HeartSolver.hpp 9.71 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
17


thomaskummer's avatar
thomaskummer committed
18
19
20
21
22

namespace LifeV
{

    
thomaskummer's avatar
thomaskummer committed
23
24
25
class HeartData
{
public:
thomaskummer's avatar
thomaskummer committed
26
    
thomaskummer's avatar
thomaskummer committed
27
28
    HeartData() {}
    
thomaskummer's avatar
thomaskummer committed
29
    virtual ~HeartData() {};
thomaskummer's avatar
thomaskummer committed
30
    
thomaskummer's avatar
thomaskummer committed
31
32
33
34
35
36
    void setup(const GetPot& datafile)
    {
        setGetPotFile(datafile);
        readFile();
    }
    
thomaskummer's avatar
thomaskummer committed
37
    const Real& dt_activation () const { return M_dt_activation; }
thomaskummer's avatar
thomaskummer committed
38
    const Real& dt_loadstep () const { return M_dt_loadstep; }
thomaskummer's avatar
thomaskummer committed
39
    const Real& activationLimit_loadstep () const { return M_activationLimit_loadstep; }
thomaskummer's avatar
thomaskummer committed
40
41
    const Real& dt_mechanics () const { return M_dt_mechanics; }
    const Real& dt_save () const { return M_dt_save; }
thomaskummer's avatar
thomaskummer committed
42
    const Real& endtime () const { return M_endtime; }
thomaskummer's avatar
thomaskummer committed
43
44
45
46
    const UInt& mechanicsLoadstepIter () const { return M_mechanicsLoadstepIter; }
    const UInt& mechanicsCouplingIter () const { return M_mechanicsCouplingIter; }
    const UInt& maxiter () const { return M_maxiter; }
    const UInt& preloadSteps () const { return M_preloadSteps; }
thomaskummer's avatar
thomaskummer committed
47

thomaskummer's avatar
thomaskummer committed
48
49
50
51
52
53
54
    const UInt& pPerturbationFe () const { return M_pPerturbationFe; }
    const UInt& pPerturbationCirc () const { return M_pPerturbationCirc; }
    const UInt& couplingError () const { return M_couplingError; }
    const UInt& couplingJFeSubIter () const { return M_couplingJFeSubIter; }
    const UInt& couplingJFeSubStart () const { return M_couplingJFeSubStart; }
    const UInt& couplingJFeIter () const { return M_couplingJFeIter; }

thomaskummer's avatar
thomaskummer committed
55
56
    const GetPot& datafile () { return M_datafile; }
    
thomaskummer's avatar
thomaskummer committed
57
protected:
thomaskummer's avatar
thomaskummer committed
58
59
    
    
thomaskummer's avatar
thomaskummer committed
60
    void setGetPotFile(const GetPot& datafile)
thomaskummer's avatar
thomaskummer committed
61
    {
thomaskummer's avatar
thomaskummer committed
62
        M_datafile = datafile;
thomaskummer's avatar
thomaskummer committed
63
64
    }
    
thomaskummer's avatar
thomaskummer committed
65
    void readFile()
thomaskummer's avatar
thomaskummer committed
66
    {
thomaskummer's avatar
thomaskummer committed
67
        M_dt_activation = M_datafile ("activation/time_discretization/timestep", 0.05 );
thomaskummer's avatar
thomaskummer committed
68
69
        M_dt_loadstep =  M_datafile ( "solid/time_discretization/dt_loadstep", 1.0 );
        M_activationLimit_loadstep =  M_datafile ( "solid/time_discretization/activation_limit_loadstep", 0.0 );
thomaskummer's avatar
thomaskummer committed
70
        M_dt_mechanics = M_datafile ("solid/time_discretization/timestep", 1.0 );
thomaskummer's avatar
thomaskummer committed
71
        M_dt_save = M_datafile ( "exporter/save", 10. );
thomaskummer's avatar
thomaskummer committed
72
        M_endtime = M_datafile ("solid/time_discretization/endtime", 100000);
thomaskummer's avatar
thomaskummer committed
73
74
75
        M_mechanicsLoadstepIter = static_cast<UInt>( M_dt_loadstep / M_dt_activation );
        M_mechanicsCouplingIter = static_cast<UInt>( M_dt_mechanics / M_dt_activation );
        M_maxiter = static_cast<UInt>( M_endtime / M_dt_activation ) ;
thomaskummer's avatar
thomaskummer committed
76
        M_preloadSteps = M_datafile ( "solid/boundary_conditions/numPreloadSteps", 0);
thomaskummer's avatar
thomaskummer committed
77

thomaskummer's avatar
thomaskummer committed
78
79
80
81
82
83
        M_pPerturbationFe = M_datafile ( "solid/coupling/pPerturbationFe", 1e-2 );
        M_pPerturbationCirc = M_datafile ( "solid/coupling/pPerturbationCirc", 1e-3 );
        M_couplingError = M_datafile ( "solid/coupling/couplingError", 1e-6 );
        M_couplingJFeSubIter = M_datafile ( "solid/coupling/couplingJFeSubIter", 1 );
        M_couplingJFeSubStart = M_datafile ( "solid/coupling/couplingJFeSubStart", 1 );
        M_couplingJFeIter = M_datafile ( "solid/coupling/couplingJFeIter", 1 );
thomaskummer's avatar
thomaskummer committed
84
        
thomaskummer's avatar
thomaskummer committed
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
    //        const Real dpMax = dataFile ( "solid/coupling/dpMax", 0.1 );
    //
    //        std::vector<std::vector<std::string> > bcNames { { "lv" , "p" } , { "rv" , "p" } };
    //        std::vector<double> bcValues { p ( "lv" ) , p ( "rv") };
    //        std::vector<double> bcValuesPre ( bcValues );
    //
    //        VectorSmall<4> ABdplv, ABdprv, ABcoef;
    //        ABcoef (0) = 55/24; ABcoef (1) = -59/24; ABcoef (2) = 37/24; ABcoef (3) = -3/8;
    //
    //        VectorSmall<2> VCirc, VCircNew, VCircPert, VFe, VFeNew, VFePert, R, dp;
    //        MatrixSmall<2,2> JFe, JCirc, JR;
    //        
    //        UInt iter (0);
    //        Real t (0);
    
thomaskummer's avatar
thomaskummer committed
100
101
102
        
    }
    
thomaskummer's avatar
thomaskummer committed
103
104
105
106
107
108
109
110
111
    Real M_dt_activation;
    Real M_dt_loadstep;
    Real M_activationLimit_loadstep;
    Real M_dt_mechanics;
    Real M_dt_save;
    Real M_endtime;
    UInt M_mechanicsLoadstepIter;
    UInt M_mechanicsCouplingIter;
    UInt M_maxiter;
thomaskummer's avatar
thomaskummer committed
112
    UInt M_preloadSteps;
thomaskummer's avatar
thomaskummer committed
113
    
thomaskummer's avatar
thomaskummer committed
114
115
116
117
118
119
    Real M_pPerturbationFe;
    Real M_pPerturbationCirc;
    Real M_couplingError;
    UInt M_couplingJFeSubIter;
    UInt M_couplingJFeSubStart;
    UInt M_couplingJFeIter;
thomaskummer's avatar
thomaskummer committed
120
    
thomaskummer's avatar
thomaskummer committed
121
    GetPot M_datafile;
thomaskummer's avatar
thomaskummer committed
122
    
thomaskummer's avatar
thomaskummer committed
123
};
thomaskummer's avatar
thomaskummer committed
124
    
thomaskummer's avatar
thomaskummer committed
125
    
thomaskummer's avatar
thomaskummer committed
126
127
128
129
template <class EmSolver>
class HeartSolver {
   
public:
thomaskummer's avatar
thomaskummer committed
130
    
thomaskummer's avatar
thomaskummer committed
131
132
    HeartSolver(EmSolver& emSolver,  Circulation& circulationSolver) :
        M_emSolver          (emSolver),
thomaskummer's avatar
thomaskummer committed
133
134
        M_circulationSolver (circulationSolver),
        M_heartData         (HeartData())
thomaskummer's avatar
thomaskummer committed
135
    {}
thomaskummer's avatar
thomaskummer committed
136
    
thomaskummer's avatar
thomaskummer committed
137
    virtual ~HeartSolver() {}
thomaskummer's avatar
thomaskummer committed
138
    
thomaskummer's avatar
thomaskummer committed
139
    const HeartData& data() const
thomaskummer's avatar
thomaskummer committed
140
141
142
143
    {
        return M_heartData;
    }
    
thomaskummer's avatar
thomaskummer committed
144
    void setupData(const GetPot& datafile)
thomaskummer's avatar
thomaskummer committed
145
    {
thomaskummer's avatar
thomaskummer committed
146
        M_heartData.setup(datafile);
thomaskummer's avatar
thomaskummer committed
147
    }
thomaskummer's avatar
thomaskummer committed
148
    
thomaskummer's avatar
thomaskummer committed
149
    template <class lambda>
thomaskummer's avatar
thomaskummer committed
150
    void preload(const lambda& modifyFeBC, const std::vector<Real>& bcValues) const
thomaskummer's avatar
thomaskummer committed
151
    {
thomaskummer's avatar
thomaskummer committed
152
        M_emSolver.structuralOperatorPtr() -> data() -> dataTime() -> setTime(0.0);
thomaskummer's avatar
thomaskummer committed
153
154
155
156
157
158
159
160
161
162
        
