EMSolver.hpp 39.6 KB
Newer Older
Simone Rossi's avatar
Simone Rossi committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
//@HEADER
/*
 *******************************************************************************

 Copyright (C) 2004, 2005, 2007 EPFL, Politecnico di Milano, INRIA
 Copyright (C) 2010 EPFL, Politecnico di Milano, Emory University

 This file is part of LifeV.

 LifeV is free software; you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 LifeV is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 Lesser General Public License for more details.

 You should have received a copy of the GNU Lesser General Public License
 along with LifeV.  If not, see <http://www.gnu.org/licenses/>.

 *******************************************************************************
 */
//@HEADER
/*!
 @file
 @brief Class for solving the Monodomain equations in electrophysiology.

 @date 02-2013
 @author Simone Rossi <simone.rossi@epfl.ch>

 @last update 02-2013

 This class provides interfaces to solve the monodomain equation
 ( reaction diffusion equation ) using the ETA framework.
 The solution can be performed using three different methods:
 -operator splitting method (at this point available only with forward Euler
 for the reaction step and backward Euler for the diffusion step. );
 -Ionic Currents Interpolation (at this point only forward Euler);
 -State Variable interpolation (at this point only forward Euler).
 */

#ifndef _EMSOLVER_H_
#define _EMSOLVER_H_

Simone Rossi's avatar
Simone Rossi committed
47
#include <lifev/core/mesh/MeshLoadingUtility.hpp>
Simone Rossi's avatar
Simone Rossi committed
48

Simone Rossi's avatar
Simone Rossi committed
49
#include <lifev/em/solver/electrophysiology/EMMonodomainSolver.hpp>
Simone Rossi's avatar
Simone Rossi committed
50
#include <lifev/em/solver/electrophysiology/IonicModelsList.hpp>
Simone Rossi's avatar
Simone Rossi committed
51
52
53
#include <lifev/em/solver/mechanics/EMStructuralOperator.hpp>


thomaskummer's avatar
thomaskummer committed
54
55
#include <lifev/structure/solver/WallTensionEstimator.hpp>

Simone Rossi's avatar
Simone Rossi committed
56
57
//#include <lifev/em/solver/activation/activeStressModels/ActiveStressActivation.hpp>
#include <lifev/em/solver/activation/ActivationModelsList.hpp>
Simone Rossi's avatar
Simone Rossi committed
58

Simone Rossi's avatar
Simone Rossi committed
59
60
61
62
63
64
65
66
67
68
69
//
//#include <lifev/em/solver/EMStructuralOperator.hpp>
//#include <lifev/em/solver/EMGeneralizedActiveHolzapfelOgdenMaterial.hpp>
//#include <lifev/em/solver/EMActiveStrainSolver.hpp>
//#include <lifev/core/interpolation/RBFlocallyRescaledVectorial.hpp>
//#include <lifev/core/interpolation/RBFlocallyRescaledScalar.hpp>
//#include <lifev/core/interpolation/RBFrescaledVectorial.hpp>
//#include <lifev/core/interpolation/RBFrescaledScalar.hpp>
////#include <lifev/core/interpolation/RBFscalar.hpp>
//#include <lifev/core/interpolation/RBFvectorial.hpp>
//
Simone Rossi's avatar
Simone Rossi committed
70
#include <lifev/bc_interface/3D/bc/BCInterface3D.hpp>
Simone Rossi's avatar
Simone Rossi committed
71
72
73
//
//
//#include <lifev/em/solver/EMEvaluate.hpp>
Simone Rossi's avatar
Simone Rossi committed
74
75
76
77
78
79

namespace LifeV
{

//! EMSolver - Class featuring the solution of the electromechanical problem with monodomain equation

Simone Rossi's avatar
Simone Rossi committed
80
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
81
82
class EMSolver
{
Simone Rossi's avatar
Simone Rossi committed
83
public:
Simone Deparis's avatar
Simone Deparis committed
84
    typedef Mesh                                              mesh_Type;
Simone Rossi's avatar
Simone Rossi committed
85

Simone Deparis's avatar
Simone Deparis committed
86
    typedef boost::shared_ptr<mesh_Type>                      meshPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
87

Simone Deparis's avatar
Simone Deparis committed
88
    typedef Epetra_Comm                                       comm_Type;
Simone Rossi's avatar
Simone Rossi committed
89

Simone Deparis's avatar
Simone Deparis committed
90
    typedef boost::shared_ptr<Epetra_Comm>                    commPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
91

Simone Deparis's avatar
Simone Deparis committed
92
    typedef VectorEpetra                                      vector_Type;
thomaskummer's avatar
thomaskummer committed
93
    
Simone Deparis's avatar
Simone Deparis committed
94
    typedef StructuralConstitutiveLawData                     structureData_Type;
Simone Rossi's avatar
Simone Rossi committed
95

Simone Deparis's avatar
Simone Deparis committed
96
    typedef boost::shared_ptr<structureData_Type>             structureDataPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
97

Simone Deparis's avatar
Simone Deparis committed
98
    typedef EMStructuralOperator< mesh_Type >                 structuralOperator_Type;
Simone Rossi's avatar
Simone Rossi committed
99

Simone Deparis's avatar
Simone Deparis committed
100
    typedef boost::shared_ptr< structuralOperator_Type >      structuralOperatorPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
101

Simone Deparis's avatar
Simone Deparis committed
102
    typedef BCHandler                                          bc_Type;
Simone Rossi's avatar
Simone Rossi committed
103

Simone Deparis's avatar
Simone Deparis committed
104
    typedef boost::shared_ptr< bc_Type >                       bcPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
105

Simone Deparis's avatar
Simone Deparis committed
106
    typedef StructuralOperator< mesh_Type >                   physicalSolver_Type;
Simone Rossi's avatar
Simone Rossi committed
107

Simone Deparis's avatar
Simone Deparis committed
108
    typedef BCInterface3D< bc_Type, physicalSolver_Type >  bcInterface_Type;
Simone Rossi's avatar
Simone Rossi committed
109

Simone Deparis's avatar
Simone Deparis committed
110
    typedef boost::shared_ptr< bcInterface_Type >              bcInterfacePtr_Type;
Simone Rossi's avatar
Simone Rossi committed
111

Simone Rossi's avatar
Simone Rossi committed
112
    typedef boost::shared_ptr<Activation>                     activationModelPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
113

Simone Deparis's avatar
Simone Deparis committed
114
    typedef ElectroSolver                                      electroSolver_Type;
Simone Rossi's avatar
Simone Rossi committed
115

Simone Deparis's avatar
Simone Deparis committed
116
    typedef boost::shared_ptr<electroSolver_Type>              electroSolverPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
117

Simone Deparis's avatar
Simone Deparis committed
118
    typedef ElectroIonicModel                                  ionicModel_Type;
Simone Rossi's avatar
Simone Rossi committed
119

Simone Deparis's avatar
Simone Deparis committed
120
    typedef boost::shared_ptr<ionicModel_Type>                 ionicModelPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
121

Simone Deparis's avatar
Simone Deparis committed
122
    typedef ExporterHDF5< Mesh >                               exporter_Type;
Simone Rossi's avatar
Simone Rossi committed
123

Simone Deparis's avatar
Simone Deparis committed
124
    typedef boost::shared_ptr<ExporterHDF5< Mesh > >           exporterPtr_Type;
Simone Rossi's avatar
Simone Rossi committed
125
126
127
128
129
130
131
132
133
134

    typedef FESpace< RegionMesh<LinearTetra>, MapEpetra >      solidFESpace_Type;

    typedef boost::shared_ptr<solidFESpace_Type>                solidFESpacePtr_Type;

    typedef ETFESpace< RegionMesh<LinearTetra>, MapEpetra, 3, 3 > solidETFESpace_Type;

    typedef boost::shared_ptr<solidETFESpace_Type>              solidETFESpacePtr_Type;

    typedef boost::function < Real (const Real& t,
Simone Deparis's avatar
Simone Deparis committed
135
136
                                    const Real&    x,
                                    const Real&    y,
Simone Rossi's avatar
Simone Rossi committed
137
138
139
140
141
                                    const Real& z,
                                    const ID&   /*i*/ ) >       function_Type;



Simone Rossi's avatar
Simone Rossi committed
142
    EMSolver(commPtr_Type comm);
Simone Rossi's avatar
Simone Rossi committed
143

Simone Deparis's avatar
Simone Deparis committed
144
    EMSolver (const EMSolver& solver);
Simone Rossi's avatar
Simone Rossi committed
145

Simone Rossi's avatar
Simone Rossi committed
146

Simone Rossi's avatar
Simone Rossi committed
147

Simone Rossi's avatar
Simone Rossi committed
148
    void loadMesh (std::string meshName, std::string meshPath)
Simone Deparis's avatar
Simone Deparis committed
149
    {
thomaskummer's avatar
thomaskummer committed
150
151
152
153
154
        if (M_commPtr -> MyPID() == 0)
        {
            std::cout << "\nEMSolver: loadMesh ...";
        }
        
Simone Rossi's avatar
Simone Rossi committed
155
        M_fullMeshPtr.reset( new Mesh() );
Simone Deparis's avatar
Simone Deparis committed
156
        MeshUtility::loadMesh (M_localMeshPtr, M_fullMeshPtr, meshName, meshPath);
Simone Rossi's avatar
Simone Rossi committed
157
158
159
160
161
162
163
164
165
        if(M_commPtr)
        {
			M_localMeshPtr->setComm(M_commPtr);
			M_fullMeshPtr->setComm(M_commPtr);
        }
        else
        {
        	M_commPtr = M_localMeshPtr -> comm();
        }
thomaskummer's avatar
thomaskummer committed
166
167
168
169
170
        
        if (M_commPtr -> MyPID() == 0)
        {
            std::cout << " done";
        }
Simone Deparis's avatar
Simone Deparis committed
171
    }
Simone Rossi's avatar
Simone Rossi committed
172

thomaskummer's avatar
thomaskummer committed
173
    void setupElectroExporter ( std::string problemFolder = "./", std::string outputFileName = "ElectroSolution" )
Simone Deparis's avatar
Simone Deparis committed
174
175
176
    {
        M_electroSolverPtr -> setupExporter (*M_electroExporterPtr, outputFileName, problemFolder);
    }
Simone Rossi's avatar
Simone Rossi committed
177

Simone Rossi's avatar
Simone Rossi committed
178
    void setupActivationExporter ( std::string problemFolder = "./", std::string outputFileName = "ActivationSolution" )
Simone Rossi's avatar
Simone Rossi committed
179
    {
Simone Deparis's avatar
Simone Deparis committed
180
        EMUtility::setupExporter<Mesh> (*M_activationExporterPtr, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
Simone Rossi's avatar
Simone Rossi committed
181
    }
thomaskummer's avatar
thomaskummer committed
182
    
thomaskummer's avatar
thomaskummer committed
183
184
185
186
//    void setupActivationTimeExporter ( std::string problemFolder = "./", std::string outputFileName = "ActivationTimeSolution" )
//    {
//        EMUtility::setupExporter<Mesh> (*M_activationTimeExporterPtr, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
//    }
Simone Rossi's avatar
Simone Rossi committed
187

thomaskummer's avatar
thomaskummer committed
188
189
190
191
    void setupVonMisesStressExporter ( std::string problemFolder = "./", std::string outputFileName = "VonMisesStress" )
    {
        EMUtility::setupExporter<Mesh> (*M_vonMisesStressExporterPtr, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
    }
thomaskummer's avatar
thomaskummer committed
192
    
thomaskummer's avatar
thomaskummer committed
193
194
195
196
197
198
199
200
201
//    void setupVonMisesStressExporterP ( std::string problemFolder = "./", std::string outputFileName = "VonMisesStressP" )
//    {
//        EMUtility::setupExporter<Mesh> (*M_vonMisesStressExporterPtrP, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
//    }
//    
//    void setupVonMisesStressExporterA ( std::string problemFolder = "./", std::string outputFileName = "VonMisesStressA" )
//    {
//        EMUtility::setupExporter<Mesh> (*M_vonMisesStressExporterPtrA, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
//    }
thomaskummer's avatar
thomaskummer committed
202

thomaskummer's avatar
thomaskummer committed
203
    void setupMechanicsExporter ( std::string problemFolder = "./", std::string outputFileName = "MechanicalSolution" )
Simone Rossi's avatar
Simone Rossi committed
204
    {
Simone Deparis's avatar
Simone Deparis committed
205
206
207
208
        if (M_mechanicsExporterPtr)
        {
            EMUtility::setupExporter<Mesh> (*M_mechanicsExporterPtr, M_localMeshPtr, M_commPtr, outputFileName, problemFolder);
        }
Simone Rossi's avatar
Simone Rossi committed
209
210
    }

211
212
    void importHdf5 ();

Simone Deparis's avatar
Simone Deparis committed
213
214
215
    void setupExporters (std::string problemFolder   = "./",
                         std::string electroFileName = "ElectroSolution",
                         std::string activationFileName  = "ActivationSolution",
thomaskummer's avatar
thomaskummer committed
216
                         //std::string activationTimeFileName  = "ActivationTimeSolution",
thomaskummer's avatar
thomaskummer committed
217
                         std::string mechanicsFileName  = "MechanicalSolution",
thomaskummer's avatar
thomaskummer committed
218
                         std::string vonMisesStressFileName  = "VonMisesStress");
Simone Rossi's avatar
Simone Rossi committed
219

Thomas Kummer's avatar
Thomas Kummer committed
220
221
222
223
    void setupElectroSolver ( GetPot& dataFile, Teuchos::ParameterList& list)
    {
        setupElectroSolver (dataFile);
    }
Simone Rossi's avatar
Simone Rossi committed
224

Thomas Kummer's avatar
Thomas Kummer committed
225
226
    void setupElectroSolver ( GetPot& dataFile );
    
Simone Deparis's avatar
Simone Deparis committed
227
    void setupMechanicalSolver ( GetPot& dataFile);
Simone Rossi's avatar
Simone Rossi committed
228

Simone Deparis's avatar
Simone Deparis committed
229
230
231
    void setupMechanicalBC (std::string data_file_name,
                            std::string section,
                            solidFESpacePtr_Type dFESpace);
Simone Rossi's avatar
Simone Rossi committed
232

Simone Rossi's avatar
Simone Rossi committed
233
    void setupActivation (const MapEpetra& map)
Simone Deparis's avatar
Simone Deparis committed
234
235
236
    {
        if (M_commPtr -> MyPID() == 0)
        {
thomaskummer's avatar
thomaskummer committed
237
            std::cout << "\nEMSolver: setupActivation ... " << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
238
        }
thomaskummer's avatar
thomaskummer committed
239
        
