| Line |
Branch |
Exec |
Source |
| 1 |
|
|
// ______ ______ _ _ _____ ______ |
| 2 |
|
|
// | ____| ____| | (_)/ ____| | ____| |
| 3 |
|
|
// | |__ | |__ | | _| (___ ___| |__ |
| 4 |
|
|
// | __| | __| | | | |\___ \ / __| __| |
| 5 |
|
|
// | | | |____| |____| |____) | (__| |____ |
| 6 |
|
|
// |_| |______|______|_|_____/ \___|______| |
| 7 |
|
|
// Finite Elements for Life Sciences and Engineering |
| 8 |
|
|
// |
| 9 |
|
|
// License: LGL2.1 License |
| 10 |
|
|
// FELiScE default license: LICENSE in root folder |
| 11 |
|
|
// |
| 12 |
|
|
// Main authors: J. Foulon & M. Fragu |
| 13 |
|
|
// |
| 14 |
|
|
|
| 15 |
|
|
#ifndef _MODEL_HPP |
| 16 |
|
|
#define _MODEL_HPP |
| 17 |
|
|
|
| 18 |
|
|
// System includes |
| 19 |
|
|
#include <unordered_map> |
| 20 |
|
|
#include <string> |
| 21 |
|
|
#include <vector> |
| 22 |
|
|
|
| 23 |
|
|
// External includes |
| 24 |
|
|
#ifdef FELISCE_WITH_SLEPC |
| 25 |
|
|
#include "Core/NoThirdPartyWarning/Slepc/slepc.hpp" |
| 26 |
|
|
#endif |
| 27 |
|
|
|
| 28 |
|
|
// Project includes |
| 29 |
|
|
#include "Solver/linearProblem.hpp" |
| 30 |
|
|
#include "Core/commandLineOption.hpp" |
| 31 |
|
|
#include "Core/felisceParam.hpp" |
| 32 |
|
|
#include "Core/felisceTransient.hpp" |
| 33 |
|
|
#include "Core/mpiInfo.hpp" |
| 34 |
|
|
#include "Core/shared_pointers.hpp" |
| 35 |
|
|
#include "Model/initialCondition.hpp" |
| 36 |
|
|
#include "Model/solutionBackup.hpp" |
| 37 |
|
|
|
| 38 |
|
|
namespace felisce |
| 39 |
|
|
{ |
| 40 |
|
|
///@name felisce Globals |
| 41 |
|
|
///@{ |
| 42 |
|
|
|
| 43 |
|
|
///@} |
| 44 |
|
|
///@name Type Definitions |
| 45 |
|
|
///@{ |
| 46 |
|
|
|
| 47 |
|
|
///@} |
| 48 |
|
|
///@name Enum's |
| 49 |
|
|
///@{ |
| 50 |
|
|
|
| 51 |
|
|
///@} |
| 52 |
|
|
///@name Functions |
| 53 |
|
|
///@{ |
| 54 |
|
|
|
| 55 |
|
|
///@} |
| 56 |
|
|
///@name felisce Classes |
| 57 |
|
|
///@{ |
| 58 |
|
|
|
| 59 |
|
|
/*! |
| 60 |
|
|
\class Model |
| 61 |
|
|
\authors J. Foulon & M. Fragu |
| 62 |
|
|
\date 04/02/2011 |
| 63 |
|
|
\brief Manage a general Felisce Model. |
| 64 |
|
|
*/ |
| 65 |
|
|
class Model { |
| 66 |
|
|
public: |
| 67 |
|
|
///@name Type Definitions |
| 68 |
|
|
///@{ |
| 69 |
|
|
|
| 70 |
|
|
/// Pointer definition of Model |
| 71 |
|
|
FELISCE_CLASS_POINTER_DEFINITION(Model); |
| 72 |
|
|
|
| 73 |
|
|
///@} |
| 74 |
|
|
///@name Life Cycle |
| 75 |
|
|
///@{ |
| 76 |
|
|
|
| 77 |
|
|
///Constructor. |
| 78 |
|
|
//============= |
| 79 |
|
|
Model(); |
| 80 |
|
|
|
| 81 |
|
|
///Destructor. |
| 82 |
|
|
//============ |
| 83 |
|
|
virtual ~Model(); |
| 84 |
|
|
|
| 85 |
|
|
///@} |
| 86 |
|
|
///@name Operators |
| 87 |
|
|
///@{ |
| 88 |
|
|
|
| 89 |
|
|
///@} |
| 90 |
|
|
///@name Operations |
| 91 |
|
|
///@{ |
| 92 |
|
|
|
| 93 |
|
|
/// Function to initialize model |
| 94 |
|
|
//============================== |
| 95 |
|
|
virtual void initializeModel( |
| 96 |
|
|
CommandLineOption& opt, |
| 97 |
|
|
FelisceTransient& fstransient, |
| 98 |
|
|
const MPI_Comm comm = MPI_COMM_WORLD, |
| 99 |
|
|
const bool callPetscInitialize = true |
| 100 |
|
|
); |
| 101 |
|
|
|
| 102 |
|
239 |
virtual void initializeDerivedModel() {} |
| 103 |
|
|
|
| 104 |
|
451 |
virtual void initializeDerivedLinearProblem() {} |
| 105 |
|
|
|
| 106 |
|
163 |
virtual void setExternalVec() {} |
| 107 |
|
|
|
| 108 |
|
|
/*! |
| 109 |
|
|
* \brief Function to initialize linear problem m_linearProblem[k]. |
| 110 |
|
|
* |
| 111 |
|
|
* \param[in] doUseSNES True if you are handling an non-linear problem and using Petsc's SNES Newton-Raphson method |
| 112 |
|
|
* to manage it. |
| 113 |
|
|
*/ |
| 114 |
|
|
void initializeLinearProblem(LinearProblem* linearPb, bool doUseSNES = false); |
| 115 |
|
|
|
| 116 |
|
|
/*! |
| 117 |
|
|
\brief Initialization of all linear systems. |
| 118 |
|
|
\param[in] linearPb the vector of pointer to the linear problems. |
| 119 |
|
|
*/ |
| 120 |
|
|
void initializeLinearProblem(const std::vector<LinearProblem*>& linearPb, bool doUseSNES = false); |
| 121 |
|
|
|
| 122 |
|
|
void initializeLinearProblem(const std::vector<LinearProblem*>& linearPb, const std::vector<bool>& doUseSNES); |
| 123 |
|
|
|
| 124 |
|
|
/*! |
| 125 |
|
|
* \brief Function to finalizes linear problem m_linearProblem[k]. |
| 126 |
|
|
* |
| 127 |
|
|
* \param[in] doUseSNES True if you are handling an non-linear problem and using Petsc's SNES Newton-Raphson method |
| 128 |
|
|
* to manage it. |
| 129 |
|
|
*/ |
| 130 |
|
|
void finalizeLinearProblem(LinearProblem* linearPb); |
| 131 |
|
|
|
| 132 |
|
|
void finalizeLinearProblem(const std::vector<LinearProblem*>& linearPb); |
| 133 |
|
|
|
| 134 |
|
|
//================ |
| 135 |
|
|
|
| 136 |
|
|
/// Virtual function to specify special action before assembling(duplicate a matrix, work specific on RHS,...) |
| 137 |
|
296 |
virtual void preAssemblingMatrixRHS(std::size_t iProblem=0) { |
| 138 |
|
|
(void) iProblem; |
| 139 |
|
296 |
} |
| 140 |
|
|
|
| 141 |
|
|
/// Virtual function to specify special action after assembling(duplicate a matrix, work specific on RHS,...) |
| 142 |
|
✗ |
virtual void postAssemblingMatrixRHS(std::size_t iProblem=0) { |
| 143 |
|
|
(void) iProblem; |
| 144 |
|
|
} |
| 145 |
|
|
|
| 146 |
|
|
/// Virtual function to specify special action before time loop (solve time-independent problem, ...) |
| 147 |
|
✗ |
virtual void preProcessing() {} |
| 148 |
|
|
|
| 149 |
|
|
/// Manage time iteration. |
| 150 |
|
|
virtual void updateTime(FlagMatrixRHS flagMatrixRHS=FlagMatrixRHS::matrix_and_rhs); |
| 151 |
|
|
|
| 152 |
|
|
/// Advance time step. |
| 153 |
|
|
virtual void forward()=0; |
| 154 |
|
|
|
| 155 |
|
|
/// Solve the problem with the initial conditions. |
| 156 |
|
|
virtual void SolveStaticProblem(); |
| 157 |
|
|
|
| 158 |
|
|
/** |
| 159 |
|
|
* @brief Solve the dynamic problem. |
| 160 |
|
|
* A call to this method performs all the work, including initial call to solve the static problem. |
| 161 |
|
|
*/ |
| 162 |
|
|
virtual void SolveDynamicProblem(); |
| 163 |
|
|
|
| 164 |
|
|
/// Get boolean to stop loop on time. |
| 165 |
|
|
bool hasFinished(); |
| 166 |
|
|
|
| 167 |
|
|
/// Make m_hasFinished true when stop loop on time according to |
| 168 |
|
|
/// another criterion (steady-state for example) before reaching timeMax or timeIterationMax |
| 169 |
|
|
void makeHasFinishedTrue() { |
| 170 |
|
|
m_hasFinished = true; |
| 171 |
|
|
} |
| 172 |
|
|
|
| 173 |
|
|
///Input and output tools |
| 174 |
|
|
//======================= |
| 175 |
|
|
|
| 176 |
|
|
// reah mesh file to define problem |
| 177 |
|
|
virtual void readMesh(); |
| 178 |
|
|
|
| 179 |
|
|
// reah mesh file to define problem |
| 180 |
|
|
virtual void writeMesh(); |
| 181 |
|
|
|
| 182 |
|
|
// build edges of mesh |
| 183 |
|
|
void buildEdges(); |
| 184 |
|
|
|
| 185 |
|
|
// build faces of mesh |
| 186 |
|
|
void buildFaces(); |
| 187 |
|
|
|
| 188 |
|
|
// write solution with ensight |
| 189 |
|
|
void writeSolution(); |
| 190 |
|
|
|
| 191 |
|
|
/*! |
| 192 |
|
|
* \brief Write the matrix in Matlab format |
| 193 |
|
|
* |
| 194 |
|
|
* \param[in] filename Name of the file to be written |
| 195 |
|
|
* \param[in] index Index in the std::vector of the linear problem which matrix is printed |
| 196 |
|
|
*/ |
| 197 |
|
|
void writeMatrixForMatlab(const std::string& filename, unsigned int index = 0) const; |
| 198 |
|
|
|
| 199 |
|
|
/*! |
| 200 |
|
|
* \brief Write the RHS in Matlab format |
| 201 |
|
|
* |
| 202 |
|
|
* \param[in] filename Name of the file to be written |
| 203 |
|
|
* \param[in] index Index in the std::vector of the linear problem which rhs is printed |
| 204 |
|
|
*/ |
| 205 |
|
|
void writeRHSForMatlab(const std::string& filename, unsigned int index = 0) const; |
| 206 |
|
|
|
| 207 |
|
|
// Function tu compute boundary stress in a specific label |
| 208 |
|
|
void ComputeStress(int coef, int label, std::vector<double>& stress); |
| 209 |
|
|
|
| 210 |
|
|
virtual void setInitialCondition(); |
| 211 |
|
|
|
| 212 |
|
✗ |
virtual void userDefinedInitialConditions(std::size_t iProblem=0) {(void) iProblem;} |
| 213 |
|
|
|
| 214 |
|
|
//Callback functions. |
| 215 |
|
|
//================== |
| 216 |
|
|
|
| 217 |
|
|
/// Register a callable (function, functor) in the callback std::unordered_map. |
| 218 |
|
|
void addCallbackXYZ (const char *callbackName, const CallbackXYZ &callbackXYZ); |
| 219 |
|
|
void addCallbackXYZT(const char *callbackName, const CallbackXYZT &callbackXYZT); |
| 220 |
|
|
|
| 221 |
|
|
/// Get result of evaluation of callable named 'name' with given arguments. |
| 222 |
|
|
double evaluateCallback(const char *name, double x, double y, double z); |
| 223 |
|
|
