TSPrePostProc Struct Reference

Set of functions called by PETSc solver used to refine and update mesh. More...

Collaboration diagram for TSPrePostProc:

Public Member Functions
	TSPrePostProc ()=default
virtual	~TSPrePostProc ()=default
MoFEMErrorCode	tsSetUp (TS ts)
	Used to setup TS solver. More...
	TSPrePostProc ()=default
virtual	~TSPrePostProc ()=default
MoFEMErrorCode	tsSetUp (TS ts)
	Used to setup TS solver. More...
SmartPetscObj< VecScatter >	getScatter (Vec x, Vec y, enum FR fr)
SmartPetscObj< Vec >	getSubVector ()

Static Public Member Functions
static MoFEMErrorCode	tsPostStage (TS ts, PetscReal stagetime, PetscInt stageindex, Vec *Y)
	[Boundary condition] More...
static MoFEMErrorCode	tsPostStep (TS ts)
static MoFEMErrorCode	tsPreStep (TS ts)

Public Attributes
Example *	fsRawPtr
SmartPetscObj< DM >	solverSubDM
SmartPetscObj< Vec >	globSol
FreeSurface *	fsRawPtr

Static Private Member Functions
static MoFEMErrorCode	tsPreProc (TS ts)
	Pre process time step. More...
static MoFEMErrorCode	tsPostProc (TS ts)
	Post process time step. More...
static MoFEMErrorCode	tsPreStage (TS ts)
static MoFEMErrorCode	tsSetIFunction (TS ts, PetscReal t, Vec u, Vec u_t, Vec f, void *ctx)
static MoFEMErrorCode	tsSetIJacobian (TS ts, PetscReal t, Vec u, Vec u_t, PetscReal a, Mat A, Mat B, void *ctx)
	Wrapper for SNES Lhs. More...
static MoFEMErrorCode	tsMonitor (TS ts, PetscInt step, PetscReal t, Vec u, void *ctx)
	Wrapper for TS monitor. More...
static MoFEMErrorCode	pcSetup (PC pc)
static MoFEMErrorCode	pcApply (PC pc, Vec pc_f, Vec pc_x)

Private Attributes
SmartPetscObj< Vec >	globRes
SmartPetscObj< Mat >	subB
SmartPetscObj< KSP >	subKSP
boost::shared_ptr< SnesCtx >	snesCtxPtr
boost::shared_ptr< TsCtx >	tsCtxPtr

Detailed Description

Set of functions called by PETSc solver used to refine and update mesh.

Note

Currently theta method is only handled by this code.

Examples

dynamic_first_order_con_law.cpp, and free_surface.cpp.

Definition at line 384 of file dynamic_first_order_con_law.cpp.

Constructor & Destructor Documentation

TSPrePostProc() [1/2]

TSPrePostProc::TSPrePostProc ( )

default

~TSPrePostProc() [1/2]

virtual TSPrePostProc::~TSPrePostProc ( )

virtualdefault

TSPrePostProc() [2/2]

TSPrePostProc::TSPrePostProc ( )

default

~TSPrePostProc() [2/2]

virtual TSPrePostProc::~TSPrePostProc ( )

virtualdefault

Member Function Documentation

getScatter()

SmartPetscObj< VecScatter > TSPrePostProc::getScatter	(	Vec	x,
		Vec	y,
		enum FR	fr
	)

Examples

free_surface.cpp.

Definition at line 3118 of file free_surface.cpp.

                                                                            {
  if (auto ptr = tsPrePostProc.lock()) {
    auto prb_ptr = ptr->fsRawPtr->mField.get_problem("SUB_SOLVER");
    if (auto sub_data = prb_ptr->getSubData()) {
      auto is = sub_data->getSmartColIs();
      VecScatter s;
      if (fr == R) {
        CHK_THROW_MESSAGE(VecScatterCreate(x, PETSC_NULL, y, is, &s),
                          "crate scatter");
      } else {
        CHK_THROW_MESSAGE(VecScatterCreate(x, is, y, PETSC_NULL, &s),
                          "crate scatter");
      }
      return SmartPetscObj<VecScatter>(s);
    }
  }
  CHK_THROW_MESSAGE(MOFEM_DATA_INCONSISTENCY, "No prb pinter");
  return SmartPetscObj<VecScatter>();
}

getSubVector()

SmartPetscObj< Vec > TSPrePostProc::getSubVector

(

)

Examples

free_surface.cpp.

Definition at line 3138 of file free_surface.cpp.

                                               {
  return createDMVector(solverSubDM);
}

pcApply()

MoFEMErrorCode TSPrePostProc::pcApply ( PC  pc, Vec  pc_f, Vec  pc_x  )

staticprivate

Examples

free_surface.cpp.

Definition at line 3098 of file free_surface.cpp.

                                                               {
  MoFEMFunctionBegin;
  if (auto ptr = tsPrePostProc.lock()) {
    auto sub_x = ptr->getSubVector();
    auto sub_f = vectorDuplicate(sub_x);
    auto scatter = ptr->getScatter(sub_x, pc_x, R);
    CHKERR VecScatterBegin(scatter, pc_f, sub_f, INSERT_VALUES,
                           SCATTER_REVERSE);
    CHKERR VecScatterEnd(scatter, pc_f, sub_f, INSERT_VALUES, SCATTER_REVERSE);
    CHKERR KSPSetOperators(ptr->subKSP, ptr->subB, ptr->subB);
    MOFEM_LOG("FS", Sev::verbose) << "PCShell solve";
    CHKERR KSPSolve(ptr->subKSP, sub_f, sub_x);
    MOFEM_LOG("FS", Sev::verbose) << "PCShell solve <- done";
    CHKERR VecScatterBegin(scatter, sub_x, pc_x, INSERT_VALUES,
                           SCATTER_FORWARD);
    CHKERR VecScatterEnd(scatter, sub_x, pc_x, INSERT_VALUES, SCATTER_FORWARD);
  }
  MoFEMFunctionReturn(0);
};

pcSetup()

MoFEMErrorCode TSPrePostProc::pcSetup ( PC  pc )

staticprivate

Examples

free_surface.cpp.

Definition at line 3088 of file free_surface.cpp.

                                           {
  MoFEMFunctionBegin;
  if (auto ptr = tsPrePostProc.lock()) {
    MOFEM_LOG("FS", Sev::verbose) << "SetUP sub PC";
    ptr->subKSP = createKSP(ptr->fsRawPtr->mField.get_comm());
    CHKERR KSPSetFromOptions(ptr->subKSP);
  }
  MoFEMFunctionReturn(0);
};

tsMonitor()

MoFEMErrorCode TSPrePostProc::tsMonitor ( TS  ts, PetscInt  step, PetscReal  t, Vec  u, void *  ctx  )

staticprivate

Wrapper for TS monitor.

Examples

free_surface.cpp.

Definition at line 3063 of file free_surface.cpp.

                                                          {
  MoFEMFunctionBegin;
  if (auto ptr = tsPrePostProc.lock()) {
    auto get_norm = [&](auto x) {
      double nrm;
      CHKERR VecNorm(x, NORM_2, &nrm);
      return nrm;
    };
 
    auto sub_u = ptr->getSubVector();
    auto scatter = ptr->getScatter(sub_u, u, R);
    CHKERR VecScatterBegin(scatter, u, sub_u, INSERT_VALUES, SCATTER_REVERSE);
    CHKERR VecScatterEnd(scatter, u, sub_u, INSERT_VALUES, SCATTER_REVERSE);
    CHKERR VecGhostUpdateBegin(sub_u, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR VecGhostUpdateEnd(sub_u, INSERT_VALUES, SCATTER_FORWARD);
 
    MOFEM_LOG("FS", Sev::verbose)
        << "u norm " << get_norm(u) << " u sub nom " << get_norm(sub_u);
 
    CHKERR TsMonitorSet(ts, step, t, sub_u, ptr->tsCtxPtr.get());
  }
  MoFEMFunctionReturn(0);
}

tsPostProc()

MoFEMErrorCode TSPrePostProc::tsPostProc ( TS  ts )

staticprivate

Post process time step.

Currently that function do not make anything major

Parameters

ts

Returns

MoFEMErrorCode

Examples

free_surface.cpp.

Definition at line 2998 of file free_surface.cpp.

