free_surface.cpp

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/**
 * \file free_surface.cpp
 * \example free_surface.cpp
 *
 * Using PipelineManager interface calculate the divergence of base functions,
 * and integral of flux on the boundary. Since the h-div space is used, volume
 * integral and boundary integral should give the same result.
 */
 
/* This file is part of MoFEM.
 * MoFEM is free software: you can redistribute it and/or modify it under
 * the terms of the GNU Lesser General Public License as published by the
 * Free Software Foundation, either version 3 of the License, or (at your
 * option) any later version.
 *
 * MoFEM is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
 * License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with MoFEM. If not, see <http://www.gnu.org/licenses/>. */
 
#include <MoFEM.hpp>
 
using namespace MoFEM;
 
static char help[] = "...\n\n";
 
#include <BasicFiniteElements.hpp>
 
constexpr int BASE_DIM = 1;
constexpr int SPACE_DIM = 2;
constexpr int U_FIELD_DIM = SPACE_DIM;
constexpr CoordinateTypes coord_type =
    CARTESIAN; ///< select coordinate system <CARTESIAN, CYLINDRICAL>;
 
template <int DIM> struct ElementsAndOps {};
 
template <> struct ElementsAndOps<2> {
  using DomainEle = PipelineManager::FaceEle;
  using DomainEleOp = DomainEle::UserDataOperator;
  using BoundaryEle = PipelineManager::EdgeEle;
  using BoundaryEleOp = BoundaryEle::UserDataOperator;
  using PostProcEle = PostProcFaceOnRefinedMesh;
};
 
template <> struct ElementsAndOps<3> {
  using DomainEle = VolumeElementForcesAndSourcesCore;
  using DomainEleOp = DomainEle::UserDataOperator;
  using BoundaryEle = PipelineManager::FaceEle;
  using BoundaryEleOp = BoundaryEle::UserDataOperator;
  using PostProcEle = PostProcVolumeOnRefinedMesh;
};
 
using DomainEle = ElementsAndOps<SPACE_DIM>::DomainEle;
using DomainEleOp = DomainEle::UserDataOperator;
using BoundaryEle = ElementsAndOps<SPACE_DIM>::BoundaryEle;
using BoundaryEleOp = BoundaryEle::UserDataOperator;
 
using EntData = EntitiesFieldData::EntData;
 
using PostProcEle = ElementsAndOps<SPACE_DIM>::PostProcEle;
using AssemblyDomainEleOp =
    FormsIntegrators<DomainEleOp>::Assembly<PETSC>::OpBase;
using AssemblyBoundaryEleOp =
    FormsIntegrators<BoundaryEleOp>::Assembly<PETSC>::OpBase;
 
using OpDomainMassU = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::BiLinearForm<GAUSS>::OpMass<BASE_DIM, U_FIELD_DIM>;
using OpDomainMassH = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::BiLinearForm<GAUSS>::OpMass<BASE_DIM, 1>;
using OpDomainMassP = OpDomainMassH;
 
using OpDomainSourceU = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::LinearForm<GAUSS>::OpSource<BASE_DIM, U_FIELD_DIM>;
using OpDomainSourceH = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::LinearForm<GAUSS>::OpSource<BASE_DIM, 1>;
 
using OpBaseTimesScalarField = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::LinearForm<GAUSS>::OpBaseTimesScalarField<1, 1>;
 
using OpMixScalarTimesDiv = FormsIntegrators<DomainEleOp>::Assembly<
    PETSC>::BiLinearForm<GAUSS>::OpMixScalarTimesDiv<SPACE_DIM, coord_type>;
 
FTensor::Index<'i', SPACE_DIM> i;
FTensor::Index<'j', SPACE_DIM> j;
FTensor::Index<'k', SPACE_DIM> k;
FTensor::Index<'l', SPACE_DIM> l;
 
constexpr auto t_kd = FTensor::Kronecker_Delta_symmetric<int>();
 
// Physical parameters
constexpr double a0 = 0.98;
constexpr double rho_m = 0.998;
constexpr double mu_m = 0.0101;
constexpr double rho_p = 0.0012;
constexpr double mu_p = 0.000182;
constexpr double lambda = 7.4;
constexpr double W = 0.25;
 
// Model parameters
constexpr double h = 0.02; // mesh size
constexpr double eta = h;
constexpr double eta2 = eta * eta;
 
