HeartSolver.hpp 14.6 KB
Newer Older
thomaskummer's avatar
thomaskummer committed
1
2
3
4
5
6
7
8
9
10
11
12
13
//
//  HeartSolver.cpp
//  LifeV
//
//  Created by Thomas Kummer on 03.05.16.
//  Copyright © 2016 Thomas Kummer. All rights reserved.
//

#ifndef _HEARTDATA_H_
#define _HEARTDATA_H_


#include <stdio.h>
thomaskummer's avatar
thomaskummer committed
14
#include <lifev/em/solver/EMSolver.hpp>
thomaskummer's avatar
thomaskummer committed
15
#include <lifev/em/solver/circulation/Circulation.hpp>
thomaskummer's avatar
thomaskummer committed
16

thomaskummer's avatar
thomaskummer committed
17
#include <lifev/em/solver/HeartData.hpp>
thomaskummer's avatar
thomaskummer committed
18

thomaskummer's avatar
thomaskummer committed
19
20
21
22

namespace LifeV
{

thomaskummer's avatar
thomaskummer committed
23
#define PI 3.14159265359
thomaskummer's avatar
thomaskummer committed
24

thomaskummer's avatar
thomaskummer committed
25
    
thomaskummer's avatar
thomaskummer committed
26
27
28
29
template <class EmSolver>
class HeartSolver {
   
public:
thomaskummer's avatar
thomaskummer committed
30
    
thomaskummer's avatar
thomaskummer committed
31
    typedef RegionMesh<LinearTetra>                         mesh_Type;
thomaskummer's avatar
thomaskummer committed
32
    typedef boost::shared_ptr<mesh_Type>                    meshPtr_Typ;
thomaskummer's avatar
thomaskummer committed
33
34
35
36
    typedef ExporterHDF5<mesh_Type>                         exporter_Type;
    typedef boost::shared_ptr<exporter_Type>                exporterPtr_Type;
    
    
thomaskummer's avatar
thomaskummer committed
37
38
    HeartSolver(EmSolver& emSolver,  Circulation& circulationSolver) :
        M_emSolver          (emSolver),
thomaskummer's avatar
thomaskummer committed
39
40
        M_circulationSolver (circulationSolver),
        M_heartData         (HeartData())
thomaskummer's avatar
thomaskummer committed
41
    {}
thomaskummer's avatar
thomaskummer committed
42
    
thomaskummer's avatar
thomaskummer committed
43
    virtual ~HeartSolver() {}
thomaskummer's avatar
thomaskummer committed
44
45
46
47
48
49
50
51
52
53

    EmSolver& emSolver()
    {
        return M_emSolver;
    }
    
    Circulation& circulation()
    {
        return M_heartData;
    }
thomaskummer's avatar
thomaskummer committed
54
    
thomaskummer's avatar
thomaskummer committed
55
    const HeartData& data() const
thomaskummer's avatar
thomaskummer committed
56
57
58
59
    {
        return M_heartData;
    }
    
thomaskummer's avatar
thomaskummer committed
60
    void setup(const GetPot& datafile)
thomaskummer's avatar
thomaskummer committed
61
    {
thomaskummer's avatar
thomaskummer committed
62
        M_heartData.setup(datafile);
thomaskummer's avatar
thomaskummer committed
63
    }
thomaskummer's avatar
thomaskummer committed
64
    
thomaskummer's avatar
thomaskummer committed
65
    template <class lambda>
thomaskummer's avatar
thomaskummer committed
66
    void preload(const lambda& modifyFeBC, const std::vector<Real>& bcValues)
thomaskummer's avatar
thomaskummer committed
67
    {
thomaskummer's avatar
thomaskummer committed
68
        M_emSolver.structuralOperatorPtr() -> data() -> dataTime() -> setTime(0.0);
thomaskummer's avatar
thomaskummer committed
69
70
71
72
73
74
75
76
77
78
        
        auto preloadPressure = [] (std::vector<double> p, const int& step, const int& steps)
        {
            for (auto& i : p) {i *= double(step) / double(steps);}
            return p;
        };
        
        LifeChrono chronoSave;
        chronoSave.start();
        
thomaskummer's avatar
thomaskummer committed
79
        M_emSolver.saveSolution (-1.0);
thomaskummer's avatar
thomaskummer committed
80
        
thomaskummer's avatar
thomaskummer committed
81
        if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
82
83
84
85
86
87
88
89
90
91
92
        {
            std::cout << "\n*****************************************************************";
            std::cout << "\nData stored in " << chronoSave.diff() << " s";
            std::cout << "\n*****************************************************************\n";
        }
        
