SCL-2: Poisson's equation (non-homogeneous BC)

Table of Contents

• Results
• Plain program
  • Implementation of User Data Operators (*.hpp)
  • Implementation of the main program (*.cpp)

Note

Prerequisite of this tutorial is SCL-1: Poisson's equation (homogeneous BC)

Note

Intended learning outcome:

• idea of Boundary element in MoFEM and how to use it
• handling of non-homogeneous boundary condition using least square approximation in MoFEM
• process of implementing additional User Data Operators (UDOs) to calculate and assemble non-homogeneous boundary condition
• practising on how to push the developed UDOs to the Pipeline

Results

Figure: Poisson nonhomogeneous visualisation. Source term: 200sin(10x)cos(10y), boundary function: sin(10x)cos(10y)

Plain program

The plain program for both the implementation of the UDOs (*.hpp) and the main program (*.cpp) are as follows

Implementation of User Data Operators (*.hpp)

#ifndef __POISSON2DNONHOMOGENEOUS_HPP__
#define __POISSON2DNONHOMOGENEOUS_HPP__
 
#include <stdlib.h>
#include <BasicFiniteElements.hpp>
 
using FaceEle = MoFEM::FaceElementForcesAndSourcesCore;
using EdgeEle = MoFEM::EdgeElementForcesAndSourcesCore;
 
using OpFaceEle = MoFEM::FaceElementForcesAndSourcesCore::UserDataOperator;
using OpEdgeEle = MoFEM::EdgeElementForcesAndSourcesCore::UserDataOperator;
 
using EntData = EntitiesFieldData::EntData;
 
namespace Poisson2DNonhomogeneousOperators {
 
FTensor::Index<'i', 2> i;
 
typedef boost::function<double(const double, const double, const double)>
    ScalarFunc;
 
struct OpDomainLhs : public OpFaceEle {
public:
  OpDomainLhs(std::string row_field_name, std::string col_field_name)
      : OpFaceEle(row_field_name, col_field_name, OpFaceEle::OPROWCOL) {
    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) {
 
      locLhs.resize(nb_row_dofs, nb_col_dofs, false);
      locLhs.clear();
 
      // get element area
      const double area = getMeasure();
 
      // get number of integration points
      const int nb_integration_points = getGaussPts().size2();
      // get integration weights
      auto t_w = getFTensor0IntegrationWeight();
 
      // get derivatives of base functions on row
      auto t_row_diff_base = row_data.getFTensor1DiffN<2>();
 
      // START THE LOOP OVER INTEGRATION POINTS TO CALCULATE LOCAL MATRIX
      for (int gg = 0; gg != nb_integration_points; gg++) {
 
        const double a = t_w * area;
 
        for (int rr = 0; rr != nb_row_dofs; ++rr) {
          // get derivatives of base functions on column
          auto t_col_diff_base = col_data.getFTensor1DiffN<2>(gg, 0);
 
          for (int cc = 0; cc != nb_col_dofs; cc++) {
 
            locLhs(rr, cc) += t_row_diff_base(i) * t_col_diff_base(i) * a;
 
            // move to the derivatives of the next base functions on column
            ++t_col_diff_base;
          }
 
          // move to the derivatives of the next base functions on row
          ++t_row_diff_base;
        }
 
        // move to the weight of the next integration point
        ++t_w;
      }
 
      // FILL VALUES OF LOCAL MATRIX ENTRIES TO THE GLOBAL MATRIX
 
      // Fill value to local stiffness matrix ignoring boundary DOFs
      CHKERR MatSetValues<MoFEM::EssentialBcStorage>(
          getKSPB(), row_data, col_data, &locLhs(0, 0), ADD_VALUES);
 
      // Fill values of symmetric local stiffness matrix
      if (row_side != col_side || row_type != col_type) {
        transLocLhs.resize(nb_col_dofs, nb_row_dofs, false);
        noalias(transLocLhs) = trans(locLhs);
        CHKERR MatSetValues<MoFEM::EssentialBcStorage>(
            getKSPB(), col_data, row_data, &transLocLhs(0, 0), ADD_VALUES);
      }
    }
 