double evaluateCallback(const char *name, double x, double y, double z, double t); |
| 224 |
|
|
|
| 225 |
|
|
// CVGraph |
| 226 |
|
|
//======== |
| 227 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 228 |
|
|
virtual void startIterationCVG(); |
| 229 |
|
✗ |
virtual void cvgraphNewTimeStep(){}; |
| 230 |
|
|
|
| 231 |
|
|
/// Impose the entire solution at the interface |
| 232 |
|
|
void ImposeCVGraphInterfaceSolution(double* ImpValue); |
| 233 |
|
|
|
| 234 |
|
|
/// Impose the solution corresponding to the variable with idVariable and a computed variable needed by the users |
| 235 |
|
|
void ImposeCVGraphInterfaceSolutionAndComputedVariable(double* ImpValue, int idVariable); |
| 236 |
|
|
|
| 237 |
|
|
/// Extract the entire solution at the interface |
| 238 |
|
|
virtual void ExtractCVGraphInterfaceSolution(double* valueDofInterface); |
| 239 |
|
|
|
| 240 |
|
|
/// Extract only the solution corresponding to the variable with idVariable |
| 241 |
|
|
void ExtractCVGraphInterfaceSolution(double* valueDofInterface, int idVariable); |
| 242 |
|
|
|
| 243 |
|
|
/// Extract the solution with idVariable and a specific variable computed by the user |
| 244 |
|
|
void ExtractCVGraphInterfaceSolutionAndComputedVariable(double* valueDofInterface,int idVariable,std::vector<double>& interfaceComputedVariable); |
| 245 |
|
|
|
| 246 |
|
|
/// Store the entire solution at the interface in order to use it as previous time step solution |
| 247 |
|
|
void StoreCVGraphInterfaceSolution(double* StoringValue); |
| 248 |
|
|
#endif |
| 249 |
|
|
|
| 250 |
|
|
///@} |
| 251 |
|
|
///@name Access |
| 252 |
|
|
///@{ |
| 253 |
|
|
|
| 254 |
|
25 |
IO* io(std::size_t i=0) { |
| 255 |
|
25 |
return m_ios[i].get(); |
| 256 |
|
|
} |
| 257 |
|
|
|
| 258 |
|
335023 |
FelisceTransient::Pointer fstransient() { |
| 259 |
|
335023 |
return m_fstransient; |
| 260 |
|
|
} |
| 261 |
|
|
|
| 262 |
|
89 |
GeometricMeshRegion::Pointer mesh(const std::size_t i=0) { |
| 263 |
|
89 |
return m_mesh[i]; |
| 264 |
|
|
} |
| 265 |
|
|
|
| 266 |
|
1179 |
LinearProblem* linearProblem(const std::size_t i=0) { |
| 267 |
|
1179 |
return m_linearProblem[i]; |
| 268 |
|
|
} |
| 269 |
|
|
|
| 270 |
|
|
/// Get model name |
| 271 |
|
|
const std::string& name() const { |
| 272 |
|
|
return m_name; |
| 273 |
|
|
} |
| 274 |
|
|
|
| 275 |
|
|
/// Get model instance index |
| 276 |
|
17088985 |
std::size_t& instanceIndex() { |
| 277 |
|
17088985 |
return m_instanceIndex; |
| 278 |
|
|
} |
| 279 |
|
|
|
| 280 |
|
|
std::size_t instanceIndex() const { |
| 281 |
|
|
return m_instanceIndex; |
| 282 |
|
|
} |
| 283 |
|
|
|
| 284 |
|
|
/// print a banner with text, the time and the iteration number |
| 285 |
|
|
void printNewTimeIterationBanner(); |
| 286 |
|
|
|
| 287 |
|
|
///Get Time. |
| 288 |
|
|
double getTime() const; |
| 289 |
|
|
///Set Time. |
| 290 |
|
|
void setTime(const double time); |