// Numerical parameteres
constexpr double md = 1e-2;
constexpr double eps = 1e-12;
constexpr double tol = std::numeric_limits<float>::epsilon();
 
constexpr double rho_ave = (rho_p + rho_m) / 2;
constexpr double rho_diff = (rho_p - rho_m) / 2;
constexpr double mu_ave = (mu_p + mu_m) / 2;
constexpr double mu_diff = (mu_p - mu_m) / 2;
 
const double kappa = (3. / (4. * std::sqrt(2. * W))) * (lambda / eta);
 
auto integration_rule = [](int, int, int approx_order) {
  return 2 * approx_order;
};
 
auto cylindrical = [](const double r) {
  // When we move to C++17 add if constexpr()
  if constexpr (coord_type == CYLINDRICAL)
    return 2 * M_PI * r;
  else
    return 1.;
};
 
auto my_max = [](const double x) { return (x - 1 + std::abs(x + 1)) / 2; };
auto my_min = [](const double x) { return (x + 1 - std::abs(x - 1)) / 2; };
auto cut_off = [](const double h) {
  return my_max(my_min(h));
};
auto d_cut_off = [](const double h) {
  if (h >= -1 && h < 1)
    return 1.;
  else
    return 0.;
};
 
auto phase_function = [](const double h, const double diff, const double ave) {
  return diff * cut_off(h) + ave;
};
 
auto d_phase_function_h = [](const double h, const double diff) {
  return diff * d_cut_off(h);
};
 
auto get_f = [](const double h) { return 4 * W * h * (h * h - 1); };
auto get_f_dh = [](const double h) { return 4 * W * (3 * h * h - 1); };
 
auto get_M0 = [](auto h) { return md; };
auto get_M0_dh = [](auto h) { return 0; };
 
auto get_M2 = [](auto h_tmp) {
  const double h = cut_off(h_tmp);
  return md * (1 - h * h);
};
 
auto get_M2_dh = [](auto h_tmp) {
  const double h = cut_off(h_tmp);
  return -md * 2 * h * d_cut_off(h_tmp);
};
 
auto get_M3 = [](auto h_tmp) {
  const double h = cut_off(h_tmp);
  const double h2 = h * h;
  const double h3 = h2 * h;
  if (h >= 0)
    return md * (2 * h3 - 3 * h2 + 1);
  else
    return md * (-2 * h3 - 3 * h2 + 1);
};
 
auto get_M3_dh = [](auto h_tmp) {
  const double h = cut_off(h_tmp);
  if (h >= 0)
    return md * (6 * h * (h - 1)) * d_cut_off(h_tmp);
  else
    return md * (-6 * h * (h + 1)) * d_cut_off(h_tmp);
};
 
auto get_M = [](auto h) { return get_M0(h); };
auto get_M_dh = [](auto h) { return get_M0_dh(h); };
 
auto get_D = [](const double A) {
  FTensor::Ddg<double, SPACE_DIM, SPACE_DIM> t_D;
  t_D(i, j, k, l) = A * ((t_kd(i, k) ^ t_kd(j, l)) / 4.);
  return t_D;
};
 
auto kernel_oscillation = [](double r, double y, double) {
  constexpr int n = 3;
  constexpr double R = 0.0125;
  constexpr double A = R * 0.2;
  const double theta = atan2(r, y);
  const double w = R + A * cos(n * theta);
  const double d = std::sqrt(r * r + y * y);
  return tanh((w - d) / (eta * std::sqrt(2)));
};
 
auto kernel_eye = [](double r, double y, double) {
  constexpr double y0 = 0.5;
  constexpr double R = 0.4;
  y -= y0;
  const double d = std::sqrt(r * r + y * y);
  return tanh((R - d) / (eta * std::sqrt(2)));
};
 
auto init_h = [](double r, double y, double theta) {
  return kernel_eye(r, y, theta);
};
 
#include <FreeSurfaceOps.hpp>
using namespace FreeSurfaceOps;
 
struct FreeSurface {
 
  FreeSurface(MoFEM::Interface &m_field) : mField(m_field) {}
 
  MoFEMErrorCode runProblem();
 
private:
  MoFEMErrorCode readMesh();
  MoFEMErrorCode setupProblem();
  MoFEMErrorCode boundaryCondition();
  MoFEMErrorCode assembleSystem();
  MoFEMErrorCode solveSystem();
 
