Chaste  Release::3.4
AbstractDynamicLinearPdeSolver.hpp
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36 
37 #ifndef ABSTRACTDYNAMICLINEARPDESOLVER_HPP_
38 #define ABSTRACTDYNAMICLINEARPDESOLVER_HPP_
39 
40 #include "Exception.hpp"
41 #include "TimeStepper.hpp"
42 #include "AbstractLinearPdeSolver.hpp"
43 #include "PdeSimulationTime.hpp"
44 #include "AbstractTimeAdaptivityController.hpp"
45 #include "Hdf5DataWriter.hpp"
46 #include "Hdf5ToVtkConverter.hpp"
47 #include "Hdf5ToTxtConverter.hpp"
48 
55 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
56 class AbstractDynamicLinearPdeSolver : public AbstractLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>
57 {
58  friend class TestSimpleLinearParabolicSolver;
59 protected:
60 
62  double mTstart;
63 
65  double mTend;
66 
68  bool mTimesSet;
69 
72 
75 
81 
87 
90 
93 
99 
105 
111 
113  std::string mOutputDirectory;
114 
116  std::string mFilenamePrefix;
117 
124 
127 
129  std::vector<int> mVariableColumnIds;
130 
135  void InitialiseHdf5Writer();
136 
143  void WriteOneStep(double time, Vec solution);
144 
145 public:
146 
153 
160  void SetTimes(double tStart, double tEnd);
161 
167  void SetTimeStep(double dt);
168 
177  void SetInitialCondition(Vec initialCondition);
178 
182  virtual Vec Solve();
183 
186 
192  void SetTimeAdaptivityController(AbstractTimeAdaptivityController* pTimeAdaptivityController);
193 
197  void SetOutputToVtk(bool output);
198 
202  void SetOutputToParallelVtk(bool output);
203 
207  void SetOutputToTxt(bool output);
208 
213  void SetOutputDirectoryAndPrefix(std::string outputDirectory, std::string prefix);
214 
219  void SetPrintingTimestepMultiple(unsigned multiple);
220 };
221 
222 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
224 {
225  // Check that everything is set up correctly
226  if ((mOutputDirectory=="") || (mFilenamePrefix==""))
227  {
228  EXCEPTION("Output directory or filename prefix has not been set");
229  }
230 
231  // Create writer
232  mpHdf5Writer = new Hdf5DataWriter(*(this->mpMesh)->GetDistributedVectorFactory(),
233  mOutputDirectory,
234  mFilenamePrefix);
235 
236  // Set writer to output all nodes
237  mpHdf5Writer->DefineFixedDimension((this->mpMesh)->GetNumNodes());
238 
239  // Only used to get an estimate of the number of timesteps below
240  unsigned estimated_num_printing_timesteps = 1u + (unsigned)((mTend - mTstart)/(mIdealTimeStep*mPrintingTimestepMultiple));
241 
248  assert(mVariableColumnIds.empty());
249  for (unsigned i=0; i<PROBLEM_DIM; i++)
250  {
251  std::stringstream variable_name;
252  variable_name << "Variable_" << i;
253  mVariableColumnIds.push_back(mpHdf5Writer->DefineVariable(variable_name.str(),"undefined"));
254  }
255  mpHdf5Writer->DefineUnlimitedDimension("Time", "undefined", estimated_num_printing_timesteps);
256 
257  // End the define mode of the writer
258  mpHdf5Writer->EndDefineMode();
259 }
260 
261 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
263  : AbstractLinearPdeSolver<ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM>(pMesh),
264  mTimesSet(false),
265  mInitialCondition(NULL),
266  mMatrixIsAssembled(false),
267  mMatrixIsConstant(false),
268  mIdealTimeStep(-1.0),
269  mLastWorkingTimeStep(-1),
270  mpTimeAdaptivityController(NULL),
271  mOutputToVtk(false),
272  mOutputToParallelVtk(false),
273  mOutputToTxt(false),
274  mOutputDirectory(""),
275  mFilenamePrefix(""),
276  mPrintingTimestepMultiple(1),
277  mpHdf5Writer(NULL)
278 {
279 }
280 
281 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
283 {
284  mTstart = tStart;
285  mTend = tEnd;
286 
287  if (mTstart >= mTend)
288  {
289  EXCEPTION("Start time has to be less than end time");
290  }
291 
292  mTimesSet = true;
293 }
294 
295 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
297 {
298  if (dt <= 0)
299  {
300  EXCEPTION("Time step has to be greater than zero");
301  }
302 
303  mIdealTimeStep = dt;
