PhotonDiffusion Struct Reference

Collaboration diagram for PhotonDiffusion:

Public Member Functions
	PhotonDiffusion (MoFEM::Interface &m_field)
MoFEMErrorCode	runProgram ()
	PhotonDiffusion (MoFEM::Interface &m_field)
MoFEMErrorCode	runProgram ()

Static Public Member Functions
static double	sourceFunction (const double x, const double y, const double z)
	Pulse is infinitely short. More...

Private Member Functions
MoFEMErrorCode	readMesh ()
MoFEMErrorCode	setupProblem ()
MoFEMErrorCode	setIntegrationRules ()
MoFEMErrorCode	initialCondition ()
MoFEMErrorCode	boundaryCondition ()
MoFEMErrorCode	assembleSystem ()
MoFEMErrorCode	solveSystem ()
MoFEMErrorCode	checkResults ()
MoFEMErrorCode	outputResults ()
MoFEMErrorCode	readMesh ()
MoFEMErrorCode	setupProblem ()
MoFEMErrorCode	setIntegrationRules ()
MoFEMErrorCode	initialCondition ()
MoFEMErrorCode	boundaryCondition ()
MoFEMErrorCode	assembleSystem ()
MoFEMErrorCode	solveSystem ()
MoFEMErrorCode	outputResults ()

Private Attributes
MoFEM::Interface &	mField
boost::shared_ptr< std::vector< unsigned char > >	boundaryMarker
boost::shared_ptr< FEMethod >	domianLhsFEPtr
boost::shared_ptr< FEMethod >	boundaryLhsFEPtr
boost::shared_ptr< FEMethod >	boundaryRhsFEPtr

Detailed Description

Examples

photon_diffusion.cpp.

Definition at line 84 of file initial_diffusion.cpp.

Constructor & Destructor Documentation

PhotonDiffusion() [1/2]

PhotonDiffusion::PhotonDiffusion

(

MoFEM::Interface &

m_field

)

Examples

photon_diffusion.cpp.

Definition at line 151 of file initial_diffusion.cpp.

: mField(m_field) {}

PhotonDiffusion() [2/2]

PhotonDiffusion::PhotonDiffusion

(

MoFEM::Interface &

m_field

)

Member Function Documentation

assembleSystem() [1/2]

MoFEMErrorCode PhotonDiffusion::assembleSystem ( )

private

Examples

photon_diffusion.cpp.

Definition at line 229 of file initial_diffusion.cpp.

                                               {
  MoFEMFunctionBegin;
 
  auto bc_mng = mField.getInterface<BcManager>();
  auto &bc_map = bc_mng->getBcMapByBlockName();
 
  auto add_domain_base_ops = [&](auto &pipeline) {
    auto jac_ptr = boost::make_shared<MatrixDouble>();
    auto det_ptr = boost::make_shared<VectorDouble>();
    pipeline.push_back(new OpCalculateHOJacVolume(jac_ptr));
    pipeline.push_back(new OpInvertMatrix<3>(jac_ptr, det_ptr, nullptr));
    pipeline.push_back(new OpSetHOWeights(det_ptr));
  };
 
  auto add_domain_lhs_ops = [&](auto &pipeline) {
    pipeline.push_back(new OpDomainMass(
        "U", "U", [](const double, const double, const double) { return 1; }));
  };
 
  auto add_domain_rhs_ops = [&](auto &pipeline) {
    pipeline.push_back(new OpDomainSource("U", sourceFunction));
  };
 
  auto pipeline_mng = mField.getInterface<PipelineManager>();
  add_domain_base_ops(pipeline_mng->getOpDomainLhsPipeline());
  add_domain_base_ops(pipeline_mng->getOpDomainRhsPipeline());
  add_domain_lhs_ops(pipeline_mng->getOpDomainLhsPipeline());
  add_domain_rhs_ops(pipeline_mng->getOpDomainRhsPipeline());
 
  MoFEMFunctionReturn(0);
}

assembleSystem() [2/2]

MoFEMErrorCode PhotonDiffusion::assembleSystem ( )

private

boundaryCondition() [1/2]

MoFEMErrorCode PhotonDiffusion::boundaryCondition ( )

private

Examples

photon_diffusion.cpp.