        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
163
        M_emSolver.saveSolution (-1.0);
thomaskummer's avatar
thomaskummer committed
164
        
thomaskummer's avatar
thomaskummer committed
165
        if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
166
167
168
169
170
171
172
173
174
175
176
        {
            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
177
            if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
178
179
180
181
182
183
184
            {
                std::cout << "\n*****************************************************************";
                std::cout << "\nPreload step: " << i << " / " << data().preloadSteps();
                std::cout << "\n*****************************************************************\n";
            }
            
            // Update pressure b.c.
thomaskummer's avatar
thomaskummer committed
185
            modifyFeBC(preloadPressure(bcValues, i, data().preloadSteps() ));
thomaskummer's avatar
thomaskummer committed
186
187
            
            // Solve mechanics
thomaskummer's avatar
thomaskummer committed
188
189
            M_emSolver.bcInterfacePtr() -> updatePhysicalSolverVariables();
            M_emSolver.solveMechanics();
thomaskummer's avatar
thomaskummer committed
190
191
192
            //solver.saveSolution (i-1);
        }
        
thomaskummer's avatar
thomaskummer committed
193
        if ( 0 == M_emSolver.comm()->MyPID() )
thomaskummer's avatar
thomaskummer committed
194
195
196
197
198
199
200
        {
            std::cout << "\n*****************************************************************";
            std::cout << "\nPreload done in: " << chronoPreload.diff();
            std::cout << "\n*****************************************************************\n";
        }

    }
thomaskummer's avatar
thomaskummer committed
201
202
203
    
    
    
thomaskummer's avatar
thomaskummer committed
204
protected:
thomaskummer's avatar
thomaskummer committed
205
    
thomaskummer's avatar
thomaskummer committed
206
    
thomaskummer's avatar
thomaskummer committed
207
    EmSolver M_emSolver;
thomaskummer's avatar
thomaskummer committed
208
    Circulation M_circulationSolver;
thomaskummer's avatar
thomaskummer committed
209
    
thomaskummer's avatar
thomaskummer committed
210
    HeartData M_heartData;
thomaskummer's avatar
thomaskummer committed
211
    
thomaskummer's avatar
thomaskummer committed
212
    
thomaskummer's avatar
thomaskummer committed
213
214
215
216
    VectorSmall<2> M_pressure;
    VectorSmall<2> M_volume;

    
thomaskummer's avatar
thomaskummer committed
217

thomaskummer's avatar
thomaskummer committed
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
    
    Real patchForce (const Real& t, const Real& Tmax, const Real& tmax, const Real& tduration) const
    {
        bool time ( fmod(t-tmax+0.5*tduration, 700.) < tduration && fmod(t-tmax+0.5*tduration, 700.) > 0);
        Real force = std::pow( std::sin(fmod(t-tmax+0.5*tduration, 700.)*3.14159265359/tduration) , 2 ) * Tmax;
        return ( time ? force : 0 );
    }
    
    Real patchFunction (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/) const
    {
        Real disp = std::pow( std::sin(fmod(t, 700.) * 3.14159265359/300) , 2 )*15;
        return disp;
    }
    
    Real Iapp (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/) const
    {
        bool coords ( Y < -7. );
        //bool coords ( Y > 4. ); //( Y > 1.5 && Y < 3 );
        bool time ( fmod(t, 700.) < 4 && fmod(t, 700.) > 2);
        return ( coords && time ? 30 : 0 );
    }
    
    Real potentialMultiplyerFcn (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/) const
    {
        bool time ( fmod(t, 700.) < 4 && fmod(t, 700.) > 2);
        return 1.4 * time; // ( Y < 2.5 && Y > 0.5 ? 1.0 : 0.0 );
    }
    
thomaskummer's avatar
thomaskummer committed
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
    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
289
290
291
292
};

}

thomaskummer's avatar
thomaskummer committed
293
#endif