Simone Rossi's avatar
Simone Rossi committed
240
241
242
243
        M_activationModelPtr.reset ( Activation::EMActivationFactory::instance().createObject ( M_data.activationParameter<std::string>( "ActivationModel" ) ) );
        M_activationModelPtr->setup(M_data, map);
        M_activationModelPtr->setVariablesPtr(*M_electroSolverPtr);
        M_activationModelPtr->setI4fPtr( M_EMStructuralOperatorPtr -> I4fPtr() );
thomaskummer's avatar
thomaskummer committed
244
245
246

        if (M_commPtr -> MyPID() == 0)
        {
thomaskummer's avatar
thomaskummer committed
247
            std::cout << "EMSolver: setupActivation - done " << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
248
249
        }

Simone Deparis's avatar
Simone Deparis committed
250
    }
Simone Rossi's avatar
Simone Rossi committed
251

Thomas Kummer's avatar
Thomas Kummer committed
252
253
254
255
    void setup (GetPot& dataFile, Teuchos::ParameterList& list)
    {
        setup (dataFile);
    }
Simone Rossi's avatar
Simone Rossi committed
256

Thomas Kummer's avatar
Thomas Kummer committed
257
258
    void setup (GetPot& dataFile );
    
Simone Rossi's avatar
Simone Rossi committed
259
    void buildMechanicalSystem()
Simone Deparis's avatar
Simone Deparis committed
260
    {
Simone Rossi's avatar
Simone Rossi committed
261
262
    	//Here we call the buildSystem Of the Structural operator
    	// the coefficient is the density in front of the mass matrix
Simone Deparis's avatar
Simone Deparis committed
263
264
        M_EMStructuralOperatorPtr -> buildSystem (1.0);
    }
Simone Rossi's avatar
Simone Rossi committed
265

Simone Rossi's avatar
Simone Rossi committed
266
    void buildElectroSystem()
Simone Deparis's avatar
Simone Deparis committed
267
268
269
    {
        M_electroSolverPtr -> setupMatrices();
    }
Simone Rossi's avatar
Simone Rossi committed
270

Simone Rossi's avatar
Simone Rossi committed
271
     void buildSystem()
Simone Deparis's avatar
Simone Deparis committed
272
273
274
275
    {
        buildMechanicalSystem();
        buildElectroSystem();
    }
Simone Rossi's avatar
Simone Rossi committed
276

Simone Rossi's avatar
Simone Rossi committed
277
    void initializeElectroVariables()
Simone Deparis's avatar
Simone Deparis committed
278
279
280
    {
        M_electroSolverPtr -> setInitialConditions();
    }
Simone Rossi's avatar
Simone Rossi committed
281

Simone Rossi's avatar
Simone Rossi committed
282
    void initialize()
Simone Deparis's avatar
Simone Deparis committed
283
284
285
    {
        initializeElectroVariables();
    }
Simone Rossi's avatar
Simone Rossi committed
286

Simone Rossi's avatar
Simone Rossi committed
287
    bcInterfacePtr_Type bcInterfacePtr()
Simone Deparis's avatar
Simone Deparis committed
288
289
290
    {
        return M_bcInterfacePtr;
    }
Simone Rossi's avatar
Simone Rossi committed
291
292


293
294
295
296
297
    void setupFiberVector( const std::string& fileName,
						   const std::string& fieldName,
						   const std::string& postDir = "./",
						   const std::string& polynomialDegree = "P1"  )
    {
thomaskummer's avatar
thomaskummer committed
298
299
        if (M_commPtr -> MyPID() == 0) std::cout << "\nsetupFiberVector ... " << '\r' << std::flush;

300
301
    	setupMechanicalFiberVector(fileName, fieldName, postDir, polynomialDegree);
    	M_electroSolverPtr->setFiberPtr(getMechanicsFibers());
thomaskummer's avatar
thomaskummer committed
302
303
304
        
        if (M_commPtr -> MyPID() == 0) std::cout << "setupFiberVector - done" << '\r' << std::flush;

305
306
307
308
309
310
311
    }

    void setupMechanicalFiberVector( const std::string& fileName,
    		                         const std::string& fieldName,
									 const std::string& postDir = "./",
                                     const std::string& polynomialDegree = "P1"  )
    {
thomaskummer's avatar
thomaskummer committed
312
        if (M_commPtr -> MyPID() == 0) std::cout << "\nsetupMechanicalFiberVector ... " << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
313
        
314
        ElectrophysiologyUtility::importVectorField (getMechanicsFibers(),  fileName,  fieldName, M_localMeshPtr, postDir, polynomialDegree );
thomaskummer's avatar
thomaskummer committed
315
316
317
318
319
320
321
322
        
//        if ( polynomialDegree == "P1" )
//        {
//            FESpace<RegionMesh<LinearTetra> , MapEpetra > p2FESpace ( fullMeshPtr(), "P2", 1, fullMeshPtr() -> comm() );
//            vector_Type p2FibersRep (*getMechanicsFibers(), Repeated);
//            vector_Type p1FibersRep = M_EMStructuralOperatorPtr -> dispFESpacePtr() -> feToFEInterpolate(p2FESpace, p2FibersRep);
//            getMechanicsFibers().reset ( new vector_Type (p1FibersRep, Unique) );
//        }
thomaskummer's avatar
thomaskummer committed
323
        if (M_commPtr -> MyPID() == 0) std::cout << "setupMechanicalFiberVector - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
324

325
326
327
328
329
330
331
    }

    void setupMechanicalSheetVector( const std::string& fileName,
    		                         const std::string& fieldName,
									 const std::string& postDir = "./",
                                     const std::string& polynomialDegree = "P1"  )
    {
thomaskummer's avatar
thomaskummer committed
332
333
        if (M_commPtr -> MyPID() == 0) std::cout << "\nsetupMechanicalSheetVector ... " << '\r' << std::flush;

334
        ElectrophysiologyUtility::importVectorField (getMechanicsSheets(),  fileName,  fieldName, M_localMeshPtr, postDir, polynomialDegree );
thomaskummer's avatar
thomaskummer committed
335
336
        if (M_commPtr -> MyPID() == 0) std::cout << "setupMechanicalSheetVector - done" << '\r' << std::flush;

337
338
339
340
341
342
343
344
345
346
347
348
    }

    void setupElectroFiberVector( const std::string& fileName,
								  const std::string& fieldName,
								  const std::string& postDir = "./",
								  const std::string& polynomialDegree = "P1"  )
    {
        ElectrophysiologyUtility::importVectorField (getElectroFibers(), fileName,  fieldName, M_localMeshPtr, postDir, polynomialDegree );
    }



Simone Rossi's avatar
Simone Rossi committed
349
    void setupMechanicalFiberVector ( Real fx, Real fy, Real fz )
Simone Deparis's avatar
Simone Deparis committed
350
351
352
    {
        M_EMStructuralOperatorPtr -> EMMaterial() -> setupFiberVector ( fx, fy, fz);
    }
Simone Rossi's avatar
Simone Rossi committed
353

Simone Rossi's avatar
Simone Rossi committed
354
    void setupElectroFiberVector ( VectorSmall<3>& fibers)
Simone Deparis's avatar
Simone Deparis committed
355
356
357
    {
        M_electroSolverPtr -> setupFibers (fibers);
    }
Simone Rossi's avatar
Simone Rossi committed
358
359


Simone Rossi's avatar
Simone Rossi committed
360
    void setupFiberVector ( Real fx, Real fy, Real fz )
Simone Deparis's avatar
Simone Deparis committed
361
362
363
364
365
366
    {
        VectorSmall<3> f;
        f[0] = fx;
        f[1] = fy;
        f[2] = fz;
        setupElectroFiberVector (f);
Simone Rossi's avatar
Simone Rossi committed
367
        M_EMStructuralOperatorPtr -> EMMaterial() -> setupFiberVector(fx, fy, fz);
Simone Deparis's avatar
Simone Deparis committed
368
    }
Simone Rossi's avatar
Simone Rossi committed
369

Simone Rossi's avatar
Simone Rossi committed
370
371
372
373
374
375
    void setupSheetVector ( Real sx, Real sy, Real sz )
    {
        M_EMStructuralOperatorPtr -> EMMaterial() -> setupSheetVector(sx, sy, sz);
    }

    electroSolverPtr_Type electroSolverPtr()
Simone Deparis's avatar
Simone Deparis committed
376
377
378
    {
        return M_electroSolverPtr;
    }
Simone Rossi's avatar
Simone Rossi committed
379

Simone Rossi's avatar
Simone Rossi committed
380
    structuralOperatorPtr_Type structuralOperatorPtr()
Simone Deparis's avatar
Simone Deparis committed
381
382
383
    {
        return M_EMStructuralOperatorPtr;
    }
Simone Rossi's avatar
Simone Rossi committed
384

Simone Rossi's avatar
Simone Rossi committed
385
    activationModelPtr_Type  activationModelPtr()
Simone Deparis's avatar
Simone Deparis committed
386
387
388
    {
        return M_activationModelPtr;
    }
thomaskummer's avatar
thomaskummer committed
389
    
thomaskummer's avatar
thomaskummer committed
390
391
392
393
//    vectorPtr_Type activationTimePtr()
//    {
//        return M_activationTimePtr;
//    }
Simone Rossi's avatar
Simone Rossi committed
394

thomaskummer's avatar
thomaskummer committed
395
    void saveSolution (Real time, const bool& restart = 0);
thomaskummer's avatar
restart    
thomaskummer committed
396
397
398
    
    void setTimeIndex (const UInt& time);

Simone Rossi's avatar
Simone Rossi committed
399

Simone Deparis's avatar
Simone Deparis committed
400
    void closeExporters();
Simone Rossi's avatar
Simone Rossi committed
401

Simone Deparis's avatar
Simone Deparis committed
402
    void oneWayCoupling();
Simone Rossi's avatar
Simone Rossi committed
403

Simone Deparis's avatar
Simone Deparis committed
404
    void twoWayCoupling();
Simone Rossi's avatar
Simone Rossi committed
405

Simone Rossi's avatar
Simone Rossi committed
406
    void setAppliedCurrent (function_Type& stimulus, Real time = 0.0)
Simone Deparis's avatar
Simone Deparis committed
407
408
409
    {
        M_electroSolverPtr -> setAppliedCurrentFromFunction (stimulus, time);
    }
Simone Rossi's avatar
Simone Rossi committed
410
411


Simone Rossi's avatar
Simone Rossi committed
412
    void solveMechanics()
Simone Deparis's avatar
Simone Deparis committed
413
414
415
    {
        M_EMStructuralOperatorPtr -> iterate ( M_bcInterfacePtr -> handler() );
    }
Simone Rossi's avatar
Simone Rossi committed
416

417
418
419
420
421
    void solveMechanicsLin()
    {
        M_EMStructuralOperatorPtr -> solveLin ();
    }

Simone Rossi's avatar
Simone Rossi committed
422
423
    void solveElectrophysiology (function_Type& stimulus, Real time = 0.0);

Simone Rossi's avatar
Simone Rossi committed
424

Simone Rossi's avatar
Simone Rossi committed
425
    void solveActivation (Real dt);
thomaskummer's avatar
thomaskummer committed
426
    
thomaskummer's avatar
thomaskummer committed
427
    void computeI4f (VectorEpetra& i4f, VectorEpetra& f0_, VectorEpetra& disp, solidFESpacePtr_Type feSpacePtr);
Simone Rossi's avatar
Simone Rossi committed
428

Simone Rossi's avatar
Simone Rossi committed
429
430
431
432
433
434
435
436
437
438
439
440
441
    vectorPtr_Type getElectroFibers()
    {
    	return M_electroSolverPtr -> fiberPtr();
    }
    vectorPtr_Type getMechanicsFibers()
    {
    	return M_EMStructuralOperatorPtr -> EMMaterial() -> fiberVectorPtr();
    }
    vectorPtr_Type getMechanicsSheets()
    {
    	return M_EMStructuralOperatorPtr -> EMMaterial() -> sheetVectorPtr();
    }
    //  bcInterface_Type bcInterface()
Simone Deparis's avatar
Simone Deparis committed
442
443
444
    //  {
    //      return *M_bcInterfacePtr;
    //  }
Simone Rossi's avatar
Simone Rossi committed
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
    EMData& data()
    {
    	return M_data;
    }


    commPtr_Type comm() const
    {
    	return M_commPtr;
    }

    void setComm(commPtr_Type comm)
    {
    	M_commPtr = comm;
    }
Simone Rossi's avatar
Simone Rossi committed
460

461
    void showMe() const {}
462
463
464
465
466
467
468
469
470
471
    
    meshPtr_Type fullMeshPtr()
    {
        return M_fullMeshPtr;
    }
    
    meshPtr_Type localMeshPtr()
    {
        return M_localMeshPtr;
    }
472

thomaskummer's avatar
thomaskummer committed
473
    std::vector<meshPtr_Type> mesh()
thomaskummer's avatar
thomaskummer committed
474
    {
thomaskummer's avatar
thomaskummer committed
475
        std::vector<meshPtr_Type> meshVector;
thomaskummer's avatar
thomaskummer committed
476
477
        meshVector.push_back(M_fullMeshPtr);
        meshVector.push_back(M_localMeshPtr);
thomaskummer's avatar
thomaskummer committed
478
        return meshVector;
thomaskummer's avatar
thomaskummer committed
479
    }
480
    
Simone Rossi's avatar
Simone Rossi committed
481
protected:
Simone Rossi's avatar
Simone Rossi committed
482
public:
Simone Deparis's avatar
Simone Deparis committed
483
484
485
486
    electroSolverPtr_Type                M_electroSolverPtr;
    activationModelPtr_Type              M_activationModelPtr;
    bcInterfacePtr_Type                  M_bcInterfacePtr;
    structuralOperatorPtr_Type           M_EMStructuralOperatorPtr;
Simone Rossi's avatar
Simone Rossi committed
487

Simone Deparis's avatar
Simone Deparis committed
488
489
490
    exporterPtr_Type                     M_electroExporterPtr;
    exporterPtr_Type                     M_activationExporterPtr;
    exporterPtr_Type                     M_mechanicsExporterPtr;
thomaskummer's avatar
thomaskummer committed
491
//    exporterPtr_Type                     M_activationTimeExporterPtr;
thomaskummer's avatar
thomaskummer committed
492
    exporterPtr_Type                     M_vonMisesStressExporterPtr;
thomaskummer's avatar
thomaskummer committed
493
494
//    exporterPtr_Type                     M_vonMisesStressExporterPtrP;
//    exporterPtr_Type                     M_vonMisesStressExporterPtrA;
thomaskummer's avatar
thomaskummer committed
495
    
Simone Deparis's avatar
Simone Deparis committed
496
497
    meshPtr_Type                         M_localMeshPtr;
    meshPtr_Type                         M_fullMeshPtr;
thomaskummer's avatar
thomaskummer committed
498
    
thomaskummer's avatar
thomaskummer committed
499
    //vectorPtr_Type                       M_activationTimePtr;
Simone Rossi's avatar
Simone Rossi committed
500
501

    bool                                 M_oneWayCoupling;
thomaskummer's avatar
thomaskummer committed
502
    
thomaskummer's avatar
thomaskummer committed
503
    WallTensionEstimator<RegionMesh<LinearTetra> > M_wteTotal;
thomaskummer's avatar
thomaskummer committed
504
505
//    WallTensionEstimator<RegionMesh<LinearTetra> > M_wtePassive;
//    WallTensionEstimator<RegionMesh<LinearTetra> > M_wteActive;
thomaskummer's avatar
thomaskummer committed
506

Simone Rossi's avatar
Simone Rossi committed
507

Simone Deparis's avatar
Simone Deparis committed
508
    commPtr_Type                         M_commPtr;
Simone Rossi's avatar
Simone Rossi committed
509

Simone Rossi's avatar
Simone Rossi committed
510
511
    EMData                               M_data;

Simone Rossi's avatar
Simone Rossi committed
512

Simone Rossi's avatar
Simone Rossi committed
513
};
Simone Rossi's avatar
Simone Rossi committed
514
515
516

/////////////////////
// CONSTRUCTORS
Simone Rossi's avatar
Simone Rossi committed
517
518
template<typename Mesh , typename ElectroSolver>
EMSolver<Mesh, ElectroSolver>::EMSolver(commPtr_Type comm) :
Simone Rossi's avatar
Simone Rossi committed
519
520
521
522
523
524
525
526
527
    M_electroSolverPtr       ( ),
    M_activationModelPtr    ( ),
    M_bcInterfacePtr        ( ),
    M_EMStructuralOperatorPtr(),
    M_electroExporterPtr ( ),
    M_activationExporterPtr ( ),
    M_mechanicsExporterPtr  ( ),
    M_localMeshPtr      ( ),
    M_fullMeshPtr      ( ),
thomaskummer's avatar
thomaskummer committed
528
    //M_activationTimePtr     ( ),
Simone Rossi's avatar
Simone Rossi committed
529
    M_oneWayCoupling     (true),
thomaskummer's avatar
thomaskummer committed
530
    M_wteTotal ( ),
thomaskummer's avatar
thomaskummer committed
531
532
//    M_wtePassive ( ),
//    M_wteActive ( ),
Simone Rossi's avatar
Simone Rossi committed
533
534
    M_commPtr               (comm),
    M_data                    ()
Simone Rossi's avatar
Simone Rossi committed
535
536
537
538
539
540
{
}


/////////////////////
// COPY CONSTRUCTORS
Simone Rossi's avatar
Simone Rossi committed
541
542
template<typename Mesh , typename ElectroSolver>
EMSolver<Mesh, ElectroSolver>::EMSolver (const EMSolver& solver) :
Simone Deparis's avatar
Simone Deparis committed
543
544
    M_electroSolverPtr (solver.M_electroSolverPtr),
    M_activationModelPtr (solver.M_activationModelPtr),
Simone Rossi's avatar
Simone Rossi committed
545
    M_bcInterfacePtr        ( solver.M_bcInterfacePtr),
Simone Deparis's avatar
Simone Deparis committed
546
    M_EMStructuralOperatorPtr (solver.M_EMStructuralOperatorPtr),
Simone Rossi's avatar
Simone Rossi committed
547
548
549
550
551
    M_electroExporterPtr ( solver.M_electroExporterPtr),
    M_activationExporterPtr ( solver.M_activationExporterPtr),
    M_mechanicsExporterPtr  ( solver.M_mechanicsExporterPtr),
    M_localMeshPtr      ( solver.M_localMeshPtr),
    M_fullMeshPtr      ( solver.M_fullMeshPtr),
thomaskummer's avatar
thomaskummer committed
552
    //M_activationTimePtr     ( solver.M_activationTimePtr),
Simone Rossi's avatar
Simone Rossi committed
553
    M_oneWayCoupling     ( solver.M_oneWayCoupling),
thomaskummer's avatar
thomaskummer committed
554
    M_wteTotal                   (solver.M_wteTotal),
thomaskummer's avatar
thomaskummer committed
555
556
//    M_wtePassive                   (solver.M_wtePassive),
//    M_wteActive                   (solver.M_wteActive),
Simone Rossi's avatar
Simone Rossi committed
557
558
    M_commPtr               ( solver.M_commPtr),
    M_data                   (solver.M_data)
Simone Rossi's avatar
Simone Rossi committed
559
560
561
562
563
564
565

{
}


/////////////////////
// Setting up the electrophysiology solver
Simone Rossi's avatar
Simone Rossi committed
566

Simone Rossi's avatar
Simone Rossi committed
567
568
569
570


/////////////////////
// Setting up the electrophysiology solver
Simone Rossi's avatar
Simone Rossi committed
571
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
572
void
Thomas Kummer's avatar
Thomas Kummer committed
573
EMSolver<Mesh, ElectroSolver>::setup ( GetPot& dataFile )
Simone Rossi's avatar
Simone Rossi committed
574
{
Simone Rossi's avatar
Simone Rossi committed
575
    M_data.setup (dataFile);
thomaskummer's avatar
thomaskummer committed
576
    
Simone Deparis's avatar
Simone Deparis committed
577
578
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
579
        std::cout << "\n\nEMSolver: setup (simulation endtime = " << M_data.activationParameter<Real>("endtime") << ")" << " ...";
Simone Deparis's avatar
Simone Deparis committed
580
    }
thomaskummer's avatar
thomaskummer committed
581
582
    
    setupElectroSolver ( dataFile );
Simone Deparis's avatar
Simone Deparis committed
583
584
    setupMechanicalSolver ( dataFile );
    setupActivation ( M_electroSolverPtr -> potentialPtr() ->map() );
thomaskummer's avatar
thomaskummer committed
585
586
587
    
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
588
        std::cout << "\nEMSolver: setup (simulation endtime = " << M_data.activationParameter<Real>("endtime") << ")" << " - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
589
590
    }

Simone Rossi's avatar
Simone Rossi committed
591
592
}

Simone Rossi's avatar
Simone Rossi committed
593
594


Simone Rossi's avatar
Simone Rossi committed
595
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
596
void
Thomas Kummer's avatar
Thomas Kummer committed
597
EMSolver<Mesh, ElectroSolver>::setupElectroSolver ( GetPot& dataFile )
Simone Rossi's avatar
Simone Rossi committed
598
{
Simone Deparis's avatar
Simone Deparis committed
599
600
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
601
        std::cout << "\nEMSolver: setupElectroSolver ... " << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
602
    }
Simone Rossi's avatar
Simone Rossi committed
603
604
605
606
607
	ionicModelPtr_Type ionicModelPtr;
	std::string ionicModelName = M_data.electroParameter<std::string>("IonicModel");
	ionicModelPtr.reset (ionicModel_Type::IonicModelFactory::instance().createObject ( ionicModelName ) );

//    M_electroSolverPtr.reset( new ElectroSolver ( meshName, meshPath, dataFile , ionicModelPtr ) );
Simone Deparis's avatar
Simone Deparis committed
608
609
610

    M_electroSolverPtr.reset ( new ElectroSolver() );
    M_electroSolverPtr -> setIonicModelPtr (ionicModelPtr);
Simone Rossi's avatar
Simone Rossi committed
611
    M_electroSolverPtr->setParameters();
thomaskummer's avatar
thomaskummer committed
612
    //if (M_commPtr -> MyPID() == 0) M_electroSolverPtr ->showParameters();
Simone Rossi's avatar
Simone Rossi committed
613
	M_electroSolverPtr -> setParametersFromEMData ( M_data );
thomaskummer's avatar
thomaskummer committed
614
    //if (M_commPtr -> MyPID() == 0) M_electroSolverPtr ->showParameters();
Thomas Kummer's avatar
Thomas Kummer committed
615
    M_electroSolverPtr->init (M_localMeshPtr); //(M_commPtr);
Simone Rossi's avatar
Simone Rossi committed
616

Thomas Kummer's avatar
Thomas Kummer committed
617
618
619
//    if (M_localMeshPtr)
//    {
//        M_electroSolverPtr -> setLocalMeshPtr (M_localMeshPtr);
Simone Deparis's avatar
Simone Deparis committed
620
621
622
623
624
        if (M_fullMeshPtr)
        {
            M_electroSolverPtr -> setFullMeshPtr (M_fullMeshPtr);
        }
        M_electroSolverPtr ->  setup (dataFile, ionicModelPtr->Size() );
Thomas Kummer's avatar
Thomas Kummer committed
625
//    }
thomaskummer's avatar
thomaskummer committed
626
    
Simone Deparis's avatar
Simone Deparis committed
627
628
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
629
        std::cout << "\nEMSolver: setupElectroSolver - done" << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
630
    }
Simone Rossi's avatar
Simone Rossi committed
631

Simone Rossi's avatar
Simone Rossi committed
632
633
634
}


Simone Rossi's avatar
Simone Rossi committed
635
636
/////////////////////
// Setting up the electrophysiology solver
Simone Rossi's avatar
Simone Rossi committed
637
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
638
void
Simone Rossi's avatar
Simone Rossi committed
639
EMSolver<Mesh, ElectroSolver>::setupMechanicalSolver ( GetPot& dataFile)
Simone Rossi's avatar
Simone Rossi committed
640
{
Simone Deparis's avatar
Simone Deparis committed
641
642
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
643
        std::cout << "\nEMSolver: setupMechanicalSolver ... " << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
644
    }
thomaskummer's avatar
thomaskummer committed
645
    
Simone Rossi's avatar
Simone Rossi committed
646
647
648
649
650
651
    boost::shared_ptr<StructuralConstitutiveLawData> dataStructure (new StructuralConstitutiveLawData( ) );
    dataStructure->setup (dataFile);

    std::string dOrder =  dataFile ( "solid/space_discretization/order", "P1");
    solidFESpacePtr_Type dFESpace ( new solidFESpace_Type (M_localMeshPtr, dOrder, 3, M_commPtr) );
    solidETFESpacePtr_Type dETFESpace ( new solidETFESpace_Type ( M_localMeshPtr,
Simone Deparis's avatar
Simone Deparis committed
652
653
654
655
656
                                                                  & (dFESpace->refFE() ),
                                                                  & (dFESpace->fe().geoMap() ),
                                                                  M_commPtr) );
    std::string data_file_name = dataFile.get (0, "NO_DATA_FILENAME_FOUND");

thomaskummer's avatar
thomaskummer committed
657
    dFESpace->setQuadRule(quadRuleTetra4pt);
thomaskummer's avatar
thomaskummer committed
658
659
    //if (M_commPtr -> MyPID() == 0) std::cout << "\nPolynomial degree: " << dFESpace->polynomialDegree();
    //if (M_commPtr -> MyPID() == 0) std::cout << "\nDof: " << dFESpace->dof() << std::endl;
thomaskummer's avatar
thomaskummer committed
660
    
Simone Deparis's avatar
Simone Deparis committed
661
662
663
664
665
666
667
    setupMechanicalBC (data_file_name, "solid",  dFESpace);
    M_EMStructuralOperatorPtr.reset (new structuralOperator_Type() );
    M_EMStructuralOperatorPtr->setup ( dataStructure,
                                       dFESpace,
                                       dETFESpace,
                                       M_bcInterfacePtr->handler(),
                                       M_commPtr);
Simone Rossi's avatar
Simone Rossi committed
668
    M_EMStructuralOperatorPtr->setDataFromGetPot (dataFile);
thomaskummer's avatar
thomaskummer committed
669
    M_EMStructuralOperatorPtr->EMMaterial()->setParameters(M_data, dataFile);
Simone Rossi's avatar
Simone Rossi committed
670

thomaskummer's avatar
thomaskummer committed
671
    M_wteTotal.setup(dataStructure, dFESpace, dETFESpace, M_commPtr, 0, M_EMStructuralOperatorPtr->EMMaterial());
thomaskummer's avatar
thomaskummer committed
672
673
//    M_wtePassive.setup(dataStructure, dFESpace, dETFESpace, M_commPtr, 0, "passive");
//    M_wteActive.setup(dataStructure, dFESpace, dETFESpace, M_commPtr, 0, "active");
thomaskummer's avatar
thomaskummer committed
674
675
676
    
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
677
        std::cout << "\nEMSolver: setupMechanicalSolver - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
678
679
    }

Simone Rossi's avatar
Simone Rossi committed
680
681
682
683
}

/////////////////////
// Setting up the electrophysiology solver
Simone Rossi's avatar
Simone Rossi committed
684
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
685
void
Simone Rossi's avatar
Simone Rossi committed
686
EMSolver<Mesh, ElectroSolver>::setupMechanicalBC (std::string data_file_name,
Simone Deparis's avatar
Simone Deparis committed
687
688
                                                                   std::string section,
                                                                   solidFESpacePtr_Type dFESpace)
Simone Rossi's avatar
Simone Rossi committed
689
{
Simone Deparis's avatar
Simone Deparis committed
690
691
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
692
        std::cout << "\nEMSolver: setupMechanicalBC ... " << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
693
    }
thomaskummer's avatar
thomaskummer committed
694

Simone Deparis's avatar
Simone Deparis committed
695
    M_bcInterfacePtr.reset (new bcInterface_Type() );
Simone Rossi's avatar
Simone Rossi committed
696
697
    M_bcInterfacePtr->createHandler();
    M_bcInterfacePtr->fillHandler ( data_file_name, "solid" );
698
    // M_bcInterfacePtr->handler()->bcUpdate ( *dFESpace->mesh(), dFESpace->feBd(), dFESpace->dof() );
thomaskummer's avatar
thomaskummer committed
699
700
701
    
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
702
        std::cout << "EMSolver: setupMechanicalBC - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
703
    }
Simone Rossi's avatar
Simone Rossi committed
704
705
}

706
707
708
709
710
711
712
    
/////////////////////
//restart hdf5
template<typename Mesh , typename ElectroSolver>
void
EMSolver<Mesh, ElectroSolver>::importHdf5 ()
{
thomaskummer's avatar
thomaskummer committed
713
714
    M_electroExporterPtr -> import (30);
    M_activationExporterPtr -> importHdf5 (30);
thomaskummer's avatar
thomaskummer committed
715
    //M_activationTimeExporterPtr -> importHdf5 (30);
thomaskummer's avatar
thomaskummer committed
716
    M_vonMisesStressExporterPtr -> importHdf5 (30);
thomaskummer's avatar
thomaskummer committed
717
718
    //M_vonMisesStressExporterPtrP -> importHdf5 (30);
    //M_vonMisesStressExporterPtrA -> importHdf5 (30);
thomaskummer's avatar
thomaskummer committed
719
    M_mechanicsExporterPtr -> importHdf5 (30);
720
721
}
                                                   
