writer;
937 }
938 PetscTools::Destroy(electrics_solution);
939 PetscTools::Destroy(calcium_data);
940 delete p_electrics_solver;
941
942 MechanicsEventHandler::EndEvent(MechanicsEventHandler::ALL);
943}
944
945template<unsigned DIM, unsigned ELEC_PROB_DIM>
947{
948 double max = -1e200;
949 for (unsigned i=0; i<vec.size(); i++)
950 {
951 if (vec[i]>max) max=vec[i];
952 }
953 return max;
954}
955
956template<unsigned DIM, unsigned ELEC_PROB_DIM>
961
962template<unsigned DIM, unsigned ELEC_PROB_DIM>
964{
965 mIsWatchedLocation = true;
966 mWatchedLocation = watchedLocation;
967}
968
969template<unsigned DIM, unsigned ELEC_PROB_DIM>
971{
972 mNumTimestepsToOutputDeformationGradientsAndStress = (unsigned) floor((timeStep/mpProblemDefinition->GetMechanicsSolveTimestep())+0.5);
973 if (fabs(mNumTimestepsToOutputDeformationGradientsAndStress*mpProblemDefinition->GetMechanicsSolveTimestep() - timeStep) > 1e-6)
974 {
975 EXCEPTION("Timestep provided for SetOutputDeformationGradientsAndStress() is not a multiple of mechanics solve timestep");
976 }
977}
978
979template<unsigned DIM, unsigned ELEC_PROB_DIM>
981{
982 return mpMechanicsSolver->rGetDeformedPosition();
983}
984
985// Explicit instantiation
986
987//note: 1d incompressible material doesn't make sense
#define EXCEPTION(message)
#define NEVER_REACHED
const unsigned UNSIGNED_UNSET
Definition Exception.hpp:53
#define CHASTE_PETSC_NULLPTR
A macro to define PETSc null pointer based on the PETSc version.
boost::numeric::ublas::c_matrix< T, 1, 1 > Inverse(const boost::numeric::ublas::c_matrix< T, 1, 1 > &rM)
void SetTimes(double tStart, double tEnd)
unsigned GetNumNodes() const
unsigned GetNodeGlobalIndex(unsigned localIndex) const
virtual void WriteFilesUsingMesh(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)
double Max(std::vector< double > &vec)
CardiacElectroMechanicsProblem(CompressibilityType compressibilityType, ElectricsProblemType electricsProblemType, TetrahedralMesh< DIM, DIM > *pElectricsMesh, QuadraticMesh< DIM > *pMechanicsMesh, AbstractCardiacCellFactory< DIM > *pCellFactory, ElectroMechanicsProblemDefinition< DIM > *pProblemDefinition, std::string outputDirectory)
c_matrix< double, DIM, DIM > & rCalculateModifiedConductivityTensor(unsigned elementIndex, const c_matrix< double, DIM, DIM > &rOriginalConductivity, unsigned domainIndex)
void SetWatchedPosition(c_vector< double, DIM > watchedLocation)
std::vector< c_vector< double, DIM > > & rGetDeformedPosition()
void WriteWatchedLocationData(double time, Vec voltage)
AbstractCardiacProblem< DIM, DIM, ELEC_PROB_DIM > * mpElectricsProblem
void WriteCmguiScript(std::string fieldBaseName="", std::string undeformedBaseName="")
void WriteDeformationPositions(std::vector< c_vector< double, DIM > > &rDeformedPositions, unsigned counter)
void WriteInitialMesh(std::string fileName="")
void SetAdditionalFieldNames(std::vector< std::string > &rFieldNames)
void SetRegionNames(std::vector< std::string > &rRegionNames)
bool OptionExists(const std::string &rOption)
static CommandLineArguments * Instance()
static AbstractCardiacProblem< DIM, DIM, 1u > * Create(ElectricsProblemType problemType, AbstractCardiacCellFactory< DIM > *pCellFactory)
static AbstractCardiacProblem< DIM, DIM, 2u > * Create(ElectricsProblemType problemType, AbstractCardiacCellFactory< DIM > *pCellFactory)
static AbstractCardiacProblem< DIM, DIM, PROBLEM_DIM > * Create(ElectricsProblemType problemType, AbstractCardiacCellFactory< DIM > *pCellFactory)
double GetPdeTimeStep() const
void SetPrintingTimeStep(double printingTimeStep)
void SetOutputDirectory(const std::string &rOutputDirectory)
void SetOutputFilenamePrefix(const std::string &rOutputFilenamePrefix)
static void Reset()
std::string GetOutputDirectory() const
static HeartConfig * Instance()
void Set(unsigned level, const std::string &rDirectory, const std::string &rFileName="log.txt")
Definition LogFile.cpp:73
static LogFile * Instance()
Definition LogFile.cpp:52
void WriteElapsedTime(std::string pre="")
Definition LogFile.cpp:116
void WriteHeader(std::string simulationType="")
Definition LogFile.cpp:111
static void Close()
Definition LogFile.cpp:101
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
static void Destroy(Vec &rVec)
static void Barrier(const std::string callerId="")
bool IsTimeAtEnd() const
double GetTime() const
void AdvanceOneTimeStep()
double GetNextTime() const