Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ExtendedBidomainTissue.hpp
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35
36
37#ifndef EXTENDEDBIDOMAINTISSUE_HPP_
38#define EXTENDEDBIDOMAINTISSUE_HPP_
39
41#include <boost/serialization/base_object.hpp>
42
43#include <vector>
45
46#include "AbstractStimulusFunction.hpp"
47#include "AbstractStimulusFactory.hpp"
48#include "AbstractConductivityTensors.hpp"
49
50#include "AbstractCardiacTissue.hpp"
51
76template <unsigned SPACE_DIM>
77class ExtendedBidomainTissue : public virtual AbstractCardiacTissue<SPACE_DIM>
78{
79private:
80 friend class TestExtendedBidomainTissue; // for testing.
81
90 template<class Archive>
91 void serialize(Archive & archive, const unsigned int version)
92 {
93 archive & boost::serialization::base_object<AbstractCardiacTissue<SPACE_DIM> >(*this);
94 // Conductivity tensors are dealt with by HeartConfig, and the caches get regenerated.
95
96 archive & mAmFirstCell;
97 archive & mAmSecondCell;
98 archive & mAmGap;
99 archive & mCmFirstCell;
100 archive & mCmSecondCell;
101 archive & mGGap;
103 }
104
107
112 c_vector<double, SPACE_DIM> mIntracellularConductivitiesSecondCell;
113
114
117
123
129
135
141
143 std::vector< AbstractCardiacCellInterface* > mCellsDistributedSecondCell;
144
146 std::vector<boost::shared_ptr<AbstractStimulusFunction> > mExtracellularStimuliDistributed;
147
149 std::vector<double> mGgapDistributed;
150
156 double mAmGap;
162 double mGGap;
163
169
174
189 void UpdateAdditionalCaches(unsigned globalIndex, unsigned localIndex, double nextTime);
190
202
204 std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > mGgapHeterogeneityRegions;
206 std::vector<double> mGgapValues;
207
208public:
209
217
227 ExtendedBidomainTissue(std::vector<AbstractCardiacCellInterface*> & rCellsDistributed,
228 std::vector<AbstractCardiacCellInterface*> & rSecondCellsDistributed,
229 std::vector<boost::shared_ptr<AbstractStimulusFunction> > & rExtraStimuliDistributed,
230 std::vector<double>& rGgapsDistributed,
232 c_vector<double, SPACE_DIM> intracellularConductivitiesSecondCell);
233
237 virtual ~ExtendedBidomainTissue();
238
244 void SetIntracellularConductivitiesSecondCell(c_vector<double, SPACE_DIM> conductivities);
245
251 AbstractCardiacCellInterface* GetCardiacSecondCell( unsigned globalIndex );
252
253
259 boost::shared_ptr<AbstractStimulusFunction> GetExtracellularStimulus( unsigned globalIndex );
260
264 const std::vector<AbstractCardiacCellInterface*>& rGetSecondCellsDistributed() const;
265
269 const std::vector<double>& rGetGapsDistributed() const;
270
271
275 const std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rGetExtracellularStimulusDistributed() const;
276
277
281 c_vector<double, SPACE_DIM> GetIntracellularConductivitiesSecondCell() const;
282
292 virtual void SolveCellSystems(Vec existingSolution, double time, double nextTime, bool updateVoltage = false);
293
298
305 void SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<SPACE_DIM> > > & rGgapHeterogeneityRegions, std::vector<double> rGgapValues);
306
313
318 const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetExtracellularConductivityTensor(unsigned elementIndex);
319
324 const c_matrix<double, SPACE_DIM, SPACE_DIM>& rGetIntracellularConductivityTensorSecondCell(unsigned elementIndex);
325
326
329
332
335
338
342 double GetAmFirstCell();
343
347 double GetAmSecondCell();
348
352 double GetAmGap();
353
357 double GetCmFirstCell();
358
362 double GetCmSecondCell();
363
367 double GetGGap();
368
372 void SetAmFirstCell(double value);
373
377 void SetAmSecondCell(double value);
378
382 void SetAmGap(double value);
383
387 void SetCmFirstCell(double value);
388
392 void SetCmSecondCell(double value);
393
397 void SetGGap(double value);
398
407
416