    MoFEMFunctionReturn(0);
  }
 
private:
  boost::shared_ptr<std::vector<unsigned char>> boundaryMarker;
  MatrixDouble locLhs, transLocLhs;
};
 
struct OpDomainRhs : public OpFaceEle {
public:
  OpDomainRhs(std::string field_name, ScalarFunc source_term_function)
      : OpFaceEle(field_name, OpFaceEle::OPROW),
        sourceTermFunc(source_term_function) {}
 
  MoFEMErrorCode doWork(int side, EntityType type, EntData &data) {
    MoFEMFunctionBegin;
 
    const int nb_dofs = data.getIndices().size();
 
    if (nb_dofs) {
 
      locRhs.resize(nb_dofs, false);
      locRhs.clear();
 
      // get element area
      const double area = getMeasure();
 
      // get number of integration points
      const int nb_integration_points = getGaussPts().size2();
      // get integration weights
      auto t_w = getFTensor0IntegrationWeight();
      // get coordinates of the integration point
      auto t_coords = getFTensor1CoordsAtGaussPts();
 
      // get base functions
      auto t_base = data.getFTensor0N();
 
      // START THE LOOP OVER INTEGRATION POINTS TO CALCULATE LOCAL VECTOR
      for (int gg = 0; gg != nb_integration_points; gg++) {
 
        const double a = t_w * area;
        double body_source =
            sourceTermFunc(t_coords(0), t_coords(1), t_coords(2));
 
        for (int rr = 0; rr != nb_dofs; rr++) {
 
          locRhs[rr] += t_base * body_source * a;
 
          // move to the next base function
          ++t_base;
        }
 
        // move to the weight of the next integration point
        ++t_w;
        // move to the coordinates of the next integration point
        ++t_coords;
      }
 
      // FILL VALUES OF THE GLOBAL VECTOR ENTRIES FROM THE LOCAL ONES
      CHKERR VecSetValues<MoFEM::EssentialBcStorage>(
          getKSPf(), data, &*locRhs.begin(), ADD_VALUES);
    }
 
    MoFEMFunctionReturn(0);
  }
 
private:
  ScalarFunc sourceTermFunc;
  VectorDouble locRhs;
};
 
struct OpBoundaryLhs : public OpEdgeEle {
public:
  OpBoundaryLhs(std::string row_field_name, std::string col_field_name)
      : OpEdgeEle(row_field_name, col_field_name, OpEdgeEle::OPROWCOL) {
    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) {
 
      locBoundaryLhs.resize(nb_row_dofs, nb_col_dofs, false);
      locBoundaryLhs.clear();
 
      // get (boundary) element length
      const double edge = getMeasure();
 
      // get number of integration points
      const int nb_integration_points = getGaussPts().size2();
      // get integration weights
      auto t_w = getFTensor0IntegrationWeight();
 
      // get base functions on row
      auto t_row_base = row_data.getFTensor0N();
 
      // START THE LOOP OVER INTEGRATION POINTS TO CALCULATE LOCAL MATRIX
      for (int gg = 0; gg != nb_integration_points; gg++) {
        const double a = t_w * edge;
 
        for (int rr = 0; rr != nb_row_dofs; ++rr) {
          // get base functions on column
          auto t_col_base = col_data.getFTensor0N(gg, 0);
 
          for (int cc = 0; cc != nb_col_dofs; cc++) {
 
            locBoundaryLhs(rr, cc) += t_row_base * t_col_base * a;
 
            // move to the next base functions on column
            ++t_col_base;
          }
          // move to the next base functions on row
          ++t_row_base;
        }
 