                                              {
  if (auto ptr = tsPrePostProc.lock()) {
    auto &m_field = ptr->fsRawPtr->mField;
    MOFEM_LOG_CHANNEL("SYNC");
    MOFEM_TAG_AND_LOG("SYNC", Sev::verbose, "FS") << "PostProc done";
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::verbose);
  }
  return 0;
}

tsPostStage()

MoFEMErrorCode TSPrePostProc::tsPostStage ( TS  ts, PetscReal  stagetime, PetscInt  stageindex, Vec *  Y  )

static

[Boundary condition]

Examples

dynamic_first_order_con_law.cpp.

Definition at line 581 of file dynamic_first_order_con_law.cpp.

                                                                       {
  MoFEMFunctionBegin;
  // cerr << "tsPostStage " <<"\n";
  if (auto ptr = tsPrePostProc.lock()) {
    auto &m_field = ptr->fsRawPtr->mField;
    auto *simple = m_field.getInterface<Simple>();
    auto *pipeline_mng = m_field.getInterface<PipelineManager>();
 
    auto fb = m_field.getInterface<FieldBlas>();
    double dt;
    CHKERR TSGetTimeStep(ts, &dt);
    double time;
    CHKERR TSGetTime(ts, &time);
    PetscInt num_stages;
    Vec *stage_solutions;
 
    CHKERR TSGetStages(ts, &num_stages, &stage_solutions);
    PetscPrintf(PETSC_COMM_WORLD, "Check timestep %d time %e dt %e\n",
                num_stages, time, dt);
 
    const double inv_num_step = (double)num_stages;
    CHKERR fb->fieldCopy(1., "x_1", "x_2");
    CHKERR fb->fieldAxpy(dt, "V", "x_2");
    CHKERR fb->fieldCopy(1., "x_2", "x_1");
 
    CHKERR fb->fieldCopy(-inv_num_step / dt, "F_0", "F_dot");
    CHKERR fb->fieldAxpy(inv_num_step / dt, "F", "F_dot");
    CHKERR fb->fieldCopy(1., "F", "F_0");
  }
  MoFEMFunctionReturn(0);
}

tsPostStep()

MoFEMErrorCode TSPrePostProc::tsPostStep ( TS  ts )

static

Examples

dynamic_first_order_con_law.cpp.

Definition at line 614 of file dynamic_first_order_con_law.cpp.

                                              {
  MoFEMFunctionBegin;
 
  if (auto ptr = tsPrePostProc.lock()) {
    auto &m_field = ptr->fsRawPtr->mField;
    auto fb = m_field.getInterface<FieldBlas>();
    double dt;
    CHKERR TSGetTimeStep(ts, &dt);
    double time;
    CHKERR TSGetTime(ts, &time);
  }
  MoFEMFunctionReturn(0);
}

tsPreProc()

MoFEMErrorCode TSPrePostProc::tsPreProc ( TS  ts )

staticprivate

Pre process time step.

Refine mesh and update fields

Parameters

ts

Returns

MoFEMErrorCode

cut-off values at nodes, i.e. abs("H") <= 1

Examples

free_surface.cpp.

Definition at line 2877 of file free_surface.cpp.

                                             {
  MoFEMFunctionBegin;
 
  if (auto ptr = tsPrePostProc.lock()) {
 
    /**
     * @brief cut-off values at nodes, i.e. abs("H") <= 1
     *
     */
    auto cut_off_dofs = [&]() {
      MoFEMFunctionBegin;
 
      auto &m_field = ptr->fsRawPtr->mField;
 
      Range current_verts;
      auto bit_mng = m_field.getInterface<BitRefManager>();
      CHKERR bit_mng->getEntitiesByTypeAndRefLevel(
          bit(get_current_bit()), BitRefLevel().set(), MBVERTEX, current_verts);
 
      auto cut_off_verts = [&](boost::shared_ptr<FieldEntity> ent_ptr) {
        MoFEMFunctionBegin;
        for (auto &h : ent_ptr->getEntFieldData()) {
          h = cut_off(h);
        }
        MoFEMFunctionReturn(0);
      };
 
      auto field_blas = m_field.getInterface<FieldBlas>();
      CHKERR field_blas->fieldLambdaOnEntities(cut_off_verts, "H",
                                               &current_verts);
      MoFEMFunctionReturn(0);
    };
 
