reaction_diffusion.cpp

/**
 * \file reaction_diffusion.cpp
 * \example reaction_diffusion.cpp
 *
 **/
 
/* 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 <BasicFiniteElements.hpp>
using namespace MoFEM;
 
static char help[] = "...\n\n";
 
namespace ReactionDiffusionEquation {
 
using Ele = FaceElementForcesAndSourcesCore;
using OpEle = FaceElementForcesAndSourcesCore::UserDataOperator;
using EntData = EntitiesFieldData::EntData;
 
const double D = 2e-3; ///< diffusivity
const double r = 1;    ///< rate factor
const double k = 1;    ///< caring capacity
 
const double u0 = 0.1; ///< inital vale on blocksets
 
const int save_every_nth_step = 4;
 
/**
 * @brief Common data
 *
 * Common data are used to keep and pass data between elements
 *
 */
struct CommonData {
 
  MatrixDouble grad;    ///< Gradients of field "u" at integration points
  VectorDouble val;     ///< Values of field "u" at integration points
  VectorDouble dot_val; ///< Rate of values of field "u" at integration points
 
  SmartPetscObj<Mat> M;   ///< Mass matrix
  SmartPetscObj<KSP> ksp; ///< Linear solver
};
 
/**
 * @brief Assemble mass matrix
 */
struct OpAssembleMass : OpEle {
  OpAssembleMass(boost::shared_ptr<CommonData> &data)
      : OpEle("u", "u", OpEle::OPROWCOL), commonData(data) {
    sYmm = true;
  }
  MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
                        EntityType col_type, EntData &row_data,
                        EntData &col_data) {
    MoFEMFunctionBegin;
    const int nb_row_dofs = row_data.getIndices().size();
    const int nb_col_dofs = col_data.getIndices().size();
    if (nb_row_dofs && nb_col_dofs) {
      const int nb_integration_pts = getGaussPts().size2();
      mat.resize(nb_row_dofs, nb_col_dofs, false);
      mat.clear();
      auto t_row_base = row_data.getFTensor0N();
      auto t_w = getFTensor0IntegrationWeight();
      const double vol = getMeasure();
      for (int gg = 0; gg != nb_integration_pts; ++gg) {
        const double a = t_w * vol;
        for (int rr = 0; rr != nb_row_dofs; ++rr) {
          auto t_col_base = col_data.getFTensor0N(gg, 0);
          for (int cc = 0; cc != nb_col_dofs; ++cc) {
            mat(rr, cc) += a * t_row_base * t_col_base;
            ++t_col_base;
          }
          ++t_row_base;
        }
        ++t_w;
      }
 
      CHKERR MatSetValues(commonData->M, row_data, col_data, &mat(0, 0),
                          ADD_VALUES);
      if (row_side != col_side || row_type != col_type) {
        transMat.resize(nb_col_dofs, nb_row_dofs, false);
        noalias(transMat) = trans(mat);
        CHKERR MatSetValues(commonData->M, col_data, row_data, &transMat(0, 0),
                            ADD_VALUES);
      }
    }
    MoFEMFunctionReturn(0);
  }
 
private:
  MatrixDouble mat, transMat;
  boost::shared_ptr<CommonData> commonData;
};
 
/**
 * @brief Assemble slow part
 *
 * Solve problem \f$ F(t,u,\dot{u}) = G(t,u) \f$ where here the right hand side
 * \f$ G(t,u) \f$ is implemented.
 *
 */
struct OpAssembleSlowRhs : OpEle {
  OpAssembleSlowRhs(boost::shared_ptr<CommonData> &data)
      : OpEle("u", OpEle::OPROW), commonData(data) {}
  MoFEMErrorCode doWork(int side, EntityType type, EntData &data) {
    MoFEMFunctionBegin;
    const int nb_dofs = data.getIndices().size();
    if (nb_dofs) {
      vecF.resize(nb_dofs, false);
      vecF.clear();
 
      const int nb_integration_pts = getGaussPts().size2();
      auto t_val = getFTensor0FromVec(commonData->val);
      auto t_base = data.getFTensor0N();
      auto t_w = getFTensor0IntegrationWeight();
 
      const double vol = getMeasure();
      for (int gg = 0; gg != nb_integration_pts; ++gg) {
        const double a = vol * t_w;
        const double f = a * r * t_val * (1 - t_val / k);
        for (int rr = 0; rr != nb_dofs; ++rr) {
          const double b = f * t_base;
          vecF[rr] += b;
          ++t_base;
        }
 