| 291 |
|
|
|
| 292 |
|
|
/// Function to get size of the state std::vector. |
| 293 |
|
✗ |
virtual int getNstate() const { |
| 294 |
|
✗ |
return 0; |
| 295 |
|
|
} |
| 296 |
|
✗ |
virtual int getNstate(PhysicalVariable variable) const { |
| 297 |
|
|
(void) variable; |
| 298 |
|
✗ |
return 0; |
| 299 |
|
|
} |
| 300 |
|
|
|
| 301 |
|
|
/// Function to get state vector. |
| 302 |
|
✗ |
virtual void getState(double* & state) { |
| 303 |
|
|
(void) state; |
| 304 |
|
|
} |
| 305 |
|
|
|
| 306 |
|
|
/// Function to std::set state std::vector. |
| 307 |
|
✗ |
virtual void setState(double* & state) { |
| 308 |
|
|
(void) state; |
| 309 |
|
|
} |
| 310 |
|
|
|
| 311 |
|
|
inline const MapCallbackXYZ& mapCallbackXYZ () const { |
| 312 |
|
|
return m_mapCallbackXYZ; |
| 313 |
|
|
} |
| 314 |
|
|
inline MapCallbackXYZ& mapCallbackXYZ () { |
| 315 |
|
|
return m_mapCallbackXYZ; |
| 316 |
|
|
} |
| 317 |
|
|
inline const MapCallbackXYZT& mapCallbackXYZT() const { |
| 318 |
|
|
return m_mapCallbackXYZT; |
| 319 |
|
|
} |
| 320 |
|
|
inline MapCallbackXYZT& mapCallbackXYZT() { |
| 321 |
|
|
return m_mapCallbackXYZT; |
| 322 |
|
|
} |
| 323 |
|
|
|
| 324 |
|
|
CallbackXYZ& callbackXYZ (const char* name); |
| 325 |
|
|
CallbackXYZT& callbackXYZT(const char* name); |
| 326 |
|
|
|
| 327 |
|
|
///@} |
| 328 |
|
|
///@name Inquiry |
| 329 |
|
|
///@{ |
| 330 |
|
|
|
| 331 |
|
|
///@} |
| 332 |
|
|
///@name Input and output |
| 333 |
|
|
///@{ |
| 334 |
|
|
|
| 335 |
|
|
///@} |
| 336 |
|
|
///@name Friends |
| 337 |
|
|
///@{ |
| 338 |
|
|
|
| 339 |
|
|
///@} |
| 340 |
|
|
protected: |
| 341 |
|
|
///@name Protected Life Cycle |
| 342 |
|
|
///@{ |
| 343 |
|
|
|
| 344 |
|
|
///@} |
| 345 |
|
|
///@name Protected static Member Variables |
| 346 |
|
|
///@{ |
| 347 |
|
|
|
| 348 |
|
|
///@} |
| 349 |
|
|
///@name Protected member Variables |
| 350 |
|
|
///@{ |
| 351 |
|
|
|
| 352 |
|
|
/// model name |
| 353 |
|
|
std::string m_name = "GIVE_A_NAME_TO_YOUR_MODEL"; |
| 354 |
|
|
|
| 355 |
|
|
/// Instance index |
| 356 |
|
|
std::size_t m_instanceIndex = 0; |
| 357 |
|
|
|
| 358 |
|
|
/// Global mesh |
| 359 |
|
|
std::vector<GeometricMeshRegion::Pointer> m_mesh; |
| 360 |
|
|
|
| 361 |
|
|
/// InputOutput manager |
| 362 |
|
|
std::vector<IO::Pointer> m_ios; |
| 363 |
|
|
|
| 364 |
|
|
FelisceTransient::Pointer m_fstransient = nullptr; |
| 365 |
|
|
|
| 366 |
|
|
/// Linear Problem |
| 367 |
|
|
std::vector<LinearProblem*> m_linearProblem; |
| 368 |
|
|
|
| 369 |
|
|
// Has finished flag |
| 370 |
|
|
bool m_hasFinished = false; |
| 371 |
|
|
|
| 372 |
|
|
//CVGraphInterface |
| 373 |
|
|
CVGraphInterface::Pointer m_cvgraphInterf = nullptr; |
| 374 |
|
|
|
| 375 |
|
|
// initialization flags |
| 376 |
|
|
bool m_modelIsInitialized = false; |
| 377 |
|
|
bool m_linearProblemIsInitialized = false; |
| 378 |
|
|
bool m_eigenProblemIsInitialized = false; |
| 379 |