304 }
305 
306 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
308 {
309  assert(initialCondition != NULL);
310  mInitialCondition = initialCondition;
311 }
312 
313 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
315 {
316  mpHdf5Writer->PutUnlimitedVariable(time);
317  if (PROBLEM_DIM == 1)
318  {
319  mpHdf5Writer->PutVector(mVariableColumnIds[0], solution);
320  }
321  else
322  {
323  mpHdf5Writer->PutStripedVector(mVariableColumnIds, solution);
324  }
325 }
326 
327 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
329 {
330  // Begin by checking that everything has been set up correctly
331  if (!mTimesSet)
332  {
333  EXCEPTION("SetTimes() has not been called");
334  }
335  if ((mIdealTimeStep <= 0.0) && (mpTimeAdaptivityController==NULL))
336  {
337  EXCEPTION("SetTimeStep() has not been called");
338  }
339  if (mInitialCondition == NULL)
340  {
341  EXCEPTION("SetInitialCondition() has not been called");
342  }
343 
344  // If required, initialise HDF5 writer and output initial condition to HDF5 file
345  bool print_output = (mOutputToVtk || mOutputToParallelVtk || mOutputToTxt);
346  if (print_output)
347  {
348  InitialiseHdf5Writer();
349  WriteOneStep(mTstart, mInitialCondition);
350  mpHdf5Writer->AdvanceAlongUnlimitedDimension();
351  }
352 
353  this->InitialiseForSolve(mInitialCondition);
354 
355  if (mIdealTimeStep < 0) // hasn't been set, so a controller must have been given
356  {
357  mIdealTimeStep = mpTimeAdaptivityController->GetNextTimeStep(mTstart, mInitialCondition);
358  }
359 
360  /*
361  * Note: we use the mIdealTimeStep here (the original timestep that was passed in, or
362  * the last timestep suggested by the controller), rather than the last timestep used
363  * (mLastWorkingTimeStep), because the timestep will be very slightly altered by the
364  * stepper in the final timestep of the last printing-timestep-loop, and these floating
365  * point errors can add up and eventually cause exceptions being thrown.
366  */
367  TimeStepper stepper(mTstart, mTend, mIdealTimeStep, mMatrixIsConstant);
368 
369  Vec solution = mInitialCondition;
370  Vec next_solution;
371 
372  while (!stepper.IsTimeAtEnd())
373  {
374  bool timestep_changed = false;
375 
377 
378  // Determine timestep to use
379  double new_dt;
380  if (mpTimeAdaptivityController)
381  {
382  // Get the timestep the controller wants to use and store it as the ideal timestep
383  mIdealTimeStep = mpTimeAdaptivityController->GetNextTimeStep(stepper.GetTime(), solution);
384 
385  // Tell the stepper to use this timestep from now on...
386  stepper.ResetTimeStep(mIdealTimeStep);
387 
388  // ..but now get the timestep from the stepper, as the stepper might need
389  // to trim the timestep if it would take us over the end time
390  new_dt = stepper.GetNextTimeStep();
391  // Changes in timestep bigger than 0.001% will trigger matrix re-computation
392  timestep_changed = (fabs(new_dt/mLastWorkingTimeStep - 1.0) > 1e-5);
393  }
394  else
395  {
396  new_dt = stepper.GetNextTimeStep();
397 
398  //new_dt should be roughly the same size as mIdealTimeStep - we should never need to take a tiny step
399 
400  if (mMatrixIsConstant && fabs(new_dt/mIdealTimeStep - 1.0) > 1e-5)
401  {
402  // Here we allow for changes of up to 0.001%
403  // Note that the TimeStepper guarantees that changes in dt are no bigger than DBL_EPSILON*current_time
405  }
406  }
407 
408  // Save the timestep as the last one use, and also put it in PdeSimulationTime
409  // so everyone can see it
410  mLastWorkingTimeStep = new_dt;
412 
413  // Solve
414  try
415  {
416  // (This runs the cell ODE models in heart simulations)
417  this->PrepareForSetupLinearSystem(solution);
418  }
419  catch(Exception& e)
420  {
421  // We only need to clean up memory if we are NOT on the first PDE time step,
422  // as someone else cleans up the mInitialCondition vector in higher classes.