  MoFEM::Interface &mField;
 
  boost::shared_ptr<FEMethod> domianLhsFEPtr;
};
 
//! [Run programme]
MoFEMErrorCode FreeSurface::runProblem() {
  MoFEMFunctionBegin;
  CHKERR readMesh();
  CHKERR setupProblem();
  CHKERR boundaryCondition();
  CHKERR assembleSystem();
  CHKERR solveSystem();
  MoFEMFunctionReturn(0);
}
//! [Run programme]
 
//! [Read mesh]
MoFEMErrorCode FreeSurface::readMesh() {
  MoFEMFunctionBegin;
 
  auto simple = mField.getInterface<Simple>();
  CHKERR simple->getOptions();
  CHKERR simple->loadFile();
 
  MoFEMFunctionReturn(0);
}
//! [Read mesh]
 
//! [Set up problem]
MoFEMErrorCode FreeSurface::setupProblem() {
  MoFEMFunctionBegin;
 
  auto simple = mField.getInterface<Simple>();
 
  // Fields on domain
  
  // Velocity field
  CHKERR simple->addDomainField("U", H1, AINSWORTH_LEGENDRE_BASE, U_FIELD_DIM);
  // Pressure field
  CHKERR simple->addDomainField("P", H1, AINSWORTH_LEGENDRE_BASE, 1);
  // Order/phase fild
  CHKERR simple->addDomainField("H", H1, AINSWORTH_LEGENDRE_BASE, 1);
  //Chemical potential
  CHKERR simple->addDomainField("G", H1, AINSWORTH_LEGENDRE_BASE, 1);
 
  // Field on boundary
  CHKERR simple->addBoundaryField("U", H1, AINSWORTH_LEGENDRE_BASE, U_FIELD_DIM);
  CHKERR simple->addBoundaryField("H", H1, AINSWORTH_LEGENDRE_BASE, 1);
  // Lagrange multiplier which constrains slip conditions
  CHKERR simple->addBoundaryField("L", H1, AINSWORTH_LEGENDRE_BASE, 1);
 
  constexpr int order = 3;
  CHKERR simple->setFieldOrder("U", order);
  CHKERR simple->setFieldOrder("P", order - 1);
  CHKERR simple->setFieldOrder("H", order);
  CHKERR simple->setFieldOrder("G", order);
  CHKERR simple->setFieldOrder("L", order);
  CHKERR simple->setUp();
 
  MoFEMFunctionReturn(0);
}
//! [Set up problem]
 
//! [Boundary condition]
MoFEMErrorCode FreeSurface::boundaryCondition() {
  MoFEMFunctionBegin;
 
  auto simple = mField.getInterface<Simple>();
  auto pipeline_mng = mField.getInterface<PipelineManager>();
  auto bc_mng = mField.getInterface<BcManager>();
  auto dm = simple->getDM();
 
  auto h_ptr = boost::make_shared<VectorDouble>();
  auto grad_h_ptr = boost::make_shared<MatrixDouble>();
  auto g_ptr = boost::make_shared<VectorDouble>();
  auto grad_g_ptr = boost::make_shared<MatrixDouble>();
 
  auto post_proc = [&]() {
    MoFEMFunctionBegin;
    auto post_proc_fe = boost::make_shared<PostProcEle>(mField);
    post_proc_fe->generateReferenceElementMesh();
 
    auto det_ptr = boost::make_shared<VectorDouble>();
    auto jac_ptr = boost::make_shared<MatrixDouble>();
    auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
 
    post_proc_fe->addFieldValuesPostProc("H");
    post_proc_fe->addFieldValuesPostProc("G");
    post_proc_fe->addFieldValuesGradientPostProc("G", 2);
    post_proc_fe->addFieldValuesGradientPostProc("H", 2);
 
    CHKERR DMoFEMLoopFiniteElements(dm, "dFE", post_proc_fe);
    CHKERR post_proc_fe->writeFile("out_init.h5m");
 
    MoFEMFunctionReturn(0);
  };
 
  auto solve_init = [&]() {
    MoFEMFunctionBegin;
 
    auto set_generic = [&](auto &pipeline) {
      auto det_ptr = boost::make_shared<VectorDouble>();
      auto jac_ptr = boost::make_shared<MatrixDouble>();
      auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
      pipeline.push_back(new OpSetHOWeightsOnFace());
      pipeline.push_back(new OpCalculateHOJacForFace(jac_ptr));
      pipeline.push_back(
          new OpInvertMatrix<SPACE_DIM>(jac_ptr, det_ptr, inv_jac_ptr));
      pipeline.push_back(new OpSetInvJacH1ForFace(inv_jac_ptr));
 
      pipeline.push_back(new OpCalculateScalarFieldValues("H", h_ptr));
      pipeline.push_back(
          new OpCalculateScalarFieldGradient<SPACE_DIM>("H", grad_h_ptr));
 
      pipeline.push_back(new OpCalculateScalarFieldValues("G", g_ptr));
      pipeline.push_back(
          new OpCalculateScalarFieldGradient<SPACE_DIM>("G", grad_g_ptr));
    };
 
    auto set_domain_rhs = [&](auto &pipeline) {
      pipeline.push_back(new OpRhsH<true>("H", nullptr, nullptr, h_ptr,
                                          grad_h_ptr, grad_g_ptr));
      pipeline.push_back(new OpRhsG<true>("G", h_ptr, grad_h_ptr, g_ptr));
    };
 
    auto set_domain_lhs = [&](auto &pipeline) {
      pipeline.push_back(new OpLhsH_dH<true>("H", nullptr, h_ptr, grad_g_ptr));
      pipeline.push_back(new OpLhsH_dG<true>("H", "G", h_ptr));
      pipeline.push_back(new OpLhsG_dH<true>("G", "H", h_ptr));
      pipeline.push_back(new OpLhsG_dG("G"));
    };
 
    auto create_subdm = [&]() {
      DM subdm;
      CHKERR DMCreate(mField.get_comm(), &subdm);
      CHKERR DMSetType(subdm, "DMMOFEM");
      CHKERR DMMoFEMCreateSubDM(subdm, dm, "SUB");
      CHKERR DMMoFEMAddElement(subdm, simple->getDomainFEName().c_str());
      CHKERR DMMoFEMSetSquareProblem(subdm, PETSC_TRUE);
      CHKERR DMMoFEMAddSubFieldRow(subdm, "H");
      CHKERR DMMoFEMAddSubFieldRow(subdm, "G");
      CHKERR DMMoFEMAddSubFieldCol(subdm, "H");
      CHKERR DMMoFEMAddSubFieldCol(subdm, "G");
      CHKERR DMSetUp(subdm);
      return SmartPetscObj<DM>(subdm);
    };
 
    auto subdm = create_subdm();
    CHKERR pipeline_mng->setDomainRhsIntegrationRule(integration_rule);
    CHKERR pipeline_mng->setDomainLhsIntegrationRule(integration_rule);
 
    set_generic(pipeline_mng->getOpDomainRhsPipeline());
    set_domain_rhs(pipeline_mng->getOpDomainRhsPipeline());
    set_generic(pipeline_mng->getOpDomainLhsPipeline());
    set_domain_lhs(pipeline_mng->getOpDomainLhsPipeline());
 
    auto D = smartCreateDMVector(subdm);
    auto snes = pipeline_mng->createSNES(subdm);
 
    auto set_section_monitor = [&](auto solver) {
      MoFEMFunctionBegin;
      PetscViewerAndFormat *vf;
      CHKERR PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,
                                        PETSC_VIEWER_DEFAULT, &vf);
      CHKERR SNESMonitorSet(
          solver,
          (MoFEMErrorCode(*)(SNES, PetscInt, PetscReal,
                             void *))SNESMonitorFields,
          vf, (MoFEMErrorCode(*)(void **))PetscViewerAndFormatDestroy);
      auto section = mField.getInterface<ISManager>()->sectionCreate("SUB");
      PetscInt num_fields;
      CHKERR PetscSectionGetNumFields(section, &num_fields);
      for (int f = 0; f < num_fields; ++f) {
        const char *field_name;
        CHKERR PetscSectionGetFieldName(section, f, &field_name);
        MOFEM_LOG("FS", Sev::inform)
            << "Field " << f << " " << std::string(field_name);
      }
      MoFEMFunctionReturn(0);
    };
 
    CHKERR set_section_monitor(snes);
 
    CHKERR SNESSetFromOptions(snes);
    CHKERR SNESSolve(snes, PETSC_NULL, D);
 
    CHKERR VecGhostUpdateBegin(D, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR VecGhostUpdateEnd(D, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR DMoFEMMeshToLocalVector(subdm, D, INSERT_VALUES, SCATTER_REVERSE);
 
    MoFEMFunctionReturn(0);
  };
 
  CHKERR solve_init();
  CHKERR post_proc();
 
  CHKERR bc_mng->removeBlockDOFsOnEntities(simple->getProblemName(),
                                           "SYMETRY", "U", 0, 0);
  CHKERR bc_mng->removeBlockDOFsOnEntities(simple->getProblemName(),
                                           "SYMETRY", "L", 0, 0);
  CHKERR bc_mng->removeBlockDOFsOnEntities(simple->getProblemName(), "FIX",
                                           "U", 0, SPACE_DIM);
  CHKERR bc_mng->removeBlockDOFsOnEntities(simple->getProblemName(), "FIX",
                                           "L", 0, 0);
  // Clear pipelines
  pipeline_mng->getOpDomainRhsPipeline().clear();
  pipeline_mng->getOpDomainLhsPipeline().clear();
 
  MoFEMFunctionReturn(0);
}
//! [Boundary condition]
 
//! [Push operators to pipeline]
MoFEMErrorCode FreeSurface::assembleSystem() {
  MoFEMFunctionBegin;
 
  auto dot_u_ptr = boost::make_shared<MatrixDouble>();
  auto u_ptr = boost::make_shared<MatrixDouble>();
  auto grad_u_ptr = boost::make_shared<MatrixDouble>();
  auto dot_h_ptr = boost::make_shared<VectorDouble>();
  auto h_ptr = boost::make_shared<VectorDouble>();
  auto grad_h_ptr = boost::make_shared<MatrixDouble>();
  auto g_ptr = boost::make_shared<VectorDouble>();
  auto grad_g_ptr = boost::make_shared<MatrixDouble>();
  auto lambda_ptr = boost::make_shared<VectorDouble>();
  auto p_ptr = boost::make_shared<VectorDouble>();
  auto div_u_ptr = boost::make_shared<VectorDouble>();
 
  // Push element from reference configuration to current configuration in 3d
  // space
  auto set_domain_general = [&](auto &pipeline) {
    auto det_ptr = boost::make_shared<VectorDouble>();
    auto jac_ptr = boost::make_shared<MatrixDouble>();
    auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
    pipeline.push_back(new OpSetHOWeightsOnFace());
    pipeline.push_back(new OpCalculateHOJacForFace(jac_ptr));
    pipeline.push_back(
        new OpInvertMatrix<SPACE_DIM>(jac_ptr, det_ptr, inv_jac_ptr));
    pipeline.push_back(new OpSetInvJacH1ForFace(inv_jac_ptr));
 
    pipeline.push_back(
        new OpCalculateVectorFieldValuesDot<U_FIELD_DIM>("U", dot_u_ptr));
    pipeline.push_back(
        new OpCalculateVectorFieldValues<U_FIELD_DIM>("U", u_ptr));
    pipeline.push_back(
        new OpCalculateVectorFieldGradient<U_FIELD_DIM, SPACE_DIM>("U",
                                                                   grad_u_ptr));
 
    pipeline.push_back(new OpCalculateScalarFieldValuesDot("H", dot_h_ptr));
    pipeline.push_back(new OpCalculateScalarFieldValues("H", h_ptr));
    pipeline.push_back(
        new OpCalculateScalarFieldGradient<SPACE_DIM>("H", grad_h_ptr));
    pipeline.push_back(new OpCalculateScalarFieldValues("G", g_ptr));
    pipeline.push_back(
        new OpCalculateScalarFieldGradient<SPACE_DIM>("G", grad_g_ptr));
    pipeline.push_back(new OpCalculateScalarFieldValues("P", p_ptr));
    pipeline.push_back(
        new OpCalculateDivergenceVectorFieldValues<SPACE_DIM, coord_type>(
            "U", div_u_ptr));
  };
 
  auto set_domain_rhs = [&](auto &pipeline) {
    pipeline.push_back(new OpRhsU("U", dot_u_ptr, u_ptr, grad_u_ptr, h_ptr,
                                  grad_h_ptr, g_ptr, p_ptr));
    pipeline.push_back(new OpRhsH<false>("H", u_ptr, dot_h_ptr, h_ptr,
                                         grad_h_ptr, grad_g_ptr));
    pipeline.push_back(new OpRhsG<false>("G", h_ptr, grad_h_ptr, g_ptr));
    pipeline.push_back(new OpBaseTimesScalarField(
        "P", div_u_ptr, [](const double r, const double, const double) {
          return cylindrical(r);
        }));
    pipeline.push_back(new OpBaseTimesScalarField(
        "P", p_ptr, [](const double r, const double, const double) {
          return eps * cylindrical(r) ;
        }));
  };
 
  auto set_domain_lhs = [&](auto &pipeline) {
    pipeline.push_back(new OpLhsU_dU("U", u_ptr, grad_u_ptr, h_ptr));
    pipeline.push_back(
        new OpLhsU_dH("U", "H", dot_u_ptr, u_ptr, grad_u_ptr, h_ptr, g_ptr));
    pipeline.push_back(new OpLhsU_dG("U", "G", grad_h_ptr));
 
    pipeline.push_back(new OpLhsH_dU("H", "U", grad_h_ptr));
    pipeline.push_back(new OpLhsH_dH<false>("H", u_ptr, h_ptr, grad_g_ptr));
    pipeline.push_back(new OpLhsH_dG<false>("H", "G", h_ptr));
 
    pipeline.push_back(new OpLhsG_dH<false>("G", "H", h_ptr));
    pipeline.push_back(new OpLhsG_dG("G"));
 
    pipeline.push_back(new OpMixScalarTimesDiv(
        "P", "U",
        [](const double r, const double, const double) {
          return cylindrical(r);
        },
        true, false));
    pipeline.push_back(
        new OpDomainMassP("P", "P", [](double r, double, double) {
          return eps * cylindrical(r);
        }));
  };
 
  auto set_boundary_rhs = [&](auto &pipeline) {
    pipeline.push_back(
        new OpCalculateVectorFieldValues<U_FIELD_DIM>("U", u_ptr));
    pipeline.push_back(new OpCalculateScalarFieldValues("L", lambda_ptr));
    pipeline.push_back(new OpNormalConstrainRhs("L", u_ptr));
    pipeline.push_back(new OpNormalForcebRhs("U", lambda_ptr));
  };
 
  auto set_boundary_lhs = [&](auto &pipeline) {
    pipeline.push_back(new OpNormalConstrainLhs("L", "U"));
  };
 
  auto *pipeline_mng = mField.getInterface<PipelineManager>();
 
  CHKERR pipeline_mng->setDomainRhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setDomainLhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setBoundaryRhsIntegrationRule(integration_rule);
  CHKERR pipeline_mng->setBoundaryLhsIntegrationRule(integration_rule);
 
  set_domain_general(pipeline_mng->getOpDomainRhsPipeline());
  set_domain_general(pipeline_mng->getOpDomainLhsPipeline());
  set_domain_rhs(pipeline_mng->getOpDomainRhsPipeline());
  set_domain_lhs(pipeline_mng->getOpDomainLhsPipeline());
  set_boundary_rhs(pipeline_mng->getOpBoundaryRhsPipeline());
  set_boundary_lhs(pipeline_mng->getOpBoundaryLhsPipeline());
 
  domianLhsFEPtr = pipeline_mng->getDomainLhsFE();
 
  MoFEMFunctionReturn(0);
}
//! [Push operators to pipeline]
 
/**
 * @brief Monitor solution
 *
 * This functions is called by TS solver at the end of each step. It is used
 * to output results to the hard drive.
 */
struct Monitor : public FEMethod {
  Monitor(
      SmartPetscObj<DM> dm, boost::shared_ptr<PostProcEle> post_proc,
      std::pair<boost::shared_ptr<BoundaryEle>, boost::shared_ptr<VectorDouble>>
          p)
      : dM(dm), postProc(post_proc), liftFE(p.first), liftVec(p.second) {}
  MoFEMErrorCode postProcess() {
    MoFEMFunctionBegin;
    constexpr int save_every_nth_step = 1;
    if (ts_step % save_every_nth_step == 0) {
      CHKERR DMoFEMLoopFiniteElements(dM, "dFE", postProc,
                                      this->getCacheWeakPtr());
      CHKERR postProc->writeFile(
          "out_step_" + boost::lexical_cast<std::string>(ts_step) + ".h5m");
 