|
|
bool m_meshIsRead = false; |
| 380 |
|
|
bool m_meshIsWritten = false; |
| 381 |
|
|
bool m_initializeCVGraphInterface = false; |
| 382 |
|
|
bool m_callPetscInitialize = false; |
| 383 |
|
|
|
| 384 |
|
|
// Callback maps |
| 385 |
|
|
MapCallbackXYZ m_mapCallbackXYZ; |
| 386 |
|
|
MapCallbackXYZT m_mapCallbackXYZT; |
| 387 |
|
|
|
| 388 |
|
|
///Initialization vectors. |
| 389 |
|
|
PetscVector m_U_0; |
| 390 |
|
|
std::vector<SolutionBackup> m_solutionBackup; |
| 391 |
|
|
InitialCondition m_initialCondition; |
| 392 |
|
|
|
| 393 |
|
|
///@} |
| 394 |
|
|
///@name Protected Operators |
| 395 |
|
|
///@{ |
| 396 |
|
|
|
| 397 |
|
|
///@} |
| 398 |
|
|
///@name Protected Operations |
| 399 |
|
|
///@{ |
| 400 |
|
|
|
| 401 |
|
|
///@} |
| 402 |
|
|
///@name Protected Operators |
| 403 |
|
|
///@{ |
| 404 |
|
|
|
| 405 |
|
|
///@} |
| 406 |
|
|
///@name Protected Operations |
| 407 |
|
|
///@{ |
| 408 |
|
|
|
| 409 |
|
|
///@} |
| 410 |
|
|
///@name Protected Access |
| 411 |
|
|
///@{ |
| 412 |
|
|
|
| 413 |
|
|
///@} |
| 414 |
|
|
///@name Protected Inquiry |
| 415 |
|
|
///@{ |
| 416 |
|
|
|
| 417 |
|
|
///@} |
| 418 |
|
|
///@name Protected LifeCycle |
| 419 |
|
|
///@{ |
| 420 |
|
|
|
| 421 |
|
|
///@} |
| 422 |
|
|
private: |
| 423 |
|
|
///@name Private Life Cycle |
| 424 |
|
|
///@{ |
| 425 |
|
|
|
| 426 |
|
|
///@} |
| 427 |
|
|
///@name Private Operators |
| 428 |
|
|
///@{ |
| 429 |
|
|
|
| 430 |
|
|
///@} |
| 431 |
|
|
///@name Private Operations |
| 432 |
|
|
///@{ |
| 433 |
|
|
|
| 434 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 435 |
|
|
void rhsWithoutBC_zeroEntries(); |
| 436 |
|
|
void rhsWithoutBC_restore(); |
| 437 |
|
|
#endif |
| 438 |
|
|
|
| 439 |
|
|
///@} |
| 440 |
|
|
///@name Private static Member Variables |
| 441 |
|
|
///@{ |
| 442 |
|
|
|
| 443 |
|
|
///@} |
| 444 |
|
|
///@name Private member Variables |
| 445 |
|
|
///@{ |
| 446 |
|
|
|
| 447 |
|
|
#ifdef FELISCE_WITH_CVGRAPH |
| 448 |
|
|
PetscVector m_rhsWithForceTermWithoutBC; |
| 449 |
|
|
bool m_rhsWithoutBC_zeroed; |
| 450 |
|
|
#endif |
| 451 |
|
|
|
| 452 |
|
|
///@} |
| 453 |
|
|
///@name Private Operators |
| 454 |
|
|
///@{ |
| 455 |
|
|
|
| 456 |
|
|
///@} |
| 457 |
|
|
///@name Private Operations |
| 458 |
|
|
///@{ |
| 459 |
|
|
|
| 460 |
|
|
void checkConnectionVariablesMeshs(); |
| 461 |
|
|
|
| 462 |
|
|
///@} |
| 463 |
|
|
///@name Private Access |
| 464 |
|
|
///@{ |
| 465 |
|
|
|
| 466 |
|
|
///@} |
| 467 |
|
|
///@name Private Inquiry |
| 468 |
|
|
///@{ |
| 469 |
|
|
|
| 470 |
|
|
///@} |
| 471 |
|
|
///@name Private LifeCycle |
| 472 |
|
|
///@{ |
| 473 |
|
|
|
| 474 |
|
|
///@} |
| 475 |
|
|
}; |
| 476 |
|
|
|
| 477 |
|
|
///@} |
| 478 |
|
|
///@name Type Definitions |
| 479 |
|
|
///@{ |
| 480 |
|
|
|
| 481 |
|
|
///@} |
| 482 |
|
|
|
| 483 |
|
|
} // namespace felisce |
| 484 |
|
|
|
| 485 |
|
|
#endif |
| 486 |
|
|
|