        // move to the weight of the next integration point
        ++t_w;
      }
 
      // FILL VALUES OF LOCAL MATRIX ENTRIES TO THE GLOBAL MATRIX
      CHKERR MatSetValues<MoFEM::EssentialBcStorage>(
          getKSPB(), row_data, col_data, &locBoundaryLhs(0, 0), ADD_VALUES);
      if (row_side != col_side || row_type != col_type) {
        transLocBoundaryLhs.resize(nb_col_dofs, nb_row_dofs, false);
        noalias(transLocBoundaryLhs) = trans(locBoundaryLhs);
        CHKERR MatSetValues<MoFEM::EssentialBcStorage>(
            getKSPB(), col_data, row_data, &transLocBoundaryLhs(0, 0),
            ADD_VALUES);
      }
    }
 
    MoFEMFunctionReturn(0);
  }
 
private:
  MatrixDouble locBoundaryLhs, transLocBoundaryLhs;
};
 
struct OpBoundaryRhs : public OpEdgeEle {
public:
  OpBoundaryRhs(std::string field_name, ScalarFunc boundary_function)
      : OpEdgeEle(field_name, OpEdgeEle::OPROW),
        boundaryFunc(boundary_function) {}
 
  MoFEMErrorCode doWork(int side, EntityType type, EntData &data) {
    MoFEMFunctionBegin;
 
    const int nb_dofs = data.getIndices().size();
 
    if (nb_dofs) {
 
      locBoundaryRhs.resize(nb_dofs, false);
      locBoundaryRhs.clear();
 
      // get (boundary) element length
      const double edge = getMeasure();
 
      // get number of integration points
      const int nb_integration_points = getGaussPts().size2();
      // get integration weights
      auto t_w = getFTensor0IntegrationWeight();
      // get coordinates at integration point
      auto t_coords = getFTensor1CoordsAtGaussPts();
 
      // get base function
      auto t_base = data.getFTensor0N();
 
      // START THE LOOP OVER INTEGRATION POINTS TO CALCULATE LOCAL VECTOR
      for (int gg = 0; gg != nb_integration_points; gg++) {
 
        const double a = t_w * edge;
        double boundary_term =
            boundaryFunc(t_coords(0), t_coords(1), t_coords(2));
 
        for (int rr = 0; rr != nb_dofs; rr++) {
 
          locBoundaryRhs[rr] += t_base * boundary_term * a;
 
          // move to the next base function
          ++t_base;
        }
 
        // move to the weight of the next integration point
        ++t_w;
        // move to the coordinates of the next integration point
        ++t_coords;
      }
 
      // FILL VALUES OF LOCAL VECTOR ENTRIES TO THE GLOBAL VECTOR
      CHKERR VecSetValues<MoFEM::EssentialBcStorage>(
          getKSPf(), data, &*locBoundaryRhs.begin(), ADD_VALUES);
    }
 
    MoFEMFunctionReturn(0);
  }
 
private:
  ScalarFunc boundaryFunc;
  VectorDouble locBoundaryRhs;
};
 
}; // namespace Poisson2DNonhomogeneousOperators
 
#endif //__POISSON2DNONHOMOGENEOUS_HPP__

Implementation of the main program (*.cpp)

#include <stdlib.h>
#include <BasicFiniteElements.hpp>
#include <poisson_2d_nonhomogeneous.hpp>
 
using namespace MoFEM;
using namespace Poisson2DNonhomogeneousOperators;
 
using PostProcFaceEle =
    PostProcBrokenMeshInMoab<FaceElementForcesAndSourcesCore>;
 
static char help[] = "...\n\n";
 
struct Poisson2DNonhomogeneous {
public:
  Poisson2DNonhomogeneous(MoFEM::Interface &m_field);
 
  // Declaration of the main function to run analysis
  MoFEMErrorCode runProgram();
 
private:
  // Declaration of other main functions called in runProgram()
  MoFEMErrorCode readMesh();
  MoFEMErrorCode setupProblem();
  MoFEMErrorCode boundaryCondition();
  MoFEMErrorCode assembleSystem();
  MoFEMErrorCode setIntegrationRules();
  MoFEMErrorCode solveSystem();
  MoFEMErrorCode outputResults();
 