        ++t_val;
        ++t_w;
      }
 
      CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
                          PETSC_TRUE);
      CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
                          ADD_VALUES);
    }
    MoFEMFunctionReturn(0);
  }
 
private:
  boost::shared_ptr<CommonData> commonData;
  VectorDouble vecF;
};
 
/**
 * @brief Assemble stiff part
 *
 * Solve problem \f$ F(t,u,\dot{u}) = G(t,u) \f$ where here the right hand side
 * \f$ F(t,u,\dot{u}) \f$ is implemented.
 *
 */
template <int DIM> struct OpAssembleStiffRhs : OpEle {
  OpAssembleStiffRhs(boost::shared_ptr<CommonData> &data)
      : OpEle("u", OpEle::OPROW), commonData(data) {}
  MoFEMErrorCode doWork(int side, EntityType type, EntData &data) {
    MoFEMFunctionBegin;
    const int nb_dofs = data.getIndices().size();
    if (nb_dofs) {
      vecF.resize(nb_dofs, false);
      vecF.clear();
 
      const int nb_integration_pts = getGaussPts().size2();
      auto t_dot_val = getFTensor0FromVec(commonData->dot_val);
      auto t_grad = getFTensor1FromMat<DIM>(commonData->grad);
      auto t_base = data.getFTensor0N();
      auto t_diff_base = data.getFTensor1DiffN<DIM>();
      auto t_w = getFTensor0IntegrationWeight();
      FTensor::Index<'i', DIM> i;
 
      const double vol = getMeasure();
      for (int gg = 0; gg != nb_integration_pts; ++gg) {
        const double a = vol * t_w;
        for (int rr = 0; rr != nb_dofs; ++rr) {
          vecF[rr] += a * (t_base * t_dot_val + D * t_diff_base(i) * t_grad(i));
          ++t_diff_base;
          ++t_base;
        }
        ++t_dot_val;
        ++t_grad;
        ++t_w;
      }
 
      CHKERR VecSetOption(getFEMethod()->ts_F, VEC_IGNORE_NEGATIVE_INDICES,
                          PETSC_TRUE);
      CHKERR VecSetValues(getFEMethod()->ts_F, data, &*vecF.begin(),
                          ADD_VALUES);
    }
    MoFEMFunctionReturn(0);
  }
 
private:
  boost::shared_ptr<CommonData> commonData;
  VectorDouble vecF;
};
 
/**
 * @brief Assemble stiff part tangent
 *
 * Solve problem \f$ F(t,u,\dot{u}) = G(t,u) \f$ where here the right hand side
 * \f$ \frac{\textrm{d} F}{\textrm{d} u^n} = a F_{\dot{u}}(t,u,\textrm{u}) +
 * F_{u}(t,u,\textrm{u}) \f$ is implemented.
 *
 */
template <int DIM> struct OpAssembleStiffLhs : OpEle {
  OpAssembleStiffLhs(boost::shared_ptr<CommonData> &data)
      : OpEle("u", "u", OpEle::OPROWCOL), commonData(data) {
    sYmm = true;
  }
  MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
                        EntityType col_type, EntData &row_data,
                        EntData &col_data) {
    MoFEMFunctionBegin;
    const int nb_row_dofs = row_data.getIndices().size();
    const int nb_col_dofs = col_data.getIndices().size();
    if (nb_row_dofs && nb_col_dofs) {
      mat.resize(nb_row_dofs, nb_col_dofs, false);
      mat.clear();
 
      const int nb_integration_pts = getGaussPts().size2();
      auto t_row_base = row_data.getFTensor0N();
      auto t_row_diff_base = row_data.getFTensor1DiffN<DIM>();
      auto t_w = getFTensor0IntegrationWeight();
      FTensor::Index<'i', DIM> i;
 
      const double ts_a = getFEMethod()->ts_a;
      const double vol = getMeasure();
      for (int gg = 0; gg != nb_integration_pts; ++gg) {
        const double a = vol * t_w;
        for (int rr = 0; rr != nb_row_dofs; ++rr) {
 
          auto t_col_base = col_data.getFTensor0N(gg, 0);
          auto t_col_diff_base = col_data.getFTensor1DiffN<DIM>(gg, 0);
 
          for (int cc = 0; cc != nb_col_dofs; ++cc) {
            mat(rr, cc) += a * (t_row_base * t_col_base * ts_a +
                                D * t_row_diff_base(i) * t_col_diff_base(i));
            ++t_col_base;
            ++t_col_diff_base;
          }
 
          ++t_row_base;
          ++t_row_diff_base;
        }
        ++t_w;
      }
 
      CHKERR MatSetValues(getFEMethod()->ts_B, row_data, col_data, &mat(0, 0),
                          ADD_VALUES);
      if (row_side != col_side || row_type != col_type) {
        transMat.resize(nb_col_dofs, nb_row_dofs, false);
        noalias(transMat) = trans(mat);
        CHKERR MatSetValues(getFEMethod()->ts_B, col_data, row_data,
                            &transMat(0, 0), ADD_VALUES);
      }
    }
    MoFEMFunctionReturn(0);
  }
 
private:
  boost::shared_ptr<CommonData> commonData;
  MatrixDouble mat, transMat;
};
 
/**
 * @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<PostProcFaceOnRefinedMesh> &post_proc)
      : dM(dm), postProc(post_proc){};
 
  MoFEMErrorCode preProcess() { return 0; }
  MoFEMErrorCode operator()() { return 0; }
 
  MoFEMErrorCode postProcess() {
    MoFEMFunctionBegin;
    if (ts_step % save_every_nth_step == 0) {
      CHKERR DMoFEMLoopFiniteElements(dM, "dFE", postProc);
      CHKERR postProc->writeFile(
          "out_level_" + boost::lexical_cast<std::string>(ts_step) + ".h5m");
    }
    MoFEMFunctionReturn(0);
  }
 
private:
  SmartPetscObj<DM> dM;
  boost::shared_ptr<PostProcFaceOnRefinedMesh> postProc;
};
 
}; // namespace ReactionDiffusionEquation
 
using namespace ReactionDiffusionEquation;
 
int main(int argc, char *argv[]) {
 
  // initialize petsc
  const char param_file[] = "param_file.petsc";
  MoFEM::Core::Initialize(&argc, &argv, param_file, help);
 
  try {
 
    // Create moab and mofem instances
    moab::Core mb_instance;
    moab::Interface &moab = mb_instance;
    MoFEM::Core core(moab);
    MoFEM::Interface &m_field = core;
 
    // Register DM Manager
    DMType dm_name = "DMMOFEM";
    CHKERR DMRegister_MoFEM(dm_name);
 
    // Simple interface
    Simple *simple_interface;
    CHKERR m_field.getInterface(simple_interface);
    CHKERR simple_interface->getOptions();
    CHKERR simple_interface->loadFile();
 
    int order = 4; ///< approximation order
    CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-order", &order, PETSC_NULL);
 
    // add fields
    CHKERR simple_interface->addDomainField("u", H1, AINSWORTH_LEGENDRE_BASE,
                                            1);
    // set fields order
    CHKERR simple_interface->setFieldOrder("u", order);
    // setup problem
    CHKERR simple_interface->setUp();
 
    // Create common data structure
    boost::shared_ptr<CommonData> data(new CommonData());
    /// Alias pointers to data in common data structure
    auto val_ptr = boost::shared_ptr<VectorDouble>(data, &data->val);
    auto dot_val_ptr = boost::shared_ptr<VectorDouble>(data, &data->dot_val);
    auto grad_ptr = boost::shared_ptr<MatrixDouble>(data, &data->grad);
 
    // Create finite element instances to integrate the right-hand side of slow
    // and stiff vector, and the tangent left-hand side for stiff part.
    boost::shared_ptr<Ele> vol_ele_slow_rhs(new Ele(m_field));
    boost::shared_ptr<Ele> vol_ele_stiff_rhs(new Ele(m_field));
    boost::shared_ptr<Ele> vol_ele_stiff_lhs(new Ele(m_field));
 
    // Push operators to integrate the slow right-hand side vector
    vol_ele_slow_rhs->getOpPtrVector().push_back(
        new OpCalculateScalarFieldValues("u", val_ptr));
    vol_ele_slow_rhs->getOpPtrVector().push_back(new OpAssembleSlowRhs(data));
 
    // PETSc IMAX and Explicit solver demans that g = M^-1 G is provided. So
    // when the slow right-hand side vector (G) is assembled is solved for g
    // vector.
    auto solve_for_g = [&]() {
      MoFEMFunctionBegin;
      if (vol_ele_slow_rhs->vecAssembleSwitch) {
        CHKERR VecGhostUpdateBegin(vol_ele_slow_rhs->ts_F, ADD_VALUES,
                                   SCATTER_REVERSE);
        CHKERR VecGhostUpdateEnd(vol_ele_slow_rhs->ts_F, ADD_VALUES,
                                 SCATTER_REVERSE);
        CHKERR VecAssemblyBegin(vol_ele_slow_rhs->ts_F);
        CHKERR VecAssemblyEnd(vol_ele_slow_rhs->ts_F);
        *vol_ele_slow_rhs->vecAssembleSwitch = false;
      }
      CHKERR KSPSolve(data->ksp, vol_ele_slow_rhs->ts_F,
                      vol_ele_slow_rhs->ts_F);
      MoFEMFunctionReturn(0);
    };
    // Add hook to the element to calculate g.
    vol_ele_slow_rhs->postProcessHook = solve_for_g;
 
    auto det_ptr = boost::make_shared<VectorDouble>();
    auto jac_ptr = boost::make_shared<MatrixDouble>();
    auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
    // Add operators to calculate the stiff right-hand side
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpCalculateHOJac<2>(jac_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpInvertMatrix<2>(jac_ptr, det_ptr, inv_jac_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpSetHOInvJacToScalarBases<2>(H1, inv_jac_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(new OpSetHOWeights(det_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpCalculateScalarFieldValuesDot("u", dot_val_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpCalculateScalarFieldGradient<2>("u", grad_ptr));
    vol_ele_stiff_rhs->getOpPtrVector().push_back(
        new OpAssembleStiffRhs<2>(data));
 
    // Add operators to calculate the stiff left-hand side
    vol_ele_stiff_lhs->getOpPtrVector().push_back(
        new OpCalculateHOJac<2>(jac_ptr));
    vol_ele_stiff_lhs->getOpPtrVector().push_back(
        new OpInvertMatrix<2>(jac_ptr, det_ptr, inv_jac_ptr));
    vol_ele_stiff_lhs->getOpPtrVector().push_back(
        new OpSetHOInvJacToScalarBases<2>(H1, inv_jac_ptr));
    vol_ele_stiff_lhs->getOpPtrVector().push_back(new OpSetHOWeights(det_ptr));
    vol_ele_stiff_lhs->getOpPtrVector().push_back(
        new OpAssembleStiffLhs<2>(data));
 
    // Set integration rules
    auto vol_rule = [](int, int, int p) -> int { return 2 * p; };
    vol_ele_slow_rhs->getRuleHook = vol_rule;
    vol_ele_stiff_rhs->getRuleHook = vol_rule;
    vol_ele_stiff_lhs->getRuleHook = vol_rule;
 
    // Crate element for post-processing
    boost::shared_ptr<PostProcFaceOnRefinedMesh> post_proc =
        boost::shared_ptr<PostProcFaceOnRefinedMesh>(
            new PostProcFaceOnRefinedMesh(m_field));
    boost::shared_ptr<ForcesAndSourcesCore> null;
    // Genarte post-processing mesh
    post_proc->generateReferenceElementMesh();
    // Postprocess only field values
    post_proc->addFieldValuesPostProc("u");
 
    // Get PETSc discrete manager
    auto dm = simple_interface->getDM();
 
    // Get surface entities form blockset, set initial values in those
    // blocksets. To keep it simple is assumed that inital values are on
    // blockset 1
    if (m_field.getInterface<MeshsetsManager>()->checkMeshset(1, BLOCKSET)) {
      Range inner_surface;
      CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
          1, BLOCKSET, 2, inner_surface, true);
      if (!inner_surface.empty()) {
        Range inner_surface_verts;
        CHKERR moab.get_connectivity(inner_surface, inner_surface_verts, false);
        CHKERR m_field.getInterface<FieldBlas>()->setField(
            u0, MBVERTEX, inner_surface_verts, "u");
      }
    }
 
    // Get skin on the body, i.e. body boundary, and apply homogenous Dirichlet
    // conditions on that boundary.
    Range surface;
    CHKERR moab.get_entities_by_dimension(0, 2, surface, false);
    Skinner skin(&m_field.get_moab());
    Range edges;
    CHKERR skin.find_skin(0, surface, false, edges);
    Range edges_part;
    ParallelComm *pcomm = ParallelComm::get_pcomm(&moab, MYPCOMM_INDEX);
    CHKERR pcomm->filter_pstatus(edges, PSTATUS_SHARED | PSTATUS_MULTISHARED,
                                 PSTATUS_NOT, -1, &edges_part);
    Range edges_verts;
    CHKERR moab.get_connectivity(edges_part, edges_verts, false);
    // Since Dirichlet b.c. are essential boundary conditions, remove DOFs from
    // the problem.
    CHKERR m_field.getInterface<ProblemsManager>()->removeDofsOnEntities(
        simple_interface->getProblemName(), "u",
        unite(edges_verts, edges_part));
 
    // Create mass matrix, calculate and assemble
    CHKERR DMCreateMatrix_MoFEM(dm, data->M);
    CHKERR MatZeroEntries(data->M);
    boost::shared_ptr<Ele> vol_mass_ele(new Ele(m_field));
    vol_mass_ele->getOpPtrVector().push_back(new OpAssembleMass(data));
    CHKERR DMoFEMLoopFiniteElements(dm, simple_interface->getDomainFEName(),
                                    vol_mass_ele);
    CHKERR MatAssemblyBegin(data->M, MAT_FINAL_ASSEMBLY);
    CHKERR MatAssemblyEnd(data->M, MAT_FINAL_ASSEMBLY);
 
    // Create and septup KSP (linear solver), we need this to calculate g(t,u) =
    // M^-1G(t,u)
    data->ksp = createKSP(m_field.get_comm());
    CHKERR KSPSetOperators(data->ksp, data->M, data->M);
    CHKERR KSPSetFromOptions(data->ksp);
    CHKERR KSPSetUp(data->ksp);
 
    // Create and setup TS solver
    auto ts = createTS(m_field.get_comm());
    // Use IMEX solver, i.e. implicit/explicit solver
    CHKERR TSSetType(ts, TSARKIMEX);
    CHKERR TSARKIMEXSetType(ts, TSARKIMEXA2);
 
    // Add element to calculate lhs of stiff part
    CHKERR DMMoFEMTSSetIJacobian(dm, simple_interface->getDomainFEName(),
                                 vol_ele_stiff_lhs, null, null);
    // Add element to calculate rhs of stiff part
    CHKERR DMMoFEMTSSetIFunction(dm, simple_interface->getDomainFEName(),
                                 vol_ele_stiff_rhs, null, null);
    // Add element to calculate rhs of slow (nonlinear) part
    CHKERR DMMoFEMTSSetRHSFunction(dm, simple_interface->getDomainFEName(),
                                   vol_ele_slow_rhs, null, null);
 
    // Add monitor to time solver
    boost::shared_ptr<Monitor> monitor_ptr(new Monitor(dm, post_proc));
    CHKERR DMMoFEMTSSetMonitor(dm, ts, simple_interface->getDomainFEName(),
                               monitor_ptr, null, null);
 
    // Create solution vector
    SmartPetscObj<Vec> X;
    CHKERR DMCreateGlobalVector_MoFEM(dm, X);
    CHKERR DMoFEMMeshToLocalVector(dm, X, INSERT_VALUES, SCATTER_FORWARD);
 
    // Solve problem
    double ftime = 1;
    CHKERR TSSetDM(ts, dm);
    CHKERR TSSetDuration(ts, PETSC_DEFAULT, ftime);
    CHKERR TSSetSolution(ts, X);
    CHKERR TSSetFromOptions(ts);
    CHKERR TSSolve(ts, X);
  }
  CATCH_ERRORS;
 
  // finish work cleaning memory, getting statistics, etc.
  MoFEM::Core::Finalize();
 
  return 0;
}