Definition at line 224 of file initial_diffusion.cpp.

                                                  {
  MoFEMFunctionBegin;
  MoFEMFunctionReturn(0);
}

boundaryCondition() [2/2]

MoFEMErrorCode PhotonDiffusion::boundaryCondition ( )

private

checkResults()

MoFEMErrorCode PhotonDiffusion::checkResults ( )

private

Definition at line 292 of file initial_diffusion.cpp.

                                             {
  MoFEMFunctionBegin;
  PipelineManager *pipeline_mng = mField.getInterface<PipelineManager>();
  pipeline_mng->getDomainLhsFE().reset();
  pipeline_mng->getDomainRhsFE().reset();
  pipeline_mng->getOpDomainRhsPipeline().clear();
  auto u_vals_at_gauss_pts = boost::make_shared<VectorDouble>();
  double l2_error = 0;
  pipeline_mng->getOpDomainRhsPipeline().push_back(
      new OpCalculateScalarFieldValues("U", u_vals_at_gauss_pts));
  pipeline_mng->getOpDomainRhsPipeline().push_back(
      new OpError(u_vals_at_gauss_pts, l2_error));
  CHKERR pipeline_mng->loopFiniteElements();
  MOFEM_LOG("INITIAL", Sev::inform) << "L2 error " << l2_error;
  MoFEMFunctionReturn(0);
}

initialCondition() [1/2]

MoFEMErrorCode PhotonDiffusion::initialCondition ( )

private

Examples

photon_diffusion.cpp.

Definition at line 219 of file initial_diffusion.cpp.

                                                 {
  MoFEMFunctionBegin;
  MoFEMFunctionReturn(0);
}

initialCondition() [2/2]

MoFEMErrorCode PhotonDiffusion::initialCondition ( )

private

outputResults() [1/2]

MoFEMErrorCode PhotonDiffusion::outputResults ( )

private

Examples

photon_diffusion.cpp.

Definition at line 309 of file initial_diffusion.cpp.

                                              {
  MoFEMFunctionBegin;
  auto *pipeline_mng = mField.getInterface<PipelineManager>();
  pipeline_mng->getDomainLhsFE().reset();
  auto post_proc_fe = boost::make_shared<PostProcEle>(mField);
  post_proc_fe->generateReferenceElementMesh();
  post_proc_fe->addFieldValuesPostProc("U");
  pipeline_mng->getDomainRhsFE() = post_proc_fe;
  CHKERR pipeline_mng->loopFiniteElements();
  CHKERR post_proc_fe->writeFile("out_initial.h5m");
  MoFEMFunctionReturn(0);
}

outputResults() [2/2]

MoFEMErrorCode PhotonDiffusion::outputResults ( )

private

readMesh() [1/2]

MoFEMErrorCode PhotonDiffusion::readMesh ( )

private

Examples

photon_diffusion.cpp.

Definition at line 153 of file initial_diffusion.cpp.

                                         {
  MoFEMFunctionBegin;
 
  auto *simple = mField.getInterface<Simple>();
  CHKERR mField.getInterface(simple);
  CHKERR simple->getOptions();
  CHKERR simple->loadFile();
 
  MoFEMFunctionReturn(0);
}

readMesh() [2/2]

MoFEMErrorCode PhotonDiffusion::readMesh ( )

private

runProgram() [1/2]

MoFEMErrorCode PhotonDiffusion::runProgram

(

)

Examples

photon_diffusion.cpp.

Definition at line 322 of file initial_diffusion.cpp.

                                           {
  MoFEMFunctionBegin;
 
  CHKERR readMesh();
  CHKERR setupProblem();
  CHKERR setIntegrationRules();
  CHKERR initialCondition();
  CHKERR boundaryCondition();
  CHKERR assembleSystem();
  CHKERR solveSystem();
  // CHKERR checkResults();
  CHKERR outputResults();
 
  MoFEMFunctionReturn(0);
}

runProgram() [2/2]

MoFEMErrorCode PhotonDiffusion::runProgram

(

)

setIntegrationRules() [1/2]

MoFEMErrorCode PhotonDiffusion::setIntegrationRules ( )

private

Examples

photon_diffusion.cpp.

Definition at line 203 of file initial_diffusion.cpp.

                                                    {
  MoFEMFunctionBegin;
 
  auto integration_rule = [](int o_row, int o_col, int approx_order) {
    return 2 * approx_order;
  };
 
  auto *pipeline_mng = mField.getInterface<PipelineManager>();
  CHKERR pipeline_mng->setDomainRhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setDomainLhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setBoundaryLhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setBoundaryRhsIntegrationRule(integration_rule);
 
  MoFEMFunctionReturn(0);
}

setIntegrationRules() [2/2]

MoFEMErrorCode PhotonDiffusion::setIntegrationRules ( )

private

setupProblem() [1/2]

MoFEMErrorCode PhotonDiffusion::setupProblem ( )

private

Examples

photon_diffusion.cpp.

Definition at line 164 of file initial_diffusion.cpp.

                                             {
  MoFEMFunctionBegin;
 
  auto *simple = mField.getInterface<Simple>();
  CHKERR simple->addDomainField("U", H1, AINSWORTH_LEGENDRE_BASE, 1);
  CHKERR simple->addBoundaryField("U", H1, AINSWORTH_LEGENDRE_BASE, 1);
 
  CHKERR PetscOptionsGetScalar(PETSC_NULL, "", "-flux_magnitude",
                               &flux_magnitude, PETSC_NULL);
  CHKERR PetscOptionsGetScalar(PETSC_NULL, "", "-slab_thickness",
                               &slab_thickness, PETSC_NULL);
  CHKERR PetscOptionsGetScalar(PETSC_NULL, "", "-spot_radius", &spot_radius,
                               PETSC_NULL);
  CHKERR PetscOptionsGetScalar(PETSC_NULL, "", "-initial_time", &initial_time,
                               PETSC_NULL);
 
  MOFEM_LOG("INITIAL", Sev::inform) << "Refractive index: " << n;
  MOFEM_LOG("INITIAL", Sev::inform) << "Speed of light (cm/ns): " << c;
  MOFEM_LOG("INITIAL", Sev::inform)
      << "Phase velocity in medium (cm/ns): " << v;
  MOFEM_LOG("INITIAL", Sev::inform)
      << "Absorption coefficient (cm^-1): " << mu_a;
  MOFEM_LOG("INITIAL", Sev::inform)
      << "Scattering coefficient (cm^-1): " << mu_sp;
  MOFEM_LOG("INITIAL", Sev::inform) << "Impulse magnitude: " << flux_magnitude;
  MOFEM_LOG("INITIAL", Sev::inform) << "Initial time (ns): " << initial_time;
 
  int order = 3;
  CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-order", &order, PETSC_NULL);
 
  MOFEM_LOG("INITIAL", Sev::inform) << "Approximation order: " << order;
 
  CHKERR simple->setFieldOrder("U", order);
 
  CHKERR simple->setUp();
 
  MoFEMFunctionReturn(0);
}

setupProblem() [2/2]

MoFEMErrorCode PhotonDiffusion::setupProblem ( )

private

solveSystem() [1/2]

MoFEMErrorCode PhotonDiffusion::solveSystem ( )

private

Examples

photon_diffusion.cpp.

Definition at line 261 of file initial_diffusion.cpp.

                                            {
  MoFEMFunctionBegin;
  auto *simple = mField.getInterface<Simple>();
  auto *pipeline_mng = mField.getInterface<PipelineManager>();
  auto solver = pipeline_mng->createKSP();
 
  CHKERR KSPSetFromOptions(solver);
  CHKERR KSPSetUp(solver);
 
  auto dm = simple->getDM();
  auto D = smartCreateDMVector(dm);
  auto F = smartVectorDuplicate(D);
 
  MOFEM_LOG("INITIAL", Sev::inform) << "Solver start";
  CHKERR KSPSolve(solver, F, D);
  CHKERR VecGhostUpdateBegin(D, INSERT_VALUES, SCATTER_FORWARD);
  CHKERR VecGhostUpdateEnd(D, INSERT_VALUES, SCATTER_FORWARD);
  CHKERR DMoFEMMeshToLocalVector(dm, D, INSERT_VALUES, SCATTER_REVERSE);
 
  MOFEM_LOG("INITIAL", Sev::inform)
      << "writing vector in binary to vector.dat ...";
  PetscViewer viewer;
  PetscViewerBinaryOpen(PETSC_COMM_WORLD, "initial_vector.dat", FILE_MODE_WRITE,
                        &viewer);
  VecView(D, viewer);
  PetscViewerDestroy(&viewer);
 
  MOFEM_LOG("INITIAL", Sev::inform) << "Solver done";
  MoFEMFunctionReturn(0);
}

solveSystem() [2/2]

MoFEMErrorCode PhotonDiffusion::solveSystem ( )

private

sourceFunction()

static double PhotonDiffusion::sourceFunction ( const double  x, const double  y, const double  z  )

static

Pulse is infinitely short.

Note

It is good approximation of pulse in femtosecond scale. To make it longer one can apply third integral over time.

Note analysis in photon_diffusion is shifted in time by initial_time.

Parameters

x
y
z

Returns

double

Definition at line 104 of file initial_diffusion.cpp.

                                                                               {
    const double A = 4 * D * v * initial_time;
    const double T =
        (v / pow(M_PI * A, 3. / 2.)) * exp(-mu_a * v * initial_time);
 
    auto phi_pulse = [&](const double r_s, const double phi_s) {
      const double xs = r_s * cos(phi_s);
      const double ys = r_s * sin(phi_s);
      const double xp = x - xs;
      const double yp = y - ys;
      const double zp1 = z + slab_thickness / 2. - 1. / mu_sp;
      const double zp2 = z + slab_thickness / 2. + 1. / mu_sp;
      const double P1 = xp * xp + yp * yp + zp1 * zp1;
      const double P2 = xp * xp + yp * yp + zp2 * zp2;
      return r_s * (exp(-P1 / A) - exp(-P2 / A));
    };
 
    auto f = [&](const double r_s) {
      auto g = [&](const double phi_s) { return phi_pulse(r_s, phi_s); };
      return gauss_kronrod<double, 42>::integrate(
          g, 0, 2 * M_PI, 0, std::numeric_limits<float>::epsilon());
    };
 
    return T * flux_magnitude *
           gauss_kronrod<double, 32>::integrate(
               f, 0, spot_radius, 0, std::numeric_limits<float>::epsilon());
  };

Member Data Documentation

boundaryLhsFEPtr

boost::shared_ptr<FEMethod> PhotonDiffusion::boundaryLhsFEPtr

private

Examples

photon_diffusion.cpp.

Definition at line 142 of file photon_diffusion.cpp.

boundaryMarker

boost::shared_ptr< std::vector< unsigned char > > PhotonDiffusion::boundaryMarker

private

Definition at line 148 of file initial_diffusion.cpp.

boundaryRhsFEPtr

boost::shared_ptr<FEMethod> PhotonDiffusion::boundaryRhsFEPtr

private

Examples

photon_diffusion.cpp.

Definition at line 143 of file photon_diffusion.cpp.

domianLhsFEPtr

boost::shared_ptr<FEMethod> PhotonDiffusion::domianLhsFEPtr

private

Examples

photon_diffusion.cpp.

Definition at line 141 of file photon_diffusion.cpp.

mField

MoFEM::Interface & PhotonDiffusion::mField

private

Examples

photon_diffusion.cpp.

Definition at line 145 of file initial_diffusion.cpp.

---

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

• users_modules/tutorials/scl-10/initial_diffusion.cpp
• users_modules/tutorials/scl-10/photon_diffusion.cpp