//                                MFEM Example 1
//                              PUMI Modification
//
// Compile with: make ex1
//
// Sample runs:
//    ex1 -m ../../data/pumi/serial/Kova.smb -p ../../data/pumi/geom/Kova.dmg
//
// Note:         Example models + meshes for the PUMI examples can be downloaded
//               from github.com/mfem/data/pumi. After downloading we recommend
//               creating a symbolic link to the above directory in ../../data.
//
// Description:  This example code demonstrates the use of MFEM to define a
//               simple finite element discretization of the Laplace problem
//               -Delta u = 1 with homogeneous Dirichlet boundary conditions.
//               Specifically, we discretize using a FE space of the specified
//               order, or if order < 1 using an isoparametric/isogeometric
//               space (i.e. quadratic for quadratic curvilinear mesh, NURBS for
//               NURBS mesh, etc.)
//
//               The example highlights the use of mesh refinement, finite
//               element grid functions, as well as linear and bilinear forms
//               corresponding to the left-hand side and right-hand side of the
//               discrete linear system. We also cover the explicit elimination
//               of essential boundary conditions, static condensation, and the
//               optional connection to the GLVis tool for visualization.
//
//               This PUMI modification demonstrates how PUMI's API can be used
//               to load a PUMI mesh classified on a geometric model and then
//               convert it to the MFEM mesh format. The inputs are a Parasolid
//               model, "*.xmt_txt" and a SCOREC mesh "*.smb". The option "-o"
//               is used for the Finite Element order and "-go" is used for the
//               geometry order. Note that they can be used independently, i.e.
//               "-o 8 -go 3" solves for 8th order FE on a third order geometry.
//
// NOTE:         Model/Mesh files for this example are in the (large) data file
//               repository of MFEM here https://github.com/mfem/data under the
//               folder named "pumi", which consists of the following sub-folders:
//               a) geom -->  model files
//               b) parallel --> parallel pumi mesh files
//               c) serial --> serial pumi mesh files

#include "mfem.hpp"
#include <fstream>
#include <iostream>

#ifdef MFEM_USE_SIMMETRIX
#include <SimUtil.h>
#include <gmi_sim.h>
#endif
#include <apfMDS.h>
#include <gmi_null.h>
#include <PCU.h>
#include <apfConvert.h>
#include <gmi_mesh.h>
#include <crv.h>

#ifndef MFEM_USE_PUMI
#error This example requires that MFEM is built with MFEM_USE_PUMI=YES
#endif

using namespace std;
using namespace mfem;

int main(int argc, char *argv[])
{
   // 1. Initialize MPI (required by PUMI) and HYPRE.
   Mpi::Init(argc, argv);
   int num_procs = Mpi::WorldSize();
   int myid = Mpi::WorldRank();
   Hypre::Init();

   // 2. Parse command-line options.
   const char *mesh_file = "../../data/pumi/serial/Kova.smb";
#ifdef MFEM_USE_SIMMETRIX
   const char *model_file = "../../data/pumi/geom/Kova.x_t";
#else
   const char *model_file = "../../data/pumi/geom/Kova.dmg";
#endif
   int order = 1;
   bool static_cond = false;
   bool visualization = 1;
   int geom_order = 1;

   OptionsParser args(argc, argv);
   args.AddOption(&mesh_file, "-m", "--mesh",
                  "Mesh file to use.");
   args.AddOption(&order, "-o", "--order",
                  "Finite element order (polynomial degree) or -1 for"
                  " isoparametric space.");
   args.AddOption(&static_cond, "-sc", "--static-condensation", "-no-sc",
                  "--no-static-condensation", "Enable static condensation.");
   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
                  "--no-visualization",
                  "Enable or disable GLVis visualization.");
   args.AddOption(&model_file, "-p", "--parasolid",
                  "Parasolid model to use.");
   args.AddOption(&geom_order, "-go", "--geometry_order",
                  "Geometric order of the model");
   args.Parse();
   if (!args.Good())
   {
      if (myid == 0)
      {
         args.PrintUsage(cout);
      }
      return 1;
   }
   if (myid == 0)
   {
      args.PrintOptions(cout);
   }

   // 3. Read the SCOREC Mesh.
   PCU_Comm_Init();
#ifdef MFEM_USE_SIMMETRIX
   Sim_readLicenseFile(0);
   gmi_sim_start();
   gmi_register_sim();
#endif
   gmi_register_mesh();

   apf::Mesh2* pumi_mesh;
   pumi_mesh = apf::loadMdsMesh(model_file, mesh_file);

   // 4. Increase the geometry order if necessary.
   if (geom_order > 1)
   {
      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
      bc.run();
   }

   pumi_mesh->verify();

   // 5. Create the MFEM mesh object from the PUMI mesh. We can handle
   //    triangular and tetrahedral meshes. Other inputs are the same as the
   //    MFEM default constructor.
   Mesh *mesh = new PumiMesh(pumi_mesh, 1, 1);
   int dim = mesh->Dimension();