    CHKERR cut_off_dofs();
  }
 
  if (auto ptr = tsPrePostProc.lock()) {
    MOFEM_LOG("FS", Sev::inform) << "Run step pre proc";
 
    auto &m_field = ptr->fsRawPtr->mField;
    auto simple = m_field.getInterface<Simple>();
    auto bit_mng = m_field.getInterface<BitRefManager>();
    auto bc_mng = m_field.getInterface<BcManager>();
    auto field_blas = m_field.getInterface<FieldBlas>();
    auto opt = m_field.getInterface<OperatorsTester>();
    auto pip_mng = m_field.getInterface<PipelineManager>();
    auto prb_mng = m_field.getInterface<ProblemsManager>();
 
    // get vector norm
    auto get_norm = [&](auto x) {
      double nrm;
      CHKERR VecNorm(x, NORM_2, &nrm);
      return nrm;
    };
 
    // refine problem and project data, including theta data
    auto refine_problem = [&]() {
      MoFEMFunctionBegin;
      MOFEM_LOG("FS", Sev::inform) << "Refine problem";
      CHKERR ptr->fsRawPtr->refineMesh(refine_overlap);
      CHKERR ptr->fsRawPtr->projectData();
      MoFEMFunctionReturn(0);
    };
 
    // set new jacobin operator, since problem and thus tangent matrix size has
    // changed
    auto set_jacobian_operators = [&]() {
      MoFEMFunctionBegin;
      ptr->subB = createDMMatrix(ptr->solverSubDM);
      CHKERR KSPReset(ptr->subKSP);
      MoFEMFunctionReturn(0);
    };
 
    // set new solution
    auto set_solution = [&]() {
      MoFEMFunctionBegin;
      MOFEM_LOG("FS", Sev::inform) << "Set solution";
 
      PetscObjectState state;
 
      // Record the state, and set it again. This is to fool PETSc that solution
      // vector is not updated. Otherwise PETSc will treat every step as a first
      // step.
 
      // globSol is updated as result mesh refinement -  this is not really set
      // a new solution.
 
      CHKERR PetscObjectStateGet(getPetscObject(ptr->globSol.get()), &state);
      CHKERR DMoFEMMeshToLocalVector(simple->getDM(), ptr->globSol,
                                     INSERT_VALUES, SCATTER_FORWARD);
      CHKERR PetscObjectStateSet(getPetscObject(ptr->globSol.get()), state);
      MOFEM_LOG("FS", Sev::verbose)
          << "Set solution, vector norm " << get_norm(ptr->globSol);
      MoFEMFunctionReturn(0);
    };
 
    PetscBool is_theta;
    PetscObjectTypeCompare((PetscObject)ts, TSTHETA, &is_theta);
    if (is_theta) {
 
      CHKERR refine_problem();         // refine problem
      CHKERR set_jacobian_operators(); // set new jacobian
      CHKERR set_solution();           // set solution
 
    } else {
      SETERRQ(PETSC_COMM_WORLD, MOFEM_NOT_IMPLEMENTED,
              "Sorry, only TSTheta handling is implemented");
    }
 
    // Need barriers, somme functions in TS solver need are called collectively
    // and requite the same state of variables
    PetscBarrier((PetscObject)ts);
 
    MOFEM_LOG_CHANNEL("SYNC");
    MOFEM_TAG_AND_LOG("SYNC", Sev::verbose, "FS") << "PreProc done";
    MOFEM_LOG_SEVERITY_SYNC(m_field.get_comm(), Sev::verbose);
  }
 
  MoFEMFunctionReturn(0);
}

tsPreStage()

static MoFEMErrorCode TSPrePostProc::tsPreStage ( TS  ts )

staticprivate

tsPreStep()

MoFEMErrorCode TSPrePostProc::tsPreStep ( TS  ts )

static

Examples

dynamic_first_order_con_law.cpp.

Definition at line 628 of file dynamic_first_order_con_law.cpp.

                                             {
  MoFEMFunctionBegin;
 
  if (auto ptr = tsPrePostProc.lock()) {
    auto &m_field = ptr->fsRawPtr->mField;
    auto *simple = m_field.getInterface<Simple>();
    auto *pipeline_mng = m_field.getInterface<PipelineManager>();
 
    double dt;
    CHKERR TSGetTimeStep(ts, &dt);
    double time;
    CHKERR TSGetTime(ts, &time);
    int step_num;
    CHKERR TSGetStepNumber(ts, &step_num);
  }
  MoFEMFunctionReturn(0);
}

tsSetIFunction()

MoFEMErrorCode TSPrePostProc::tsSetIFunction ( TS  ts, PetscReal  t, Vec  u, Vec  u_t, Vec  f, void *  ctx  )

staticprivate

Examples

free_surface.cpp.

Definition at line 3008 of file free_surface.cpp.

                                                               {
  MoFEMFunctionBegin;
  if (auto ptr = tsPrePostProc.lock()) {
    auto sub_u = ptr->getSubVector();
    auto sub_u_t = vectorDuplicate(sub_u);
    auto sub_f = vectorDuplicate(sub_u);
    auto scatter = ptr->getScatter(sub_u, u, R);
 
    auto apply_scatter_and_update = [&](auto x, auto sub_x) {
      MoFEMFunctionBegin;
      CHKERR VecScatterBegin(scatter, x, sub_x, INSERT_VALUES, SCATTER_REVERSE);
      CHKERR VecScatterEnd(scatter, x, sub_x, INSERT_VALUES, SCATTER_REVERSE);
      CHKERR VecGhostUpdateBegin(sub_x, INSERT_VALUES, SCATTER_FORWARD);
      CHKERR VecGhostUpdateEnd(sub_x, INSERT_VALUES, SCATTER_FORWARD);
      MoFEMFunctionReturn(0);
    };
 
    CHKERR apply_scatter_and_update(u, sub_u);
    CHKERR apply_scatter_and_update(u_t, sub_u_t);
 
    CHKERR TsSetIFunction(ts, t, sub_u, sub_u_t, sub_f, ptr->tsCtxPtr.get());
    CHKERR VecScatterBegin(scatter, sub_f, f, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR VecScatterEnd(scatter, sub_f, f, INSERT_VALUES, SCATTER_FORWARD);
  }
  MoFEMFunctionReturn(0);
}

tsSetIJacobian()

MoFEMErrorCode TSPrePostProc::tsSetIJacobian ( TS  ts, PetscReal  t, Vec  u, Vec  u_t, PetscReal  a, Mat  A, Mat  B, void *  ctx  )

staticprivate

Wrapper for SNES Lhs.

Examples

free_surface.cpp.

Definition at line 3036 of file free_surface.cpp.

                                                        {
  MoFEMFunctionBegin;
  if (auto ptr = tsPrePostProc.lock()) {
    auto sub_u = ptr->getSubVector();
    auto sub_u_t = vectorDuplicate(sub_u);
    auto scatter = ptr->getScatter(sub_u, u, R);
 
    auto apply_scatter_and_update = [&](auto x, auto sub_x) {
      MoFEMFunctionBegin;
      CHKERR VecScatterBegin(scatter, x, sub_x, INSERT_VALUES, SCATTER_REVERSE);
      CHKERR VecScatterEnd(scatter, x, sub_x, INSERT_VALUES, SCATTER_REVERSE);
      CHKERR VecGhostUpdateBegin(sub_x, INSERT_VALUES, SCATTER_FORWARD);
      CHKERR VecGhostUpdateEnd(sub_x, INSERT_VALUES, SCATTER_FORWARD);
      MoFEMFunctionReturn(0);
    };
 
    CHKERR apply_scatter_and_update(u, sub_u);
    CHKERR apply_scatter_and_update(u_t, sub_u_t);
 
    CHKERR TsSetIJacobian(ts, t, sub_u, sub_u_t, a, ptr->subB, ptr->subB,
                          ptr->tsCtxPtr.get());
  }
  MoFEMFunctionReturn(0);
}

tsSetUp() [1/2]

MoFEMErrorCode TSPrePostProc::tsSetUp

(

TS

ts

)

Used to setup TS solver.

Parameters

ts

Returns

MoFEMErrorCode

Examples

free_surface.cpp.

Definition at line 3142 of file free_surface.cpp.

                                           {
 
  auto &m_field = fsRawPtr->mField;
  auto simple = m_field.getInterface<Simple>();
 
  MoFEMFunctionBegin;
 
  auto dm = simple->getDM();
 
  globRes = vectorDuplicate(globSol);
  CHKERR TSSetIFunction(ts, globRes, tsSetIFunction, nullptr);
  CHKERR TSSetIJacobian(ts, PETSC_NULL, PETSC_NULL, tsSetIJacobian, nullptr);
  CHKERR TSMonitorSet(ts, tsMonitor, fsRawPtr, PETSC_NULL);
 
  SNES snes;
  CHKERR TSGetSNES(ts, &snes);
  auto snes_ctx_ptr = getDMSnesCtx(dm);
 
  auto set_section_monitor = [&](auto snes) {
    MoFEMFunctionBegin;
    CHKERR SNESMonitorSet(snes,
                          (MoFEMErrorCode(*)(SNES, PetscInt, PetscReal,
                                             void *))MoFEMSNESMonitorFields,
                          (void *)(snes_ctx_ptr.get()), nullptr);
    MoFEMFunctionReturn(0);
  };
 
  CHKERR set_section_monitor(snes);
 
  auto ksp = createKSP(m_field.get_comm());
  CHKERR KSPSetType(ksp, KSPPREONLY); // Run KSP internally in ShellPC
  auto sub_pc = createPC(fsRawPtr->mField.get_comm());
  CHKERR PCSetType(sub_pc, PCSHELL);
  CHKERR PCShellSetSetUp(sub_pc, pcSetup);
  CHKERR PCShellSetApply(sub_pc, pcApply);
  CHKERR KSPSetPC(ksp, sub_pc);
  CHKERR SNESSetKSP(snes, ksp);
 
  snesCtxPtr = getDMSnesCtx(solverSubDM);
  tsCtxPtr = getDMTsCtx(solverSubDM);
 
  CHKERR TSSetPreStep(ts, tsPreProc);
  CHKERR TSSetPostStep(ts, tsPostProc);
 
  MoFEMFunctionReturn(0);
}

tsSetUp() [2/2]

MoFEMErrorCode TSPrePostProc::tsSetUp

(

TS

ts

)

Used to setup TS solver.

Parameters

ts

Returns

MoFEMErrorCode

Member Data Documentation

fsRawPtr [1/2]

Example* TSPrePostProc::fsRawPtr

Examples

free_surface.cpp.

Definition at line 398 of file dynamic_first_order_con_law.cpp.

fsRawPtr [2/2]

FreeSurface* TSPrePostProc::fsRawPtr

Definition at line 421 of file free_surface.cpp.

globRes

SmartPetscObj<Vec> TSPrePostProc::globRes

private

Examples

free_surface.cpp.

Definition at line 457 of file free_surface.cpp.

globSol

SmartPetscObj<Vec> TSPrePostProc::globSol

Examples

free_surface.cpp.

Definition at line 420 of file free_surface.cpp.

snesCtxPtr

boost::shared_ptr<SnesCtx> TSPrePostProc::snesCtxPtr

private

Examples

free_surface.cpp.

Definition at line 462 of file free_surface.cpp.

solverSubDM

SmartPetscObj<DM> TSPrePostProc::solverSubDM

Examples

free_surface.cpp.

Definition at line 419 of file free_surface.cpp.

subB

SmartPetscObj<Mat> TSPrePostProc::subB

private

Definition at line 458 of file free_surface.cpp.

subKSP

SmartPetscObj<KSP> TSPrePostProc::subKSP

private

Definition at line 459 of file free_surface.cpp.

tsCtxPtr

boost::shared_ptr<TsCtx> TSPrePostProc::tsCtxPtr

private

Examples

free_surface.cpp.

Definition at line 464 of file free_surface.cpp.

---

The documentation for this struct was generated from the following files:

• users_modules/tutorials/adv-4/dynamic_first_order_con_law.cpp
• users_modules/tutorials/vec-5/free_surface.cpp