        LifeChrono chronoPreload;
        chronoPreload.start();
        
        for (int i (1); i <= data().preloadSteps(); i++)
        {
thomaskummer's avatar
thomaskummer committed
93
            if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
94
95
96
97
98
99
100
            {
                std::cout << "\n*****************************************************************";
                std::cout << "\nPreload step: " << i << " / " << data().preloadSteps();
                std::cout << "\n*****************************************************************\n";
            }
            
            // Update pressure b.c.
thomaskummer's avatar
thomaskummer committed
101
            modifyFeBC(preloadPressure(bcValues, i, data().preloadSteps() ));
thomaskummer's avatar
thomaskummer committed
102
103
            
            // Solve mechanics
thomaskummer's avatar
thomaskummer committed
104
105
            M_emSolver.bcInterfacePtr() -> updatePhysicalSolverVariables();
            M_emSolver.solveMechanics();
thomaskummer's avatar
thomaskummer committed
106
107
            
            // Safe preload steps
thomaskummer's avatar
thomaskummer committed
108
            if ( data().safePreload() ) M_emSolver.saveSolution (i-1);
thomaskummer's avatar
thomaskummer committed
109
110
        }
        
thomaskummer's avatar
thomaskummer committed
111
        if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
112
113
114
115
116
117
118
        {
            std::cout << "\n*****************************************************************";
            std::cout << "\nPreload done in: " << chronoPreload.diff();
            std::cout << "\n*****************************************************************\n";
        }

    }
thomaskummer's avatar
thomaskummer committed
119
120
    
    
thomaskummer's avatar
thomaskummer committed
121
    void restart(std::string& restartInput, const GetPot& command_line, Real& t)
thomaskummer's avatar
thomaskummer committed
122
    {
thomaskummer's avatar
thomaskummer committed
123
        const std::string restartDir = ""; //command_line.follow (problemFolder.c_str(), 2, "-rd", "--restartDir");
thomaskummer's avatar
thomaskummer committed
124
125
126
127
128
129
130
131
132
133
134
        
        Real dtExport = 10.;
        
        // Set time variable
        const unsigned int restartInputStr = std::stoi(restartInput);
        const unsigned int nIter = (restartInputStr - 1) * dtExport / data().dt_mechanics();
        t = nIter * data().dt_mechanics();
        
        // Set time exporter time index
        M_emSolver.setTimeIndex(restartInputStr + 1);
        //solver.importHdf5();
thomaskummer's avatar
thomaskummer committed
135

thomaskummer's avatar
thomaskummer committed
136
        // Load restart solutions from output files
thomaskummer's avatar
thomaskummer committed
137
        std::string polynomialDegree = data().elementOrder();
thomaskummer's avatar
thomaskummer committed
138

thomaskummer's avatar
thomaskummer committed
139
        ElectrophysiologyUtility::importVectorField ( M_emSolver.structuralOperatorPtr() -> displacementPtr(), "MechanicalSolution" , "displacement", M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
thomaskummer's avatar
thomaskummer committed
140
141
142
        ElectrophysiologyUtility::importScalarField (M_emSolver.activationModelPtr() -> fiberActivationPtr(), "ActivationSolution" , "Activation", M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        //ElectrophysiologyUtility::importScalarField (solver.activationTimePtr(), "ActivationTimeSolution" , "Activation Time", solver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        
thomaskummer's avatar
thomaskummer committed
143
144
145
146
        for ( unsigned int i = 0; i < M_emSolver.electroSolverPtr()->globalSolution().size() ; ++i )
        {
            ElectrophysiologyUtility::importScalarField (M_emSolver.electroSolverPtr()->globalSolution().at(i), "ElectroSolution" , ("Variable" + std::to_string(i)), M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        }
thomaskummer's avatar
thomaskummer committed
147

thomaskummer's avatar
thomaskummer committed
148
149
150
151
        if ( 0 == M_emSolver.comm()->MyPID() )
        {
            std::cout << "\nLoad from restart: " << restartInput << ",  nIterCirculation = " << nIter << ",  time = " << t << std::endl;
        }
thomaskummer's avatar
thomaskummer committed
152
        
thomaskummer's avatar
thomaskummer committed
153
        M_circulationSolver.restartFromFile ( restartDir + "solution.dat" , nIter );
thomaskummer's avatar
thomaskummer committed
154
155
    }
    