 
      // MOFEM_LOG("FS", Sev::verbose)
      //     << "writing vector in binary to vector.dat ...";
      // PetscViewer viewer;
      // PetscViewerBinaryOpen(PETSC_COMM_WORLD, "vector.dat", FILE_MODE_WRITE,
      //                       &viewer);
      // VecView(ts_u, viewer);
      // PetscViewerDestroy(&viewer);
    }
 
    liftVec->resize(SPACE_DIM, false);
    liftVec->clear();
    CHKERR DMoFEMLoopFiniteElements(dM, "bFE", liftFE, this->getCacheWeakPtr());
    MPI_Allreduce(MPI_IN_PLACE, &(*liftVec)[0], SPACE_DIM, MPI_DOUBLE, MPI_SUM,
                  MPI_COMM_WORLD);
    MOFEM_LOG("FS", Sev::inform)
        << "Step " << ts_step << " time " << ts_t
        << " lift vec x: " << (*liftVec)[0] << " y: " << (*liftVec)[1];
 
    MoFEMFunctionReturn(0);
  }
 
private:
  SmartPetscObj<DM> dM;
  boost::shared_ptr<PostProcEle> postProc;
  boost::shared_ptr<BoundaryEle> liftFE;
  boost::shared_ptr<VectorDouble> liftVec;
};
 
//! [Solve]
MoFEMErrorCode FreeSurface::solveSystem() {
  MoFEMFunctionBegin;
 
  auto *simple = mField.getInterface<Simple>();
  auto *pipeline_mng = mField.getInterface<PipelineManager>();
  auto dm = simple->getDM();
 
  auto get_fe_post_proc = [&]() {
    auto post_proc_fe = boost::make_shared<PostProcEle>(mField);
    post_proc_fe->generateReferenceElementMesh();
    auto det_ptr = boost::make_shared<VectorDouble>();
    auto jac_ptr = boost::make_shared<MatrixDouble>();
    auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
 
    post_proc_fe->getOpPtrVector().push_back(
        new OpCalculateHOJacForFace(jac_ptr));
    post_proc_fe->getOpPtrVector().push_back(
        new OpInvertMatrix<SPACE_DIM>(jac_ptr, det_ptr, inv_jac_ptr));
    post_proc_fe->getOpPtrVector().push_back(
        new OpSetInvJacH1ForFace(inv_jac_ptr));
 
    post_proc_fe->addFieldValuesPostProc("U");
    post_proc_fe->addFieldValuesPostProc("H");
    post_proc_fe->addFieldValuesPostProc("P");
    post_proc_fe->addFieldValuesPostProc("G");
    post_proc_fe->addFieldValuesGradientPostProc("U", 2);
    post_proc_fe->addFieldValuesGradientPostProc("H", 2);
    post_proc_fe->addFieldValuesGradientPostProc("G", 2);
    return post_proc_fe;
  };
 
  auto get_lift_fe = [&]() {
    auto fe = boost::make_shared<BoundaryEle>(mField);
    auto lift_ptr = boost::make_shared<VectorDouble>();
    auto p_ptr = boost::make_shared<VectorDouble>();
    auto ents_ptr = boost::make_shared<Range>();
 
    std::vector<const CubitMeshSets *> vec_ptr;
    CHKERR mField.getInterface<MeshsetsManager>()->getCubitMeshsetPtr(
        std::regex("LIFT"), vec_ptr);
    for (auto m_ptr : vec_ptr) {
      auto meshset = m_ptr->getMeshset();
      Range ents;
      CHKERR mField.get_moab().get_entities_by_dimension(meshset, SPACE_DIM - 1,
                                                         ents, true);
      ents_ptr->merge(ents);
    }
 