   // 6. Refine the mesh to increase the resolution. In this example we do
   //    'ref_levels' of uniform refinement. We choose 'ref_levels' to be the
   //    largest number that gives a final mesh with no more than 50,000
   //    elements.
   {
      int ref_levels =
         (int)floor(log(50000./mesh->GetNE())/log(2.)/dim);
      for (int l = 0; l < ref_levels; l++)
      {
         mesh->UniformRefinement();
      }
   }

   // 7. Define a finite element space on the mesh. Here we use continuous
   //    Lagrange finite elements of the specified order. If order < 1, we
   //    instead use an isoparametric/isogeometric space.
   FiniteElementCollection *fec;
   if (order > 0)
   {
      fec = new H1_FECollection(order, dim);
   }
   else if (mesh->GetNodes())
   {
      fec = mesh->GetNodes()->OwnFEC();
      cout << "Using isoparametric FEs: " << fec->Name() << endl;
   }
   else
   {
      fec = new H1_FECollection(order = 1, dim);
   }
   FiniteElementSpace *fespace = new FiniteElementSpace(mesh, fec);
   cout << "Number of finite element unknowns: "
        << fespace->GetTrueVSize() << endl;

   // 8. Determine the list of true (i.e. conforming) essential boundary dofs.
   //    In this example, the boundary conditions are defined by marking all
   //    the boundary attributes from the mesh as essential (Dirichlet) and
   //    converting them to a list of true dofs.
   Array<int> ess_tdof_list;
   if (mesh->bdr_attributes.Size())
   {
      Array<int> ess_bdr(mesh->bdr_attributes.Max());
      ess_bdr = 1;
      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
   }

   // 9. Set up the linear form b(.) which corresponds to the right-hand side of
   //    the FEM linear system, which in this case is (1,phi_i) where phi_i are
   //    the basis functions in the finite element fespace.
   LinearForm *b = new LinearForm(fespace);
   ConstantCoefficient one(1.0);
   b->AddDomainIntegrator(new DomainLFIntegrator(one));
   b->Assemble();

   // 10. Define the solution vector x as a finite element grid function
   //     corresponding to fespace. Initialize x with initial guess of zero,
   //     which satisfies the boundary conditions.
   GridFunction x(fespace);
   x = 0.0;

   // 11. Set up the bilinear form a(.,.) on the finite element space
   //     corresponding to the Laplacian operator -Delta, by adding the
   //     Diffusion domain integrator.
   BilinearForm *a = new BilinearForm(fespace);
   a->AddDomainIntegrator(new DiffusionIntegrator(one));

   // 12. Assemble the bilinear form and the corresponding linear system,
   //     applying any necessary transformations such as: eliminating boundary
   //     conditions, applying conforming constraints for non-conforming AMR,
   //     static condensation, etc.
   if (static_cond) { a->EnableStaticCondensation(); }
   a->Assemble();

   SparseMatrix A;
   Vector B, X;
   a->FormLinearSystem(ess_tdof_list, x, *b, A, X, B);

   cout << "Size of linear system: " << A.Height() << endl;

#ifndef MFEM_USE_SUITESPARSE
   // 13. Define a simple symmetric Gauss-Seidel preconditioner and use it to
   //     solve the system A X = B with PCG.
   GSSmoother M(A);
   PCG(A, M, B, X, 1, 200, 1e-12, 0.0);
#else
   // 13. If MFEM was compiled with SuiteSparse, use UMFPACK to solve the system.
   UMFPackSolver umf_solver;
   umf_solver.Control[UMFPACK_ORDERING] = UMFPACK_ORDERING_METIS;
   umf_solver.SetOperator(A);
   umf_solver.Mult(B, X);
#endif

   // 14. Recover the solution as a finite element grid function.
   a->RecoverFEMSolution(X, *b, x);

   // 15. Save the refined mesh and the solution. This output can be viewed later
   //     using GLVis: "glvis -m refined.mesh -g sol.gf".
   ofstream mesh_ofs("refined.mesh");
   mesh_ofs.precision(8);
   mesh->Print(mesh_ofs);
   ofstream sol_ofs("sol.gf");
   sol_ofs.precision(8);
   x.Save(sol_ofs);

   // 16. Send the solution by socket to a GLVis server.
   if (visualization)
   {
      char vishost[] = "localhost";
      int  visport   = 19916;
      socketstream sol_sock(vishost, visport);
      sol_sock.precision(8);
      sol_sock << "solution\n" << *mesh << x << flush;
   }

   // 17. Free the used memory.
   delete a;
   delete b;
   delete fespace;
   if (order > 0) { delete fec; }
   delete mesh;

   pumi_mesh->destroyNative();
   apf::destroyMesh(pumi_mesh);
   PCU_Comm_Free();
#ifdef MFEM_USE_SIMMETRIX
   gmi_sim_stop();
   Sim_unregisterAllKeys();
#endif

   return 0;
}