417
424 template<class Archive>
425 void SaveExtendedBidomainCells(Archive & archive, const unsigned int version) const
426 {
427 Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
428 const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed = this->rGetCellsDistributed();
429 const std::vector<AbstractCardiacCellInterface*> & r_cells_distributed_second_cell = rGetSecondCellsDistributed();
430 const std::vector<double> & r_ggaps_distributed = rGetGapsDistributed();
431
432 r_archive & this->mpDistributedVectorFactory; // Needed when loading
433 const unsigned num_cells = r_cells_distributed.size();
434 r_archive & num_cells;
435 for (unsigned i=0; i<num_cells; i++)
436 {
437 AbstractDynamicallyLoadableEntity* p_entity = dynamic_cast<AbstractDynamicallyLoadableEntity*>(r_cells_distributed[i]);
438 bool is_dynamic = (p_entity != NULL);
439 r_archive & is_dynamic;
440 if (is_dynamic)
441 {
442 #ifdef CHASTE_CAN_CHECKPOINT_DLLS
445 //r_archive & p_entity->GetLoader()->GetLoadableModulePath();
446 #else
447 // We should have thrown an exception before this point
449 #endif // CHASTE_CAN_CHECKPOINT_DLLS
450 }
451 r_archive & r_cells_distributed[i];
452 r_archive & r_cells_distributed_second_cell[i];
453 r_archive & r_ggaps_distributed[i];
454 }
455 }
456
471 template<class Archive>
472 static void LoadExtendedBidomainCells(Archive & archive, const unsigned int version,
473 std::vector<AbstractCardiacCellInterface*>& rCells,
474 std::vector<AbstractCardiacCellInterface*>& rSecondCells,
475 std::vector<double>& rGgaps,
477 {
478 assert(pMesh!=NULL);
479 DistributedVectorFactory* p_factory;
480 archive & p_factory;
481 unsigned num_cells;
482 archive & num_cells;
483 rCells.resize(p_factory->GetLocalOwnership());
484 rSecondCells.resize(p_factory->GetLocalOwnership());
485 rGgaps.resize(p_factory->GetLocalOwnership());
486 #ifndef NDEBUG
487 // Paranoia
488 assert(rCells.size() == rSecondCells.size());
489 for (unsigned i=0; i<rCells.size(); i++)
490 {
491 assert(rCells[i] == NULL);
492 assert(rSecondCells[i] == NULL);
493 }
494 #endif
495
496 // We don't store a cell index in the archive, so need to work out what global
497 // index this tissue starts up. If we're migrating (so have an
498 // original factory) we use the original low index; otherwise we use the current
499 // low index.
500 unsigned index_low = p_factory->GetOriginalFactory() ? p_factory->GetOriginalFactory()->GetLow() : p_factory->GetLow();
501
502 for (unsigned local_index=0; local_index<num_cells; local_index++)
503 {
504 unsigned global_index = index_low + local_index;
505 unsigned new_local_index = global_index - p_factory->GetLow();
506 bool local = p_factory->IsGlobalIndexLocal(global_index);
507
508 bool is_dynamic;
509 archive & is_dynamic;
510
511 if (is_dynamic)
512 {
513 #ifdef CHASTE_CAN_CHECKPOINT_DLLS
516 // Ensure the shared object file for this cell model is loaded.
517 // We need to do this here, rather than in the class' serialization code,
518 // because that code won't be available until this is done...
519// std::string shared_object_path;
520// archive & shared_object_path;
521// DynamicModelLoaderRegistry::Instance()->GetLoader(shared_object_path);
522 #else
523 // Could only happen on Mac OS X, and will probably be trapped earlier.
525 #endif // CHASTE_CAN_CHECKPOINT_DLLS
526 }
527
529 AbstractCardiacCellInterface* p_second_cell;
530 double g_gap;
531 archive & p_cell;
532 archive & p_second_cell;
533 archive & g_gap;
534 if (local)
535 {
536 rCells[new_local_index] = p_cell; // Add to local cells
537 rSecondCells[new_local_index] = p_second_cell;
538 rGgaps[new_local_index] = g_gap;
539 }
540 else
541 {
542 //not sure how to cover this, we are already looping over local cells...
544 // Non-local real cell, so free the memory.