    MOFEM_LOG("FS", Sev::inform) << "Lift ents " << (*ents_ptr);
 
    fe->getOpPtrVector().push_back(
        new OpCalculateScalarFieldValues("P", p_ptr));
    fe->getOpPtrVector().push_back(
        new OpCalculateLift("P", p_ptr, lift_ptr, ents_ptr));
 
    return std::make_pair(fe, lift_ptr);
  };
 
  auto set_ts = [&](auto solver) {
    MoFEMFunctionBegin;
    SNES snes;
    CHKERR TSGetSNES(solver, &snes);
    KSP ksp;
    CHKERR SNESGetKSP(snes, &ksp);
    MoFEMFunctionReturn(0);
  };
 
  auto ts = pipeline_mng->createTSIM();
  CHKERR TSSetType(ts, TSALPHA);
 
  auto set_post_proc_monitor = [&](auto dm) {
    MoFEMFunctionBegin;
    boost::shared_ptr<FEMethod> null_fe;
    auto monitor_ptr =
        boost::make_shared<Monitor>(dm, get_fe_post_proc(), get_lift_fe());
    CHKERR DMMoFEMTSSetMonitor(dm, ts, simple->getDomainFEName(), null_fe,
                               null_fe, monitor_ptr);
    MoFEMFunctionReturn(0);
  };
  CHKERR set_post_proc_monitor(dm);
 
  auto set_section_monitor = [&](auto solver) {
    MoFEMFunctionBegin;
    SNES snes;
    CHKERR TSGetSNES(solver, &snes);
    PetscViewerAndFormat *vf;
    CHKERR PetscViewerAndFormatCreate(PETSC_VIEWER_STDOUT_WORLD,
                                      PETSC_VIEWER_DEFAULT, &vf);
    CHKERR SNESMonitorSet(
        snes,
        (MoFEMErrorCode(*)(SNES, PetscInt, PetscReal, void *))SNESMonitorFields,
        vf, (MoFEMErrorCode(*)(void **))PetscViewerAndFormatDestroy);
 
    auto section = mField.getInterface<ISManager>()->sectionCreate(
        simple->getProblemName());
    PetscInt num_fields;
    CHKERR PetscSectionGetNumFields(section, &num_fields);
    for (int f = 0; f < num_fields; ++f) {
      const char *field_name;
      CHKERR PetscSectionGetFieldName(section, f, &field_name);
      MOFEM_LOG("FS", Sev::inform)
          << "Field " << f << " " << std::string(field_name);
    }
 
    MoFEMFunctionReturn(0);
  };
 
  // Add monitor to time solver
  double ftime = 1;
  // CHKERR TSSetMaxTime(ts, ftime);
  CHKERR TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);
 
  auto T = smartCreateDMVector(simple->getDM());
  CHKERR DMoFEMMeshToLocalVector(simple->getDM(), T, INSERT_VALUES,
                                 SCATTER_FORWARD);
  CHKERR TSSetSolution(ts, T);
  CHKERR TSSetFromOptions(ts);
  CHKERR set_ts(ts);
  CHKERR set_section_monitor(ts);
  CHKERR TSSetUp(ts);
  CHKERR TSSolve(ts, NULL);
  CHKERR TSGetTime(ts, &ftime);
 
  MoFEMFunctionReturn(0);
}
 
int main(int argc, char *argv[]) {
 
  // Initialisation of MoFEM/PETSc and MOAB data structures
  const char param_file[] = "param_file.petsc";
  MoFEM::Core::Initialize(&argc, &argv, param_file, help);
 
  // Add logging channel for example
  auto core_log = logging::core::get();
  core_log->add_sink(LogManager::createSink(LogManager::getStrmWorld(), "FS"));
  LogManager::setLog("FS");
  MOFEM_LOG_TAG("FS", "free surface");
 
  try {
 
    //! [Register MoFEM discrete manager in PETSc]
    DMType dm_name = "DMMOFEM";
    CHKERR DMRegister_MoFEM(dm_name);
    //! [Register MoFEM discrete manager in PETSc
 
    //! [Create MoAB]
    moab::Core mb_instance;              ///< mesh database
    moab::Interface &moab = mb_instance; ///< mesh database interface
    //! [Create MoAB]
 
    //! [Create MoFEM]
    MoFEM::Core core(moab);           ///< finite element database
    MoFEM::Interface &m_field = core; ///< finite element database insterface
    //! [Create MoFEM]
 
    //! [FreeSurface]
    FreeSurface ex(m_field);
    CHKERR ex.runProblem();
    //! [FreeSurface]
  }
  CATCH_ERRORS;
 
  CHKERR MoFEM::Core::Finalize();
}