thomaskummer's avatar
thomaskummer committed
156
    
thomaskummer's avatar
thomaskummer committed
157
    void createPatch (EMSolver<RegionMesh<LinearTetra>, EMMonodomainSolver<RegionMesh<LinearTetra> > >& solver, const Vector3D& center, const Real& radius, const int& currentFlag, const int& newFlag)
thomaskummer's avatar
thomaskummer committed
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
    {
        for (auto& mesh : solver.mesh())
        {
            for (int j(0); j < mesh->numBoundaryFacets(); j++)
            {
                auto& face = mesh->boundaryFacet(j);
                auto faceFlag = face.markerID();
                
                if (faceFlag == currentFlag || faceFlag == 470 || faceFlag == 471)
                {
                    int numPointsInsidePatch (0);
                    
                    for (int k(0); k < 3; ++k)
                    {
                        auto coord = face.point(k).coordinates();
                        bool pointInPatch = (coord - center).norm() < radius;
                        
                        if (pointInPatch)
                        {
                            ++numPointsInsidePatch;
                        }
                    }
                    
                    if (numPointsInsidePatch > 2)
                    {
                        face.setMarkerID(newFlag);
                    }
                    
                }
            }
        }
    }
    
thomaskummer's avatar
thomaskummer committed
191
192
193
194
195
    boost::shared_ptr<VectorEpetra> directionalVectorField (const boost::shared_ptr<FESpace<RegionMesh<LinearTetra>, MapEpetra >> dFeSpace, Vector3D& direction, const Real& disp)
    {
        boost::shared_ptr<VectorEpetra> vectorField (new VectorEpetra( dFeSpace->map(), Repeated ));
        auto nCompLocalDof = vectorField->epetraVector().MyLength() / 3;
        
thomaskummer's avatar
thomaskummer committed
196
        direction.normalize();
thomaskummer's avatar
thomaskummer committed
197
198
199
200
201
202
203
        direction *= disp;
        
        for (int j (0); j < nCompLocalDof; ++j)
        {
            UInt iGID = vectorField->blockMap().GID (j);
            UInt jGID = vectorField->blockMap().GID (j + nCompLocalDof);
            UInt kGID = vectorField->blockMap().GID (j + 2 * nCompLocalDof);
thomaskummer's avatar
thomaskummer committed
204

thomaskummer's avatar
thomaskummer committed
205
206
207
208
209
210
211
212
            (*vectorField)[iGID] = direction[0];
            (*vectorField)[jGID] = direction[1];
            (*vectorField)[kGID] = direction[2];
        }
        
        return vectorField;
    }
    
thomaskummer's avatar
thomaskummer committed
213
    static Real Iapp (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
thomaskummer's avatar
thomaskummer committed
214
215
216
217
218
219
220
    {
        bool coords ( Y < -7. );
        //bool coords ( Y > 4. ); //( Y > 1.5 && Y < 3 );
        bool time ( fmod(t, 800.) < 4 && fmod(t, 800.) > 2);
        return ( coords && time ? 30 : 0 );
    }
    
thomaskummer's avatar
thomaskummer committed
221
    Real sinSquared (const Real& time, const Real& Tmax, const Real& tmax, const Real& tduration) const
thomaskummer's avatar
thomaskummer committed
222
    {
thomaskummer's avatar
thomaskummer committed
223
        Real timeInPeriod = fmod(time-tmax+0.5*tduration, 800.);
thomaskummer's avatar
thomaskummer committed
224
        bool inPeriod ( timeInPeriod < tduration && timeInPeriod > 0);
thomaskummer's avatar
thomaskummer committed
225
        Real sinusSquared = std::pow( std::sin(timeInPeriod * PI / tduration) , 2 ) * Tmax;
thomaskummer's avatar
thomaskummer committed
226
        return ( inPeriod ? sinusSquared : 0 );
thomaskummer's avatar
thomaskummer committed
227
228
    }
    
thomaskummer's avatar
thomaskummer committed
229
    
thomaskummer's avatar
thomaskummer committed
230
    template<class bcVectorType>
thomaskummer's avatar
thomaskummer committed
231
    void extrapolate4thOrderAdamBashforth(bcVectorType& bcValues, bcVectorType& bcValuesPre, const Real& dpMax)
thomaskummer's avatar
thomaskummer committed
232
233
234
235
236
237
    {
        VectorSmall<4> ABcoef;
        ABcoef (0) = 55/24; ABcoef (1) = -59/24; ABcoef (2) = 37/24; ABcoef (3) = -3/8;
        