545 // delete p_cell;
546 // delete p_second_cell;
547 }
548 }
549 }
550
557 template<class Archive>
558 void SaveExtracellularStimulus(Archive & archive, const unsigned int version) const
559 {
560 Archive& r_archive = *ProcessSpecificArchive<Archive>::Get();
561 const std::vector<boost::shared_ptr<AbstractStimulusFunction> > & r_stimulus_distributed = rGetExtracellularStimulusDistributed();
562 r_archive & this->mpDistributedVectorFactory; // Needed when loading
563 const unsigned num_cells = r_stimulus_distributed.size();
564 r_archive & num_cells;
565 for (unsigned i=0; i<num_cells; i++)
566 {
567 r_archive & r_stimulus_distributed[i];
568 }
569 }
570
579 template<class Archive>
580 void LoadExtracellularStimulus(Archive & archive, const unsigned int version,
581 std::vector<boost::shared_ptr<AbstractStimulusFunction> >& rStimuli,
583 {
584
585 DistributedVectorFactory* p_factory;
586 archive & p_factory;
587 unsigned num_cells;
588 archive & num_cells;
589 rStimuli.resize(p_factory->GetLocalOwnership());
590#ifndef NDEBUG
591 // Paranoia
592 for (unsigned i=0; i<rStimuli.size(); i++)
593 {
594 assert(rStimuli[i] == NULL);
595 }
596#endif
597
598 // We don't store a cell index in the archive, so need to work out what global
599 // index this tissue starts up. If we're migrating (so have an
600 // original factory) we use the original low index; otherwise we use the current
601 // low index.
602 unsigned index_low = p_factory->GetOriginalFactory() ? p_factory->GetOriginalFactory()->GetLow() : p_factory->GetLow();
603
604 assert(pMesh!=NULL);
605 //unsigned num_cells = pMesh->GetNumNodes();
606 for (unsigned local_index=0; local_index<num_cells; local_index++)
607 {
608 unsigned global_index = index_low + local_index;
609
610 unsigned new_local_index = global_index - p_factory->GetLow();
611 bool local = p_factory->IsGlobalIndexLocal(global_index);
612
613 boost::shared_ptr<AbstractStimulusFunction> p_stim;
614 archive & p_stim;//get from archive
615
616 if (local)
617 {
618 rStimuli[new_local_index] = p_stim; // Add stimulus to local cells
619 }
620 //otherwise we should delete, but I think shared pointers delete themselves?
621 }
622 }
623};
624
625 // Declare identifier for the serializer
628
629 namespace boost
630 {
631 namespace serialization
632 {
633
634 template<class Archive, unsigned SPACE_DIM>
635 inline void save_construct_data(
636 Archive & ar, const ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
637 {
638 //archive the conductivity tensor of the second cell (which may not be dealt with by heartconfig)
639 c_vector<double, SPACE_DIM> intracellular_conductivities_second_cell = t->GetIntracellularConductivitiesSecondCell();
640 //note that simple: ar & intracellular_conductivities_second_cell may not be liked by some boost versions
641 for (unsigned i = 0; i < SPACE_DIM; i++)
642 {
643 ar & intracellular_conductivities_second_cell(i);
644 }
645
646 const AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* p_mesh = t->pGetMesh();
647 ar & p_mesh;
648
649 // Don't use the std::vector serialization for cardiac cells, so that we can load them
650 // more cleverly when migrating checkpoints.
651 t->SaveExtendedBidomainCells(ar, file_version);
652 t->SaveExtracellularStimulus(ar, file_version);
653
654 // Creation of conductivity tensors are called by constructor and uses HeartConfig. So make sure that it is
655 // archived too (needs doing before construction so appears here instead of usual archive location).
657 ar & *p_config;
658 ar & p_config;
659 }
660
665 template<class Archive, unsigned SPACE_DIM>
666 inline void load_construct_data(
667 Archive & ar, ExtendedBidomainTissue<SPACE_DIM> * t, const unsigned int file_version)
668 {
669 //Load conductivities of the conductivity of the second cell.
670 c_vector<double, SPACE_DIM> intra_cond_second_cell;
671 //note that simple: ar & intra_cond_second_cell may not be liked by some boost versions
672 for (unsigned i = 0; i < SPACE_DIM; i++)
673 {
674 double cond;
675 ar & cond;
676 intra_cond_second_cell(i) = cond;
677 }
678
679
680 std::vector<AbstractCardiacCellInterface*> cells_distributed;
681 std::vector<AbstractCardiacCellInterface*> cells_distributed_second_cell;
682 std::vector<boost::shared_ptr<AbstractStimulusFunction> > extra_stim;
683 std::vector<double> g_gaps;
685 ar & p_mesh;
686
687 // Load only the cells we actually own
688 t->LoadExtendedBidomainCells(
689 *ProcessSpecificArchive<Archive>::Get(), file_version, cells_distributed, cells_distributed_second_cell, g_gaps, p_mesh);
690
691 t->LoadExtracellularStimulus(
692 *ProcessSpecificArchive<Archive>::Get(), file_version, extra_stim, p_mesh);
693
694 // CreateIntracellularConductivityTensor() is called by AbstractCardiacTissue constructor and uses HeartConfig.
695 // (as does CreateExtracellularConductivityTensor). So make sure that it is
696 // archived too (needs doing before construction so appears here instead of usual archive location).
698 ar & *p_config;
699 ar & p_config;
700
701 ::new(t)ExtendedBidomainTissue<SPACE_DIM>(cells_distributed, cells_distributed_second_cell, extra_stim, g_gaps, p_mesh, intra_cond_second_cell);
702 }
703 }
704 } // namespace ...
705
706#endif /*EXTENDEDBIDOMAINTISSUE_HPP_*/
#define NEVER_REACHED
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
const std::vector< AbstractCardiacCellInterface * > & rGetCellsDistributed() const
DistributedVectorFactory * mpDistributedVectorFactory
Forward declaration which is going to be used for friendship.
DistributedVectorFactory * GetOriginalFactory()
bool IsGlobalIndexLocal(unsigned globalIndex)
ReplicatableVector mExtracellularStimulusCacheReplicated
void UpdateAdditionalCaches(unsigned globalIndex, unsigned localIndex, double nextTime)
void serialize(Archive &archive, const unsigned int version)
ReplicatableVector & rGetExtracellularStimulusCacheReplicated()
const std::vector< boost::shared_ptr< AbstractStimulusFunction > > & rGetExtracellularStimulusDistributed() const
virtual void SolveCellSystems(Vec existingSolution, double time, double nextTime, bool updateVoltage=false)
void SetGgapHeterogeneities(std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > > &rGgapHeterogeneityRegions, std::vector< double > rGgapValues)
ReplicatableVector mIionicCacheReplicatedSecondCell
std::vector< boost::shared_ptr< AbstractChasteRegion< SPACE_DIM > > > mGgapHeterogeneityRegions
std::vector< double > mGgapValues
static void LoadExtendedBidomainCells(Archive &archive, const unsigned int version, std::vector< AbstractCardiacCellInterface * > &rCells, std::vector< AbstractCardiacCellInterface * > &rSecondCells, std::vector< double > &rGgaps, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)
ReplicatableVector & rGetIionicCacheReplicatedSecondCell()
ReplicatableVector & rGetGgapCacheReplicated()
AbstractConductivityTensors< SPACE_DIM, SPACE_DIM > * mpExtracellularConductivityTensors
const std::vector< AbstractCardiacCellInterface * > & rGetSecondCellsDistributed() const
std::vector< AbstractCardiacCellInterface * > mCellsDistributedSecondCell
ReplicatableVector mIntracellularStimulusCacheReplicatedSecondCell
c_vector< double, SPACE_DIM > mIntracellularConductivitiesSecondCell
boost::shared_ptr< AbstractStimulusFunction > GetExtracellularStimulus(unsigned globalIndex)
std::vector< boost::shared_ptr< AbstractStimulusFunction > > mExtracellularStimuliDistributed
ReplicatableVector & rGetIntracellularStimulusCacheReplicatedSecondCell()
AbstractConductivityTensors< SPACE_DIM, SPACE_DIM > * mpIntracellularConductivityTensorsSecondCell
void LoadExtracellularStimulus(Archive &archive, const unsigned int version, std::vector< boost::shared_ptr< AbstractStimulusFunction > > &rStimuli, AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM > *pMesh)
void SaveExtracellularStimulus(Archive &archive, const unsigned int version) const
c_vector< double, SPACE_DIM > GetIntracellularConductivitiesSecondCell() const
const c_matrix< double, SPACE_DIM, SPACE_DIM > & rGetExtracellularConductivityTensor(unsigned elementIndex)
std::vector< double > mGgapDistributed
friend class boost::serialization::access
AbstractCardiacCellInterface * GetCardiacSecondCell(unsigned globalIndex)
const std::vector< double > & rGetGapsDistributed() const
void SetUserSuppliedExtracellularStimulus(bool flag)
void SaveExtendedBidomainCells(Archive &archive, const unsigned int version) const
void SetIntracellularConductivitiesSecondCell(c_vector< double, SPACE_DIM > conductivities)
const c_matrix< double, SPACE_DIM, SPACE_DIM > & rGetIntracellularConductivityTensorSecondCell(unsigned elementIndex)
ReplicatableVector mGgapCacheReplicated
static HeartConfig * Instance()