Simone Rossi's avatar
Simone Rossi committed
722
723
724

/////////////////////
//Setup exporters
Simone Rossi's avatar
Simone Rossi committed
725
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
726
void
thomaskummer's avatar
thomaskummer committed
727
728
729
EMSolver<Mesh, ElectroSolver>::setupExporters ( std::string problemFolder,
                                                std::string electroFileName,
                                                std::string activationFileName,
thomaskummer's avatar
thomaskummer committed
730
                                                //std::string activationTimeFileName,
thomaskummer's avatar
thomaskummer committed
731
                                                std::string mechanicsFileName,
thomaskummer's avatar
thomaskummer committed
732
                                                std::string vonMisesStressFileName)
Simone Rossi's avatar
Simone Rossi committed
733
{
Simone Deparis's avatar
Simone Deparis committed
734
735
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
736
        std::cout << "\nEMSolver: setupExporters ... " << '\r' << std::flush;
Simone Deparis's avatar
Simone Deparis committed
737
    }
thomaskummer's avatar
thomaskummer committed
738
739
    
    // Electrophysiology
Simone Deparis's avatar
Simone Deparis committed
740
741
    M_electroExporterPtr.reset (new exporter_Type() );
    setupElectroExporter (problemFolder, electroFileName);
Simone Rossi's avatar
Simone Rossi committed
742
743
744
745
746
747
    M_electroExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
                                            "fibers",
                                            M_EMStructuralOperatorPtr -> dispFESpacePtr(),
                                            M_electroSolverPtr -> fiberPtr(),
                                            UInt (0) );

thomaskummer's avatar
thomaskummer committed
748
    // Activation
Simone Deparis's avatar
Simone Deparis committed
749
750
    M_activationExporterPtr.reset (new exporter_Type() );
    setupActivationExporter (problemFolder, activationFileName );
thomaskummer's avatar
thomaskummer committed
751
752
    M_activationExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
                                             "Activation",
thomaskummer's avatar
thomaskummer committed
753
                                             M_electroSolverPtr -> feSpacePtr(),
thomaskummer's avatar
thomaskummer committed
754
755
                                             M_activationModelPtr -> fiberActivationPtr(),
                                             UInt (0) );
Simone Deparis's avatar
Simone Deparis committed
756

thomaskummer's avatar
thomaskummer committed
757
758
759
760
761
762
763
764
765
766
767
768
//    // Activation time
//    M_activationTimeExporterPtr.reset (new exporter_Type() );
//    setupActivationTimeExporter (problemFolder, activationTimeFileName );
//    
//    M_activationTimePtr.reset (new vector_Type ( M_electroSolverPtr->potentialPtr() -> map() ) );
//    *M_activationTimePtr = -1.0;
//
//    M_activationTimeExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
//                                            "Activation Time",
//                                            M_electroSolverPtr -> feSpacePtr(),
//                                            M_activationTimePtr,
//                                            UInt (0) );
thomaskummer's avatar
thomaskummer committed
769
    
thomaskummer's avatar
thomaskummer committed
770
771
772
773
774
    // Von Mises stress
    M_vonMisesStressExporterPtr.reset (new exporter_Type() );
    setupVonMisesStressExporter (problemFolder, vonMisesStressFileName );
    
    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
thomaskummer's avatar
thomaskummer committed
775
                                                "Von Mises Stress",
thomaskummer's avatar
thomaskummer committed
776
                                                M_electroSolverPtr -> feSpacePtr(),
thomaskummer's avatar
thomaskummer committed
777
778
779
                                                M_wteTotal.vonMisesStressPtr(),
                                                UInt (0) );
    
thomaskummer's avatar
thomaskummer committed
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
//    M_vonMisesStressExporterPtrP.reset (new exporter_Type() );
//    setupVonMisesStressExporterP (problemFolder, vonMisesStressFileNameP );
//    
//    M_vonMisesStressExporterPtrP -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
//                                                "Von Mises Stress Total P",
//                                                M_electroSolverPtr -> feSpacePtr(),
//                                                M_wteTotal.vonMisesStressPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtrA.reset (new exporter_Type() );
//    setupVonMisesStressExporterA (problemFolder, vonMisesStressFileNameA );
//    
//    M_vonMisesStressExporterPtrA -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
//                                                "Von Mises Stress Total A",
//                                                M_electroSolverPtr -> feSpacePtr(),
//                                                M_wteTotal.vonMisesStressPtr(),
//                                                UInt (0) );
thomaskummer's avatar
thomaskummer committed
797

thomaskummer's avatar
thomaskummer committed
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "X Stress Total",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteTotal.sigmaXPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Y Stress Total",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteTotal.sigmaYPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Z Stress Total",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteTotal.sigmaZPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
//                                                "Von Mises Stress Passive",
//                                                M_electroSolverPtr -> feSpacePtr(),
//                                                M_wtePassive.vonMisesStressPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "X Stress Passive",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wtePassive.sigmaXPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Y Stress Passive",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wtePassive.sigmaYPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Z Stress Passive",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wtePassive.sigmaZPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
//                                                "Von Mises Stress Active",
//                                                M_electroSolverPtr -> feSpacePtr(),
//                                                M_wteActive.vonMisesStressPtr(),
//                                                UInt (0) );
//    
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "X Stress Active",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteActive.sigmaXPtr(),
//                                                UInt (0) );
//
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Y Stress Active",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteActive.sigmaYPtr(),
//                                                UInt (0) );
//    
//    M_vonMisesStressExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
//                                                "Z Stress Active",
//                                                M_EMStructuralOperatorPtr -> dispFESpacePtr(),
//                                                M_wteActive.sigmaZPtr(),
//                                                UInt (0) );
thomaskummer's avatar
thomaskummer committed
863
    
thomaskummer's avatar
thomaskummer committed
864
    // Mechanics
thomaskummer's avatar
thomaskummer committed
865
    M_mechanicsExporterPtr.reset (new exporter_Type() );
Simone Deparis's avatar
Simone Deparis committed
866
867
868
869
870
871
872
873
874
875
876
    setupMechanicsExporter (problemFolder, mechanicsFileName);
    M_mechanicsExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
                                            "displacement",
                                            M_EMStructuralOperatorPtr -> dispFESpacePtr(),
                                            M_EMStructuralOperatorPtr -> displacementPtr(),
                                            UInt (0) );
    M_mechanicsExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
                                            "fibers",
                                            M_EMStructuralOperatorPtr -> dispFESpacePtr(),
                                            M_EMStructuralOperatorPtr -> EMMaterial() -> fiberVectorPtr(),
                                            UInt (0) );
Simone Rossi's avatar
Simone Rossi committed
877
878
879
880
881
    M_mechanicsExporterPtr -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::VectorField,
                                            "sheets",
                                            M_EMStructuralOperatorPtr -> dispFESpacePtr(),
                                            M_EMStructuralOperatorPtr -> EMMaterial() -> sheetVectorPtr(),
                                            UInt (0) );
thomaskummer's avatar
thomaskummer committed
882
883
884
    
