//                       MFEM Example 1 - Parallel Version
//                              PUMI Modification
//
// Compile with: make ex1p
//
// Sample runs:
//    mpirun -np 8 ex1p -m ../../data/pumi/parallel/Kova/Kova100k_8.smb
//                      -p ../../data/pumi/geom/Kova.dmg -o 1 -go 2
//
// 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 parallel PUMI mesh classified on a geometric model
//               and then generate the corresponding parallel MFEM mesh. The
//               example also performs a "uniform" refinement, similar to the
//               MFEM examples, for coarse meshes. However, the refinement is
//               performed using the PUMI API.  The inputs are a Parasolid
//               model, "*.xmt_txt" and SCOREC parallel meshes "*.smb". The
//               option "-o" is used for the Finite Element order and "-go" for
//               the geometry order. Note that they can be used independently:
//               "-o 8 -go 3" solves for 8th order FE on 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 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/parallel/Kova/Kova100k_8.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 and refine the mesh if necessary. Parallel
   //    uniform refinement is performed if the total number of elements is less
   //    than 10,000.
   int dim = pumi_mesh->getDimension();
   int nEle = pumi_mesh->count(dim);
   int ref_levels = (int)floor(log(10000./nEle)/log(2.)/dim);

   if (geom_order > 1)
   {
      crv::BezierCurver bc(pumi_mesh, geom_order, 2);
      bc.run();
   }

   // Perform Uniform refinement
   if (ref_levels > 1)
   {
      auto uniInput = ma::configureUniformRefine(pumi_mesh, ref_levels);

      if (geom_order > 1)
      {
         crv::adapt(uniInput);
      }
      else
      {
         ma::adapt(uniInput);
      }
   }

   pumi_mesh->verify();

   // 5. Create the parallel MFEM mesh object from the parallel PUMI mesh.
   //    We can handle triangular and tetrahedral meshes. Note that the
   //    mesh resolution is performed on the PUMI mesh.
   ParMesh *pmesh = new ParPumiMesh(MPI_COMM_WORLD, pumi_mesh);

   // 6. Define a parallel finite element space on the parallel 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 (pmesh->GetNodes())
   {
      fec = pmesh->GetNodes()->OwnFEC();
      if (myid == 0)
      {
         cout << "Using isoparametric FEs: " << fec->Name() << endl;
      }
   }
   else
   {
      fec = new H1_FECollection(order = 1, dim);
   }
   ParFiniteElementSpace *fespace = new ParFiniteElementSpace(pmesh, fec);
   HYPRE_BigInt size = fespace->GlobalTrueVSize();
   if (myid == 0)
   {
      cout << "Number of finite element unknowns: " << size << endl;
   }

   // 7. Determine the list of true (i.e. parallel 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 (pmesh->bdr_attributes.Size())
   {
      Array<int> ess_bdr(pmesh->bdr_attributes.Max());
      ess_bdr = 1;
      fespace->GetEssentialTrueDofs(ess_bdr, ess_tdof_list);
   }

   // 8. Set up the parallel 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 fespace.
   ParLinearForm *b = new ParLinearForm(fespace);
   ConstantCoefficient one(1.0);
   b->AddDomainIntegrator(new DomainLFIntegrator(one));
   b->Assemble();

   // 9. Define the solution vector x as a parallel finite element grid function
   //    corresponding to fespace. Initialize x with initial guess of zero,
   //    which satisfies the boundary conditions.
   ParGridFunction x(fespace);
   x = 0.0;

   // 10. Set up the parallel bilinear form a(.,.) on the finite element space
   //     corresponding to the Laplacian operator -Delta, by adding the Diffusion
   //     domain integrator.
   ParBilinearForm *a = new ParBilinearForm(fespace);
   a->AddDomainIntegrator(new DiffusionIntegrator(one));

   // 11. Assemble the parallel bilinear form and the corresponding linear
   //     system, applying any necessary transformations such as: parallel
   //     assembly, eliminating boundary conditions, applying conforming
   //     constraints for non-conforming AMR, static condensation, etc.
   if (static_cond) { a->EnableStaticCondensation(); }
   a->Assemble();

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

   if (myid == 0)
   {
      cout << "Size of linear system: " << A.GetGlobalNumRows() << endl;
   }

   // 12. Define and apply a parallel PCG solver for AX=B with the BoomerAMG
   //     preconditioner from hypre.
   HypreSolver *amg = new HypreBoomerAMG(A);
   HyprePCG *pcg = new HyprePCG(A);
   pcg->SetTol(1e-12);
   pcg->SetMaxIter(200);
   pcg->SetPrintLevel(2);
   pcg->SetPreconditioner(*amg);
   pcg->Mult(B, X);

   // 13. Recover the parallel grid function corresponding to X. This is the
   //     local finite element solution on each processor.
   a->RecoverFEMSolution(X, *b, x);

   // 14. Save the refined mesh and the solution in parallel. This output can
   //     be viewed later using GLVis: "glvis -np <np> -m mesh -g sol".
   {
      ostringstream mesh_name, sol_name;
      mesh_name << "mesh." << setfill('0') << setw(6) << myid;
      sol_name << "sol." << setfill('0') << setw(6) << myid;

      ofstream mesh_ofs(mesh_name.str().c_str());
      mesh_ofs.precision(8);
      pmesh->Print(mesh_ofs);

      ofstream sol_ofs(sol_name.str().c_str());
      sol_ofs.precision(8);
      x.Save(sol_ofs);
   }

   // 15. Send the solution by socket to a GLVis server.
   if (visualization)
   {
      char vishost[] = "localhost";
      int  visport   = 19916;
      socketstream sol_sock(vishost, visport);
      sol_sock << "parallel " << num_procs << " " << myid << "\n";
      sol_sock.precision(8);
      sol_sock << "solution\n" << *pmesh << x << flush;
   }

   // 16. Free the used memory.
   delete pcg;
   delete amg;
   delete a;
   delete b;
   delete fespace;
   if (order > 0) { delete fec; }
   delete pmesh;

   pumi_mesh->destroyNative();
   apf::destroyMesh(pumi_mesh);
   PCU_Comm_Free();

#ifdef MFEM_USE_SIMMETRIX
   gmi_sim_stop();
   Sim_unregisterAllKeys();
#endif

   return 0;
}