  // Function to calculate the Source term
  static double sourceTermFunction(const double x, const double y,
                                   const double z) {
    return 200 * sin(x * 10.) * cos(y * 10.);
    // return 1;
  }
  // Function to calculate the Boundary term
  static double boundaryFunction(const double x, const double y,
                                 const double z) {
    return sin(x * 10.) * cos(y * 10.);
    // return 0;
  }
 
  // Main interfaces
  MoFEM::Interface &mField;
  Simple *simpleInterface;
 
  // Field name and approximation order
  std::string domainField;
  int oRder;
 
  // Object to mark boundary entities for the assembling of domain elements
  boost::shared_ptr<std::vector<unsigned char>> boundaryMarker;
 
  // Boundary entities marked for fieldsplit (block) solver - optional
  Range boundaryEntitiesForFieldsplit;
};
 
Poisson2DNonhomogeneous::Poisson2DNonhomogeneous(MoFEM::Interface &m_field)
    : domainField("U"), mField(m_field) {}
 
MoFEMErrorCode Poisson2DNonhomogeneous::readMesh() {
  MoFEMFunctionBegin;
 
  CHKERR mField.getInterface(simpleInterface);
  CHKERR simpleInterface->getOptions();
  CHKERR simpleInterface->loadFile();
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::setupProblem() {
  MoFEMFunctionBegin;
 
  CHKERR simpleInterface->addDomainField(domainField, H1,
                                         AINSWORTH_BERNSTEIN_BEZIER_BASE, 1);
  CHKERR simpleInterface->addBoundaryField(domainField, H1,
                                           AINSWORTH_BERNSTEIN_BEZIER_BASE, 1);
 
  int oRder = 3;
  CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-order", &oRder, PETSC_NULL);
  CHKERR simpleInterface->setFieldOrder(domainField, oRder);
 
  CHKERR simpleInterface->setUp();
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::boundaryCondition() {
  MoFEMFunctionBegin;
 
  // Get boundary edges marked in block named "BOUNDARY_CONDITION"
  auto get_entities_on_mesh = [&]() {
    Range boundary_entities;
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(mField, BLOCKSET, it)) {
      std::string entity_name = it->getName();
      if (entity_name.compare(0, 18, "BOUNDARY_CONDITION") == 0) {
        CHKERR it->getMeshsetIdEntitiesByDimension(mField.get_moab(), 1,
                                                   boundary_entities, true);
      }
    }
    // Add vertices to boundary entities
    Range boundary_vertices;
    CHKERR mField.get_moab().get_connectivity(boundary_entities,
                                              boundary_vertices, true);
    boundary_entities.merge(boundary_vertices);
 
    // Store entities for fieldsplit (block) solver
    boundaryEntitiesForFieldsplit = boundary_entities;
 
    return boundary_entities;
  };
 
  auto mark_boundary_dofs = [&](Range &&skin_edges) {
    auto problem_manager = mField.getInterface<ProblemsManager>();
    auto marker_ptr = boost::make_shared<std::vector<unsigned char>>();
    problem_manager->markDofs(simpleInterface->getProblemName(), ROW,
                              skin_edges, *marker_ptr);
    return marker_ptr;
  };
 
  // Get global local vector of marked DOFs. Is global, since is set for all
  // DOFs on processor. Is local since only DOFs on processor are in the
  // vector. To access DOFs use local indices.
  boundaryMarker = mark_boundary_dofs(get_entities_on_mesh());
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::assembleSystem() {
  MoFEMFunctionBegin;
 
  auto pipeline_mng = mField.getInterface<PipelineManager>();
  auto det_ptr = boost::make_shared<VectorDouble>();
  auto jac_ptr = boost::make_shared<MatrixDouble>();
  auto inv_jac_ptr = boost::make_shared<MatrixDouble>();
 