423  if (solution != mInitialCondition)
424  {
425  HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
426  PetscTools::Destroy(solution);
427  HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
428  }
429  throw e;
430  }
431 
432  bool compute_matrix = (!mMatrixIsConstant || !mMatrixIsAssembled || timestep_changed);
433 
434  this->SetupLinearSystem(solution, compute_matrix);
435 
436  this->FinaliseLinearSystem(solution);
437 
438  if (compute_matrix)
439  {
440  this->mpLinearSystem->ResetKspSolver();
441  }
442 
443  next_solution = this->mpLinearSystem->Solve(solution);
444 
445  if (mMatrixIsConstant)
446  {
447  mMatrixIsAssembled = true;
448  }
449 
450  this->FollowingSolveLinearSystem(next_solution);
451 
452  stepper.AdvanceOneTimeStep();
453 
454  // Avoid memory leaks
455  if (solution != mInitialCondition)
456  {
457  HeartEventHandler::BeginEvent(HeartEventHandler::COMMUNICATION);
458  PetscTools::Destroy(solution);
459  HeartEventHandler::EndEvent(HeartEventHandler::COMMUNICATION);
460  }
461  solution = next_solution;
462 
463  // If required, output next solution to HDF5 file
464  if (print_output && (stepper.GetTotalTimeStepsTaken()%mPrintingTimestepMultiple == 0) )
465  {
466  WriteOneStep(stepper.GetTime(), solution);
467  mpHdf5Writer->AdvanceAlongUnlimitedDimension();
468  }
469  }
470 
471  // Avoid memory leaks
472  if (mpHdf5Writer != NULL)
473  {
474  delete mpHdf5Writer;
475  mpHdf5Writer = NULL;
476  }
477 
478  // Convert HDF5 output to other formats as required
479 
480  if (mOutputToVtk)
481  {
483  mFilenamePrefix, this->mpMesh, false, false);
484  }
485  if (mOutputToParallelVtk)
486  {
488  mFilenamePrefix, this->mpMesh, true, false);
489  }
490  if (mOutputToTxt)
491  {
493  mFilenamePrefix, this->mpMesh);
494  }
495 
496  return solution;
497 }
498 
499 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
501 {
502  mMatrixIsAssembled = false;
503 }
504 
505 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
507 {
508  assert(pTimeAdaptivityController != NULL);
509  assert(mpTimeAdaptivityController == NULL);
510  mpTimeAdaptivityController = pTimeAdaptivityController;
511 }
512 
513 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
515 {
516  mOutputToVtk = output;
517 }
518 
519 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
521 {
522  mOutputToParallelVtk = output;
523 }
524 
525 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
527 {
528  mOutputToTxt = output;
529 }
530 
531 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
533 {
534  mOutputDirectory = outputDirectory;
535  mFilenamePrefix = prefix;
536 }
537 
538 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
540 {
541  mPrintingTimestepMultiple = multiple;
542 }
543 
544 #endif /*ABSTRACTDYNAMICLINEARPDESOLVER_HPP_*/
double GetNextTimeStep()
double GetTime() const
#define EXCEPTION(message)
Definition: Exception.hpp:143
void ResetTimeStep(double dt)
void SetOutputDirectoryAndPrefix(std::string outputDirectory, std::string prefix)
#define NEVER_REACHED
Definition: Exception.hpp:206
void AdvanceOneTimeStep()
bool IsTimeAtEnd() const
void SetTimes(double tStart, double tEnd)
AbstractTimeAdaptivityController * mpTimeAdaptivityController
unsigned GetTotalTimeStepsTaken() const
static void Destroy(Vec &rVec)
Definition: PetscTools.hpp:351
void SetTimeAdaptivityController(AbstractTimeAdaptivityController *pTimeAdaptivityController)
void WriteOneStep(double time, Vec solution)
static void SetTime(double time)
double GetNextTime() const
static void SetPdeTimeStepAndNextTime(double timestep, double next_time)
AbstractDynamicLinearPdeSolver(AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh)