subdomains_ex2.C

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2019 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
 
// This library 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 2.1 of the License, or (at your option) any later version.
 
// This library 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 this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
 
 
// <h1>Subdomains Example 2 - Subdomain-Restricted Variables</h1>
// \author Benjamin S. Kirk
// \date 2011
//
// This example builds on the fourth example program by showing how
// to restrict solution fields to a subdomain (or union of
// subdomains).
 
 
// C++ include files that we need
#include <iostream>
#include <algorithm>
#include <math.h>
 
// Basic include file needed for the mesh functionality.
#include "libmesh/libmesh.h"
#include "libmesh/mesh.h"
#include "libmesh/mesh_generation.h"
#include "libmesh/exodusII_io.h"
#include "libmesh/gnuplot_io.h"
#include "libmesh/linear_implicit_system.h"
#include "libmesh/equation_systems.h"
 
// Define the Finite Element object.
#include "libmesh/fe.h"
 
// Define Gauss quadrature rules.
#include "libmesh/quadrature_gauss.h"
 
// Define the DofMap, which handles degree of freedom
// indexing.
#include "libmesh/dof_map.h"
 
// Define useful datatypes for finite element
// matrix and vector components.
#include "libmesh/sparse_matrix.h"
#include "libmesh/numeric_vector.h"
#include "libmesh/dense_matrix.h"
#include "libmesh/dense_vector.h"
 
// Define the PerfLog, a performance logging utility.
// It is useful for timing events in a code and giving
// you an idea where bottlenecks lie.
#include "libmesh/perf_log.h"
 
// The definition of a geometric element
#include "libmesh/elem.h"
 
#include "libmesh/string_to_enum.h"
#include "libmesh/getpot.h"
#include "libmesh/enum_solver_package.h"
 
// Bring in everything from the libMesh namespace
using namespace libMesh;
 
 
 
// Function prototype.  This is the function that will assemble
// the linear system for our Poisson problem.  Note that the
// function will take the EquationSystems object and the
// name of the system we are assembling as input.  From the
// EquationSystems object we have access to the Mesh and
// other objects we might need.
void assemble_poisson(EquationSystems & es,
                      const std::string & system_name);
 
// Exact solution function prototype.
Real exact_solution (const Real x,
                     const Real y = 0.,
                     const Real z = 0.);
 
// Begin the main program.
int main (int argc, char ** argv)
{
  // Initialize libMesh and any dependent libraries, like in example 2.
  LibMeshInit init (argc, argv);
 
  // This example requires a linear solver package.
  libmesh_example_requires(libMesh::default_solver_package() != INVALID_SOLVER_PACKAGE,
                           "--enable-petsc, --enable-trilinos, or --enable-eigen");
 
  // Declare a performance log for the main program
  // PerfLog perf_main("Main Program");
 
  // Create a GetPot object to parse the command line
  GetPot command_line (argc, argv);
 
  // Check for proper calling arguments.
  if (argc < 3)
    {
      // This handy function will print the file name, line number,
      // specified message, and then throw an exception.
      libmesh_error_msg("Usage:\n" << "\t " << argv[0] << " -d 2(3)" << " -n 15");
    }
 
  // Brief message to the user regarding the program name
  // and command line arguments.
  else
    {
      libMesh::out << "Running " << argv[0];
 
      for (int i=1; i<argc; i++)
        libMesh::out << " " << argv[i];
 
      libMesh::out << std::endl << std::endl;
    }
 
 
  // Read problem dimension from command line.  Use int
  // instead of unsigned since the GetPot overload is ambiguous
  // otherwise.
  int dim = 2;
  if (command_line.search(1, "-d"))
    dim = command_line.next(dim);
 
  // Skip higher-dimensional examples on a lower-dimensional libMesh build
  libmesh_example_requires(dim <= LIBMESH_DIM, "2D/3D support");
 
  // Create a mesh with user-defined dimension on the default MPI
  // communicator.
  Mesh mesh (init.comm(), dim);
 
  // Read number of elements from command line
  int ps = 15;
  if (command_line.search(1, "-n"))
    ps = command_line.next(ps);
 
  // Read FE order from command line
  std::string order = "SECOND";
  if (command_line.search(2, "-Order", "-o"))
    order = command_line.next(order);
 
  // Read FE Family from command line
  std::string family = "LAGRANGE";
  if (command_line.search(2, "-FEFamily", "-f"))
    family = command_line.next(family);
 
  // Cannot use discontinuous basis.
  if ((family == "MONOMIAL") || (family == "XYZ"))
    {
      if (mesh.processor_id() == 0)
        libmesh_error_msg("This example requires a C^0 (or higher) FE basis.");
    }
 
  // Use the MeshTools::Generation mesh generator to create a uniform
  // grid on the square [-1,1]^D.  We instruct the mesh generator
  // to build a mesh of 8x8 Quad9 elements in 2D, or Hex27
  // elements in 3D.  Building these higher-order elements allows
  // us to use higher-order approximation, as in example 3.
 
  Real halfwidth = dim > 1 ? 1. : 0.;
  Real halfheight = dim > 2 ? 1. : 0.;
 
  if ((family == "LAGRANGE") && (order == "FIRST"))
    {
      // No reason to use high-order geometric elements if we are
      // solving with low-order finite elements.
      MeshTools::Generation::build_cube (mesh,
                                         ps,
                                         (dim>1) ? ps : 0,
                                         (dim>2) ? ps : 0,
                                         -1., 1.,
                                         -halfwidth, halfwidth,
                                         -halfheight, halfheight,
                                         (dim==1)    ? EDGE2 :
                                         ((dim == 2) ? QUAD4 : HEX8));
    }
 
  else
    {
      MeshTools::Generation::build_cube (mesh,
                                         ps,
                                         (dim>1) ? ps : 0,
                                         (dim>2) ? ps : 0,
                                         -1., 1.,
                                         -halfwidth, halfwidth,
                                         -halfheight, halfheight,
                                         (dim==1)    ? EDGE3 :
                                         ((dim == 2) ? QUAD9 : HEX27));
    }
 
  for (auto & elem : mesh.element_ptr_range())
    {
      const Point cent = elem->centroid();
      if (dim > 1)
        {
          if ((cent(0) > 0) == (cent(1) > 0))
            elem->subdomain_id() = 1;
        }
      else if (cent(0) > 0)
        elem->subdomain_id() = 1;
    }
 
  // Print information about the mesh to the screen.
  mesh.print_info();
 
  // Create an equation systems object.
  EquationSystems equation_systems (mesh);
 
  // Declare the system and its variables.
  // Create a system named "Poisson"
  LinearImplicitSystem & system =
    equation_systems.add_system<LinearImplicitSystem> ("Poisson");
 
 
  std::set<subdomain_id_type> active_subdomains;
 
 
  // Add the variable "u" to "Poisson".  "u"
  // will be approximated using second-order approximation.
  active_subdomains.clear(); active_subdomains.insert(0);
  system.add_variable("u",
                      Utility::string_to_enum<Order>   (order),
                      Utility::string_to_enum<FEFamily>(family),
                      &active_subdomains);
 
  // Add the variable "v" to "Poisson".  "v"
  // will be approximated using second-order approximation.
  active_subdomains.clear(); active_subdomains.insert(1);
  system.add_variable("v",
                      Utility::string_to_enum<Order>   (order),
                      Utility::string_to_enum<FEFamily>(family),
                      &active_subdomains);
 
  // Give the system a pointer to the matrix assembly
  // function.
  system.attach_assemble_function (assemble_poisson);
 
  // Initialize the data structures for the equation system.
  equation_systems.init();
 
  // Print information about the system to the screen.
  equation_systems.print_info();
  mesh.print_info();
 
  // Solve the system "Poisson", just like example 2.
  equation_systems.get_system("Poisson").solve();
 
  // After solving the system write the solution
  // to a GMV-formatted plot file.
  if (dim == 1)
    {
      GnuPlotIO plot(mesh, "Subdomains Example 2, 1D", GnuPlotIO::GRID_ON);
      plot.write_equation_systems("gnuplot_script", equation_systems);
    }
  else
    {
#ifdef LIBMESH_HAVE_EXODUS_API
      ExodusII_IO (mesh).write_equation_systems ((dim == 3) ?
                                                 "out_3.e" : "out_2.e", equation_systems);
#endif // #ifdef LIBMESH_HAVE_EXODUS_API
    }
 
  // All done.
  return 0;
}
 
 
 
 
//
//
//
// We now define the matrix assembly function for the
// Poisson system.  We need to first compute element
// matrices and right-hand sides, and then take into
// account the boundary conditions, which will be handled
// via a penalty method.
void assemble_poisson(EquationSystems & es,
                      const std::string & libmesh_dbg_var(system_name))
{
  // It is a good idea to make sure we are assembling
  // the proper system.
  libmesh_assert_equal_to (system_name, "Poisson");
 
  // Declare a performance log.  Give it a descriptive
  // string to identify what part of the code we are
  // logging, since there may be many PerfLogs in an
  // application.
  PerfLog perf_log ("Matrix Assembly");
 
  // Get a constant reference to the mesh object.
  const MeshBase & mesh = es.get_mesh();
 
  // The dimension that we are running
  const unsigned int dim = mesh.mesh_dimension();
 
  // Get a reference to the LinearImplicitSystem we are solving
  LinearImplicitSystem & system = es.get_system<LinearImplicitSystem>("Poisson");
 
  // A reference to the DofMap object for this system.  The DofMap
  // object handles the index translation from node and element numbers
  // to degree of freedom numbers.  We will talk more about the DofMap
  // in future examples.
  const DofMap & dof_map = system.get_dof_map();
 
  // Get a constant reference to the Finite Element type
  // for the first (and only) variable in the system.
  FEType fe_type = dof_map.variable_type(0);
 
  // Build a Finite Element object of the specified type.  Since the
  // FEBase::build() member dynamically creates memory we will
  // store the object as a std::unique_ptr<FEBase>.  This can be thought
  // of as a pointer that will clean up after itself.
  std::unique_ptr<FEBase> fe (FEBase::build(dim, fe_type));
 
  // A 5th order Gauss quadrature rule for numerical integration.
  QGauss qrule (dim, FIFTH);
 
  // Tell the finite element object to use our quadrature rule.
  fe->attach_quadrature_rule (&qrule);
 
  // Declare a special finite element object for
  // boundary integration.
  std::unique_ptr<FEBase> fe_face (FEBase::build(dim, fe_type));
 
  // Boundary integration requires one quadrature rule,
  // with dimensionality one less than the dimensionality
  // of the element.
  QGauss qface(dim-1, FIFTH);
 
  // Tell the finite element object to use our
  // quadrature rule.
  fe_face->attach_quadrature_rule (&qface);
 
  // Here we define some references to cell-specific data that
  // will be used to assemble the linear system.
  // We begin with the element Jacobian * quadrature weight at each
  // integration point.
  const std::vector<Real> & JxW = fe->get_JxW();
 
  // The physical XY locations of the quadrature points on the element.
  // These might be useful for evaluating spatially varying material
  // properties at the quadrature points.
  const std::vector<Point> & q_point = fe->get_xyz();
 
  // The element shape functions evaluated at the quadrature points.
  const std::vector<std::vector<Real>> & phi = fe->get_phi();
 
  // The element shape function gradients evaluated at the quadrature
  // points.
  const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();
 
  // Define data structures to contain the element matrix
  // and right-hand-side vector contribution.  Following
  // basic finite element terminology we will denote these
  // "Ke" and "Fe". More detail is in example 3.
  DenseMatrix<Number> Ke;
  DenseVector<Number> Fe;
 
  // This vector will hold the degree of freedom indices for
  // the element.  These define where in the global system
  // the element degrees of freedom get mapped.
  std::vector<dof_id_type> dof_indices, dof_indices2;
 
  // Now we will loop over all the "local" elements in the mesh.  We
  // will compute the element matrix and right-hand-side contribution.
  // See example 3 for a discussion of the element iterators.  Here we
  // only want to loop over elements that are owned by the local
  // processor.  This allows each processor to compute its components
  // of the global matrix.
  //
  // "PARALLEL CHANGE"
  for (const auto & elem : as_range(mesh.local_elements_begin(),
                                    mesh.local_elements_end()))
    {
      // Start logging the shape function initialization.
      // This is done through a simple function call with
      // the name of the event to log.
      perf_log.push("elem init");
 
      // Get the degree of freedom indices for the
      // current element.  These define where in the global
      // matrix and right-hand-side this element will
      // contribute to.
      dof_map.dof_indices (elem, dof_indices, 0);
      dof_map.dof_indices (elem, dof_indices2, 1);
 
      // libMesh::out << "dof_indices.size()="
      // << dof_indices.size()
      // << ", dof_indices2.size()="
      // << dof_indices2.size()
      // << std::endl;
 
      // Compute the element-specific data for the current
      // element.  This involves computing the location of the
      // quadrature points (q_point) and the shape functions
      // (phi, dphi) for the current element.
      fe->reinit (elem);
 
      // Zero the element matrix and right-hand side before
      // summing them.  We use the resize member here because
      // the number of degrees of freedom might have changed from
      // the last element.  Note that this will be the case if the
      // element type is different (i.e. the last element was a
      // triangle, now we are on a quadrilateral).
      Ke.resize (std::max(dof_indices.size(), dof_indices2.size()),
                 std::max(dof_indices.size(), dof_indices2.size()));
 
      Fe.resize (std::max(dof_indices.size(), dof_indices2.size()));
 
      // Stop logging the shape function initialization.
      // If you forget to stop logging an event the PerfLog
      // object will probably catch the error and abort.
      perf_log.pop("elem init");
 
      // Now we will build the element matrix.  This involves
      // a double loop to integrate the test functions (i) against
      // the trial functions (j).
      //
      // We have split the numeric integration into two loops
      // so that we can log the matrix and right-hand-side
      // computation separately.
      //
      // Now start logging the element matrix computation
      perf_log.push ("Ke");
 
      for (unsigned int qp=0; qp<qrule.n_points(); qp++)
        for (std::size_t i=0; i<phi.size(); i++)
          for (std::size_t j=0; j<phi.size(); j++)
            Ke(i,j) += JxW[qp]*(dphi[i][qp]*dphi[j][qp]);
 
 
      // Stop logging the matrix computation
      perf_log.pop ("Ke");
 
      // Now we build the element right-hand-side contribution.
      // This involves a single loop in which we integrate the
      // "forcing function" in the PDE against the test functions.
      //
      // Start logging the right-hand-side computation
      perf_log.push ("Fe");
 
      for (unsigned int qp=0; qp<qrule.n_points(); qp++)
        {
          // fxy is the forcing function for the Poisson equation.
          // In this case we set fxy to be a finite difference
          // Laplacian approximation to the (known) exact solution.
          //
          // We will use the second-order accurate FD Laplacian
          // approximation, which in 2D on a structured grid is
          //
          // u_xx + u_yy = (u(i-1,j) + u(i+1,j) +
          //                u(i,j-1) + u(i,j+1) +
          //                -4*u(i,j))/h^2
          //
          // Since the value of the forcing function depends only
          // on the location of the quadrature point (q_point[qp])
          // we will compute it here, outside of the i-loop
          const Real x = q_point[qp](0);
#if LIBMESH_DIM > 1
          const Real y = q_point[qp](1);
#else
          const Real y = 0;
#endif
#if LIBMESH_DIM > 2
          const Real z = q_point[qp](2);
#else
          const Real z = 0;
#endif
          const Real eps = 1.e-3;
 
          const Real uxx = (exact_solution(x-eps, y, z) +
                            exact_solution(x+eps, y, z) +
                            -2.*exact_solution(x, y, z))/eps/eps;
 
          const Real uyy = (exact_solution(x, y-eps, z) +
                            exact_solution(x, y+eps, z) +
                            -2.*exact_solution(x, y, z))/eps/eps;
 
          const Real uzz = (exact_solution(x, y, z-eps) +
                            exact_solution(x, y, z+eps) +
                            -2.*exact_solution(x, y, z))/eps/eps;
 
          Real fxy;
          if (dim==1)
            {
              // In 1D, compute the rhs by differentiating the
              // exact solution twice.
              const Real pi = libMesh::pi;
              fxy = (0.25*pi*pi)*sin(.5*pi*x);
            }
          else
            {
              fxy = - (uxx + uyy + ((dim==2) ? 0. : uzz));
            }
 
          // Add the RHS contribution
          for (std::size_t i=0; i<phi.size(); i++)
            Fe(i) += JxW[qp]*fxy*phi[i][qp];
        }
 
      // Stop logging the right-hand-side computation
      perf_log.pop ("Fe");
 
      // At this point the interior element integration has
      // been completed.  However, we have not yet addressed
      // boundary conditions.  For this example we will only
      // consider simple Dirichlet boundary conditions imposed
      // via the penalty method. This is discussed at length in
      // example 3.
      {
        // Start logging the boundary condition computation.  We use a
        // macro to log everything in this scope.
        LOG_SCOPE_WITH("BCs", "", perf_log);
 
        // The following loops over the sides of the element.
        // If the element has no neighbor on a side then that
        // side MUST live on a boundary of the domain.
        for (auto side : elem->side_index_range())
          if ((elem->neighbor_ptr(side) == nullptr) ||
              (elem->neighbor_ptr(side)->subdomain_id() != elem->subdomain_id()))
            {
 
              // The penalty value.  \frac{1}{\epsilon}
              // in the discussion above.
              const Real penalty = 1.e10;
 
              // The value of the shape functions at the quadrature
              // points.
              const std::vector<std::vector<Real>> & phi_face = fe_face->get_phi();
 
              // The Jacobian * Quadrature Weight at the quadrature
              // points on the face.
              const std::vector<Real> & JxW_face = fe_face->get_JxW();
 
              // The XYZ locations (in physical space) of the
              // quadrature points on the face.  This is where
              // we will interpolate the boundary value function.
              const std::vector<Point> & qface_point = fe_face->get_xyz();
 
              // Compute the shape function values on the element
              // face.
              fe_face->reinit(elem, side);
 
              // Loop over the face quadrature points for integration.
              for (unsigned int qp=0; qp<qface.n_points(); qp++)
                {
                  // The location on the boundary of the current
                  // face quadrature point.
                  const Real xf = qface_point[qp](0);
#if LIBMESH_DIM > 1
                  const Real yf = qface_point[qp](1);
#else
                  const Real yf = 0.;
#endif
#if LIBMESH_DIM > 2
                  const Real zf = qface_point[qp](2);
#else
                  const Real zf = 0.;
#endif
 
 
                  // The boundary value.
                  const Real value = exact_solution(xf, yf, zf);
 
                  // Matrix contribution of the L2 projection.
                  for (std::size_t i=0; i<phi_face.size(); i++)
                    for (std::size_t j=0; j<phi_face.size(); j++)
                      Ke(i,j) += JxW_face[qp]*penalty*phi_face[i][qp]*phi_face[j][qp];
 
                  // Right-hand-side contribution of the L2
                  // projection.
                  for (std::size_t i=0; i<phi_face.size(); i++)
                    Fe(i) += JxW_face[qp]*penalty*value*phi_face[i][qp];
                }
            }
      }
 
 
      // The element matrix and right-hand-side are now built
      // for this element.  Add them to the global matrix and
      // right-hand-side vector.  The PetscMatrix::add_matrix()
      // and PetscVector::add_vector() members do this for us.
      // Start logging the insertion of the local (element)
      // matrix and vector into the global matrix and vector
      LOG_SCOPE_WITH("matrix insertion", "", perf_log);
 
      if (dof_indices.size())
        {
          system.matrix->add_matrix (Ke, dof_indices);
          system.rhs->add_vector    (Fe, dof_indices);
        }
 
      if (dof_indices2.size())
        {
          system.matrix->add_matrix (Ke, dof_indices2);
          system.rhs->add_vector    (Fe, dof_indices2);
        }
    }
 
  // That's it.  We don't need to do anything else to the
  // PerfLog.  When it goes out of scope (at this function return)
  // it will print its log to the screen. Pretty easy, huh?
}