  { // Push operators to the Pipeline that is responsible for calculating LHS of
    // domain elements
    pipeline_mng->getOpDomainLhsPipeline().push_back(
        new OpCalculateHOJacForFace(jac_ptr));
    pipeline_mng->getOpDomainLhsPipeline().push_back(
        new OpInvertMatrix<2>(jac_ptr, det_ptr, inv_jac_ptr));
    pipeline_mng->getOpDomainLhsPipeline().push_back(
        new OpSetBc(domainField, true, boundaryMarker));
    pipeline_mng->getOpDomainLhsPipeline().push_back(
        new OpDomainLhs(domainField, domainField));
    pipeline_mng->getOpDomainLhsPipeline().push_back(
        new OpUnSetBc(domainField));
  }
 
  { // Push operators to the Pipeline that is responsible for calculating RHS of
    // domain elements
    pipeline_mng->getOpDomainRhsPipeline().push_back(
        new OpSetBc(domainField, true, boundaryMarker));
    pipeline_mng->getOpDomainRhsPipeline().push_back(
        new OpDomainRhs(domainField, sourceTermFunction));
    pipeline_mng->getOpDomainRhsPipeline().push_back(
        new OpUnSetBc(domainField));
  }
 
  { // Push operators to the Pipeline that is responsible for calculating LHS of
    // boundary elements
    pipeline_mng->getOpBoundaryLhsPipeline().push_back(
        new OpSetBc(domainField, false, boundaryMarker));
    pipeline_mng->getOpBoundaryLhsPipeline().push_back(
        new OpBoundaryLhs(domainField, domainField));
    pipeline_mng->getOpBoundaryLhsPipeline().push_back(
        new OpUnSetBc(domainField));
  }
 
  { // Push operators to the Pipeline that is responsible for calculating RHS of
    // boundary elements
    pipeline_mng->getOpBoundaryRhsPipeline().push_back(
        new OpSetBc(domainField, false, boundaryMarker));
    pipeline_mng->getOpBoundaryRhsPipeline().push_back(
        new OpBoundaryRhs(domainField, boundaryFunction));
    pipeline_mng->getOpBoundaryRhsPipeline().push_back(
        new OpUnSetBc(domainField));
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::setIntegrationRules() {
  MoFEMFunctionBegin;
 
  auto pipeline_mng = mField.getInterface<PipelineManager>();
 
  auto domain_rule_lhs = [](int, int, int p) -> int { return 2 * (p - 1); };
  auto domain_rule_rhs = [](int, int, int p) -> int { return 2 * (p - 1); };
  CHKERR pipeline_mng->setDomainLhsIntegrationRule(domain_rule_lhs);
  CHKERR pipeline_mng->setDomainRhsIntegrationRule(domain_rule_rhs);
 
  auto boundary_rule_lhs = [](int, int, int p) -> int { return 2 * p; };
  auto boundary_rule_rhs = [](int, int, int p) -> int { return 2 * p; };
  CHKERR pipeline_mng->setBoundaryLhsIntegrationRule(boundary_rule_lhs);
  CHKERR pipeline_mng->setBoundaryLhsIntegrationRule(boundary_rule_rhs);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::solveSystem() {
  MoFEMFunctionBegin;
 
  auto pipeline_mng = mField.getInterface<PipelineManager>();
 
  auto ksp_solver = pipeline_mng->createKSP();
  CHKERR KSPSetFromOptions(ksp_solver);
 
  // Create RHS and solution vectors
  auto dm = simpleInterface->getDM();
  auto F = smartCreateDMVector(dm);
  auto D = smartVectorDuplicate(F);
 
  // Setup fieldsplit (block) solver - optional: yes/no
  if (1) {
    PC pc;
    CHKERR KSPGetPC(ksp_solver, &pc);
    PetscBool is_pcfs = PETSC_FALSE;
    PetscObjectTypeCompare((PetscObject)pc, PCFIELDSPLIT, &is_pcfs);
 