        for ( unsigned int i = ABcoef.size() - 1; i > 0; --i )
        {
thomaskummer's avatar
thomaskummer committed
238
239
            m_ABdplv(i) = m_ABdplv(i-1);
            m_ABdprv(i) = m_ABdprv(i-1);
thomaskummer's avatar
thomaskummer committed
240
241
        }
        
thomaskummer's avatar
thomaskummer committed
242
243
        m_ABdplv(0) = bcValues[0] - bcValuesPre[0];
        m_ABdprv(0) = bcValues[1] - bcValuesPre[1];
thomaskummer's avatar
thomaskummer committed
244
245
246
        
        bcValuesPre = bcValues;
        
thomaskummer's avatar
thomaskummer committed
247
248
        bcValues[0] += std::min( std::max( ABcoef.dot( m_ABdplv ) , - dpMax ) , dpMax );
        bcValues[1] += std::min( std::max( ABcoef.dot( m_ABdprv ) , - dpMax ) , dpMax );
thomaskummer's avatar
thomaskummer committed
249
    }
thomaskummer's avatar
thomaskummer committed
250
    
thomaskummer's avatar
thomaskummer committed
251
    
thomaskummer's avatar
thomaskummer committed
252
    void setupExporter(std::string problemFolder = "./", std::string outputFileName = "heartSolution")
thomaskummer's avatar
thomaskummer committed
253
254
    {
        m_exporter.reset (new exporter_Type());
thomaskummer's avatar
thomaskummer committed
255
256
        setupExporter(*m_exporter, M_emSolver.localMeshPtr(), M_emSolver.comm(), outputFileName, problemFolder);

thomaskummer's avatar
thomaskummer committed
257
258
        m_exporter->addVariable (  ExporterData<RegionMesh<LinearTetra> >::VectorField,
                                   "displacement",
thomaskummer's avatar
thomaskummer committed
259
260
                                   M_emSolver.structuralOperatorPtr()->dispFESpacePtr(),
                                   M_emSolver.structuralOperatorPtr()->displacementPtr(),
thomaskummer's avatar
thomaskummer committed
261
262
263
264
                                   UInt (0) );
    }

    
thomaskummer's avatar
thomaskummer committed
265
266
267
268
269
270
271
272
273
274
275
276
277
278
    template<class Mesh>
    void setupExporter (ExporterHDF5<Mesh>& exporter,
                        boost::shared_ptr<Mesh> localMeshPtr,
                        boost::shared_ptr<Epetra_Comm> commPtr,
                        std::string fileName,
                        std::string folder)
    {
        exporter.setMeshProcId (localMeshPtr, commPtr->MyPID() );
        exporter.setPrefix (fileName);
        exporter.exportPID (localMeshPtr, commPtr);
        exporter.setPostDir (folder);
    }
    
    
thomaskummer's avatar
thomaskummer committed
279
    exporterPtr_Type exporter()
thomaskummer's avatar
thomaskummer committed
280
281
282
283
284
    {
        return m_exporter;
    }
    
    
thomaskummer's avatar
thomaskummer committed
285
protected:
thomaskummer's avatar
thomaskummer committed
286
    
thomaskummer's avatar
thomaskummer committed
287
    
thomaskummer's avatar
thomaskummer committed
288
289
    EmSolver& M_emSolver;
    Circulation& M_circulationSolver;
thomaskummer's avatar
thomaskummer committed
290
    
thomaskummer's avatar
thomaskummer committed
291
    HeartData M_heartData;
thomaskummer's avatar
thomaskummer committed
292
    
thomaskummer's avatar
thomaskummer committed
293
    exporterPtr_Type m_exporter;
thomaskummer's avatar
thomaskummer committed
294
    
thomaskummer's avatar
thomaskummer committed
295
296
297
    VectorSmall<2> M_pressure;
    VectorSmall<2> M_volume;

thomaskummer's avatar
thomaskummer committed
298
    VectorSmall<4> m_ABdplv, m_ABdprv;
thomaskummer's avatar
thomaskummer committed
299

thomaskummer's avatar
thomaskummer committed
300
    
thomaskummer's avatar
thomaskummer committed
301
    
thomaskummer's avatar
thomaskummer committed
302
303
304
    
    
    
thomaskummer's avatar
thomaskummer committed
305
306
307
308
309
310
311
312
313
314
315
    std::string pipeToString ( const char* command )
    {
        FILE* file = popen( command, "r" ) ;
        std::ostringstream stm ;
        char line[6] ;
        fgets( line, 6, file );
        stm << line;
        pclose(file) ;
        return stm.str() ;
    };
    
thomaskummer's avatar
thomaskummer committed
316
317
318


    Real patchDispFunNormal (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
thomaskummer's avatar
thomaskummer committed
319
    {
thomaskummer's avatar
thomaskummer committed
320
        return (-0.000 - 0.00005*t);// sinSquared(t, 0.1, 50, 100)); // -0.001;// (t * 1e-5);
thomaskummer's avatar
thomaskummer committed
321
322
    }
    
thomaskummer's avatar
thomaskummer committed
323
    Real patchFunction (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
thomaskummer's avatar
thomaskummer committed
324
    {
thomaskummer's avatar
thomaskummer committed
325
        Real disp = std::pow( std::sin(fmod(t, 800.) * 3.14159265359/300) , 2 )*15;
thomaskummer's avatar
thomaskummer committed
326
327
328
        return disp;
    }
    
thomaskummer's avatar
thomaskummer committed
329
    Real potentialMultiplyerFcn (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
thomaskummer's avatar
thomaskummer committed
330
    {
thomaskummer's avatar
thomaskummer committed
331
332
        bool time ( fmod(t, 800.) < 4 && fmod(t, 800.) > 2);
        return 1.4 * time; // ( Y < 2.5 && Y > 0.5 ? 1.0 : 0.0 );
thomaskummer's avatar
thomaskummer committed
333
334
    }
    
thomaskummer's avatar
thomaskummer committed
335
    Real patchDispFun1 (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
thomaskummer's avatar
thomaskummer committed
336
    {
thomaskummer's avatar
thomaskummer committed
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
        switch (i)
        {
            case 0:
                return (t);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return (t);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
    }
    
    Real patchDispFun2 (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
    {
        switch (i)
        {
            case 0:
                return (-t);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return (-t);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
    }
    
    Real normalDirection ( const Real& /*t*/, const Real& x , const Real& y, const Real& z, const ID& i)
    {
        Real nnorm = std::sqrt(x * x + y * y + z * z);
        switch (i)
        {
            case 0:
                return 1/std::sqrt(2);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return 1/std::sqrt(2);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
thomaskummer's avatar
thomaskummer committed
394
    }
thomaskummer's avatar
thomaskummer committed
395
396

    
thomaskummer's avatar
thomaskummer committed
397
    
thomaskummer's avatar
thomaskummer committed
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
    Real
    externalPower ( const VectorEpetra& dispCurrent,
                    const VectorEpetra& dispPrevious,
                    const boost::shared_ptr<ETFESpace< RegionMesh<LinearTetra>, MapEpetra, 3, 3 > > dispETFESpace,
                    Real pressure,
                    Real dt,
                    const unsigned int bdFlag) const
    {
        VectorEpetra traction ( dispCurrent.map() );
        VectorEpetra velocity ( (dispCurrent - dispPrevious) / dt );
        
        MatrixSmall<3,3> Id;
        Id(0,0) = 1.; Id(0,1) = 0., Id(0,2) = 0.;
        Id(1,0) = 0.; Id(1,1) = 1., Id(1,2) = 0.;
        Id(2,0) = 0.; Id(2,1) = 0., Id(2,2) = 1.;
        
        {
            using namespace ExpressionAssembly;
            
            auto I = value(Id);
            auto Grad_u = grad( dispETFESpace, dispCurrent, 0);
            auto F =  Grad_u + I;
            auto FmT = minusT(F);
            auto J = det(F);
            auto p = value(pressure);
            
            QuadratureBoundary myBDQR (buildTetraBDQR (quadRuleTria7pt) );
            
            integrate ( boundary ( dispETFESpace->mesh(), bdFlag),
                       myBDQR,
                       dispETFESpace,
                       p * J * dot( FmT * Nface,  phi_i)
                       //p * J * dot( FmT * Nface,  phi_i)
                       //value(-1.0) * J * dot (vE1, FmT * Nface) * phi_i) >> intergral
                       ) >> traction;
            
            traction.globalAssemble();
        }
        
        return traction.dot(velocity);
    }
    
    
thomaskummer's avatar
thomaskummer committed
441
442
443
444
};

}

thomaskummer's avatar
thomaskummer committed
445
#endif