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
885
        std::cout << "EMSolver: setupExporters - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
886
    }
Simone Rossi's avatar
Simone Rossi committed
887
888
}

thomaskummer's avatar
restart    
thomaskummer committed
889
890
891
892
893
894
template<typename Mesh , typename ElectroSolver>
void
EMSolver<Mesh, ElectroSolver>::setTimeIndex (const UInt& time)
{
    M_electroExporterPtr -> setTimeIndex (time);
    M_activationExporterPtr -> setTimeIndex (time);
thomaskummer's avatar
thomaskummer committed
895
    //M_activationTimeExporterPtr -> setTimeIndex (time);
thomaskummer's avatar
thomaskummer committed
896
    M_vonMisesStressExporterPtr -> setTimeIndex (time);
thomaskummer's avatar
thomaskummer committed
897
898
    //M_vonMisesStressExporterPtrP -> setTimeIndex (time);
    //M_vonMisesStressExporterPtrA -> setTimeIndex (time);
thomaskummer's avatar
restart    
thomaskummer committed
899
900
901
    M_mechanicsExporterPtr -> setTimeIndex (time);
}
    
Simone Rossi's avatar
Simone Rossi committed
902
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
903
void
thomaskummer's avatar
thomaskummer committed
904
EMSolver<Mesh, ElectroSolver>::saveSolution (Real time, const bool& restart)
Simone Rossi's avatar
Simone Rossi committed
905
{
thomaskummer's avatar
thomaskummer committed
906
907
908
909
    M_wteTotal.setDisplacement ( M_EMStructuralOperatorPtr -> displacement() );
    M_wteTotal.analyzeTensionsRecoveryVonMisesStress();
    
    M_vonMisesStressExporterPtr -> postProcess (time);
thomaskummer's avatar
thomaskummer committed
910
    M_electroExporterPtr -> postProcess (time);//, restart);
thomaskummer's avatar
thomaskummer committed
911
    M_activationExporterPtr -> postProcess (time);//, restart );
thomaskummer's avatar
thomaskummer committed
912
    //M_activationTimeExporterPtr -> postProcess (time);
thomaskummer's avatar
thomaskummer committed
913
    M_mechanicsExporterPtr -> postProcess (time);//, restart);
Simone Rossi's avatar
Simone Rossi committed
914
915
}

Simone Rossi's avatar
Simone Rossi committed
916
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
917
void
Simone Rossi's avatar
Simone Rossi committed
918
EMSolver<Mesh, ElectroSolver>::closeExporters()
Simone Rossi's avatar
Simone Rossi committed
919
{
Simone Deparis's avatar
Simone Deparis committed
920
    M_electroExporterPtr -> closeFile();
thomaskummer's avatar
thomaskummer committed
921
922
    M_activationExporterPtr -> closeFile();
    //M_activationTimeExporterPtr -> closeFile();
Simone Deparis's avatar
Simone Deparis committed
923
    M_mechanicsExporterPtr -> closeFile();
thomaskummer's avatar
thomaskummer committed
924
    M_vonMisesStressExporterPtr -> closeFile();
Simone Rossi's avatar
Simone Rossi committed
925
926
927
928
}


///////////////////////////////
Simone Rossi's avatar
Simone Rossi committed
929
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
930
void
Simone Rossi's avatar
Simone Rossi committed
931
EMSolver<Mesh, ElectroSolver>::oneWayCoupling()
Simone Rossi's avatar
Simone Rossi committed
932
{
Simone Deparis's avatar
Simone Deparis committed
933
934
    M_electroSolverPtr -> setMechanicsModifiesConductivity (false);
    M_electroSolverPtr -> displacementPtr().reset();
Simone Rossi's avatar
Simone Rossi committed
935
936
937
938
    M_activationModelPtr -> setupActivationPtrs( M_EMStructuralOperatorPtr -> EMMaterial() -> fiberActivationPtr(),
												 M_EMStructuralOperatorPtr -> EMMaterial() -> sheetActivationPtr(),
												 M_EMStructuralOperatorPtr -> EMMaterial() -> normalActivationPtr()
												 );
Simone Rossi's avatar
Simone Rossi committed
939
940
}

Simone Rossi's avatar
Simone Rossi committed
941
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
942
void
Simone Rossi's avatar
Simone Rossi committed
943
EMSolver<Mesh, ElectroSolver>::twoWayCoupling()
Simone Rossi's avatar
Simone Rossi committed
944
{
Simone Deparis's avatar
Simone Deparis committed
945
946
    M_electroSolverPtr -> setMechanicsModifiesConductivity (true);
    M_electroSolverPtr -> setDisplacementPtr ( M_EMStructuralOperatorPtr -> displacementPtr() );
Simone Rossi's avatar
Simone Rossi committed
947
948
949
950
    M_activationModelPtr -> setupActivationPtrs( M_EMStructuralOperatorPtr -> EMMaterial() -> fiberActivationPtr(),
												 M_EMStructuralOperatorPtr -> EMMaterial() -> sheetActivationPtr(),
												 M_EMStructuralOperatorPtr -> EMMaterial() -> normalActivationPtr()
												 );
Simone Rossi's avatar
Simone Rossi committed
951
952
953
}

////////////////////////////
Simone Rossi's avatar
Simone Rossi committed
954
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
955
void
Simone Rossi's avatar
Simone Rossi committed
956
EMSolver<Mesh, ElectroSolver>::solveElectrophysiology (function_Type& stimulus, Real time )
Simone Rossi's avatar
Simone Rossi committed
957
{
thomaskummer's avatar
thomaskummer committed
958
959
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
960
        std::cout << "\nEMSolver: solveElectrophysiology ... " << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
961
962
    }
    
Simone Deparis's avatar
Simone Deparis committed
963
    setAppliedCurrent ( stimulus, time );
thomaskummer's avatar
thomaskummer committed
964

Simone Rossi's avatar
Simone Rossi committed
965
    M_electroSolverPtr -> solveOneStepGatingVariablesFE();
thomaskummer's avatar
thomaskummer committed
966
    //M_electroSolverPtr -> solveOneStepGatingVariablesRL();
thomaskummer's avatar
thomaskummer committed
967
    
Simone Rossi's avatar
Simone Rossi committed
968
    M_electroSolverPtr -> solveOneICIStep();
thomaskummer's avatar
thomaskummer committed
969
    
thomaskummer's avatar
thomaskummer committed
970
    //M_electroSolverPtr -> registerActivationTime (*M_activationTimePtr, time, 0.9);
thomaskummer's avatar
thomaskummer committed
971
972
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
973
        std::cout << "EMSolver: solveElectrophysiology - done" << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
974
    }
Simone Rossi's avatar
Simone Rossi committed
975
976
}

Simone Rossi's avatar
Simone Rossi committed
977
template<typename Mesh , typename ElectroSolver>
Simone Rossi's avatar
Simone Rossi committed
978
void
Simone Rossi's avatar
Simone Rossi committed
979
EMSolver<Mesh, ElectroSolver>::solveActivation (Real dt)
thomaskummer's avatar
thomaskummer committed
980
    
thomaskummer's avatar
thomaskummer committed
981
{
thomaskummer's avatar
thomaskummer committed
982
983
    if (M_commPtr -> MyPID() == 0)
    {
thomaskummer's avatar
thomaskummer committed
984
        std::cout << "\nEMSolver: solveActivation ... " << '\r' << std::flush;
thomaskummer's avatar
thomaskummer committed
985
986
    }
    
thomaskummer's avatar
thomaskummer committed
987
    computeI4f (M_activationModelPtr->I4f(), *M_EMStructuralOperatorPtr<