    // Set up FIELDSPLIT, only when user set -pc_type fieldsplit
    // Identify the index for boundary entities, remaining will be for domain
    // Then split the fields for boundary and domain for solving
    if (is_pcfs == PETSC_TRUE) {
      IS is_domain, is_boundary;
      const MoFEM::Problem *problem_ptr;
      CHKERR DMMoFEMGetProblemPtr(dm, &problem_ptr);
      CHKERR mField.getInterface<ISManager>()->isCreateProblemFieldAndRank(
          problem_ptr->getName(), ROW, domainField, 0, 1, &is_boundary,
          &boundaryEntitiesForFieldsplit);
      // CHKERR ISView(is_boundary, PETSC_VIEWER_STDOUT_SELF);
 
      CHKERR PCFieldSplitSetIS(pc, NULL, is_boundary);
 
      CHKERR ISDestroy(&is_boundary);
    }
  }
 
  CHKERR KSPSetUp(ksp_solver);
 
  // Solve the system
  CHKERR KSPSolve(ksp_solver, F, D);
 
  // Scatter result data on the mesh
  CHKERR VecGhostUpdateBegin(D, INSERT_VALUES, SCATTER_FORWARD);
  CHKERR VecGhostUpdateEnd(D, INSERT_VALUES, SCATTER_FORWARD);
  CHKERR DMoFEMMeshToLocalVector(dm, D, INSERT_VALUES, SCATTER_REVERSE);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::outputResults() {
  MoFEMFunctionBegin;
 
  auto pipeline_mng = mField.getInterface<PipelineManager>();
  pipeline_mng->getDomainLhsFE().reset();
  pipeline_mng->getBoundaryLhsFE().reset();
  pipeline_mng->getDomainRhsFE().reset();
  pipeline_mng->getBoundaryRhsFE().reset();
 
  auto d_ptr = boost::make_shared<VectorDouble>();
  auto l_ptr = boost::make_shared<VectorDouble>();
 
  using OpPPMap = OpPostProcMapInMoab<2, 2>;
 
  auto post_proc_fe = boost::make_shared<PostProcFaceEle>(mField);
 
  post_proc_fe->getOpPtrVector().push_back(
      new OpCalculateScalarFieldValues(domainField, d_ptr));
  post_proc_fe->getOpPtrVector().push_back(
      new OpPPMap(post_proc_fe->getPostProcMesh(),
                  post_proc_fe->getMapGaussPts(), {{domainField, d_ptr}},
                  {}, {}, {}));
  pipeline_mng->getDomainRhsFE() = post_proc_fe;
 
  CHKERR pipeline_mng->loopFiniteElements();
  CHKERR post_proc_fe->writeFile("out_result.h5m");
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode Poisson2DNonhomogeneous::runProgram() {
  MoFEMFunctionBegin;
 
  readMesh();
  setupProblem();
  boundaryCondition();
  assembleSystem();
  setIntegrationRules();
  solveSystem();
  outputResults();
 
  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);
 
  // Error handling
  try {
    // Register MoFEM discrete manager in PETSc
    DMType dm_name = "DMMOFEM";
    CHKERR DMRegister_MoFEM(dm_name);
 
    // Create MOAB instance
    moab::Core mb_instance;              // mesh database
    moab::Interface &moab = mb_instance; // mesh database interface
 
    // Create MoFEM instance
    MoFEM::Core core(moab);           // finite element database
    MoFEM::Interface &m_field = core; // finite element interface
 
    // Run the main analysis
    Poisson2DNonhomogeneous poisson_problem(m_field);
    CHKERR poisson_problem.runProgram();
  }
  CATCH_ERRORS;
 
  // Finish work: cleaning memory, getting statistics, etc.
  MoFEM::Core::Finalize();
 
  return 0;
}