Merge branch 'master' into linearform-op-dev

examples/ex1p_vo.cpp

@@ -0,0 +1,348 @@
+//                       MFEM Example 1 - Parallel Version
+//
+// Compile with: make ex1p
+//
+// Sample runs:  mpirun -np 4 ex1p -m ../data/square-disc.mesh
+//               mpirun -np 4 ex1p -m ../data/star.mesh
+//               mpirun -np 4 ex1p -m ../data/star-mixed.mesh
+//               mpirun -np 4 ex1p -m ../data/escher.mesh
+//               mpirun -np 4 ex1p -m ../data/fichera.mesh
+//               mpirun -np 4 ex1p -m ../data/fichera-mixed.mesh
+//               mpirun -np 4 ex1p -m ../data/toroid-wedge.mesh
+//               mpirun -np 4 ex1p -m ../data/octahedron.mesh -o 1
+//               mpirun -np 4 ex1p -m ../data/periodic-annulus-sector.msh
+//               mpirun -np 4 ex1p -m ../data/periodic-torus-sector.msh
+//               mpirun -np 4 ex1p -m ../data/square-disc-p2.vtk -o 2
+//               mpirun -np 4 ex1p -m ../data/square-disc-p3.mesh -o 3
+//               mpirun -np 4 ex1p -m ../data/square-disc-nurbs.mesh -o -1
+//               mpirun -np 4 ex1p -m ../data/star-mixed-p2.mesh -o 2
+//               mpirun -np 4 ex1p -m ../data/disc-nurbs.mesh -o -1
+//               mpirun -np 4 ex1p -m ../data/pipe-nurbs.mesh -o -1
+//               mpirun -np 4 ex1p -m ../data/ball-nurbs.mesh -o 2
+//               mpirun -np 4 ex1p -m ../data/fichera-mixed-p2.mesh -o 2
+//               mpirun -np 4 ex1p -m ../data/star-surf.mesh
+//               mpirun -np 4 ex1p -m ../data/square-disc-surf.mesh
+//               mpirun -np 4 ex1p -m ../data/inline-segment.mesh
+//               mpirun -np 4 ex1p -m ../data/amr-quad.mesh
+//               mpirun -np 4 ex1p -m ../data/amr-hex.mesh
+//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh
+//               mpirun -np 4 ex1p -m ../data/mobius-strip.mesh -o -1 -sc
+//
+// Device sample runs:
+//               mpirun -np 4 ex1p -pa -d cuda
+//               mpirun -np 4 ex1p -pa -d occa-cuda
+//               mpirun -np 4 ex1p -pa -d raja-omp
+//               mpirun -np 4 ex1p -pa -d ceed-cpu
+//               mpirun -np 4 ex1p -pa -d ceed-cpu -o 4 -a
+//             * mpirun -np 4 ex1p -pa -d ceed-cuda
+//             * mpirun -np 4 ex1p -pa -d ceed-hip
+//               mpirun -np 4 ex1p -pa -d ceed-cuda:/gpu/cuda/shared
+//               mpirun -np 4 ex1p -m ../data/beam-tet.mesh -pa -d ceed-cpu
+//
+// 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.
+
+#include "mfem.hpp"
+#include "linalg/vector_operator.hpp"
+#include <fstream>
+#include <iostream>
+
+using namespace std;
+using namespace mfem;
+
+class CoordCoefficient : public Coefficient
+{
+private:
+   int d;
+
+   mutable Vector x;
+
+public:
+   CoordCoefficient(int d) : d(d), x(3) {}
+
+   double Eval(ElementTransformation &T, const IntegrationPoint &ip)
+   {
+      if (d == -1) { return 1.0; }
+
+      T.Transform(ip, x);
+      return x[d];
+   }
+};
+
+int main(int argc, char *argv[])
+{
+   // 1. Initialize MPI.
+   MPI_Session mpi;
+   int num_procs = mpi.WorldSize();
+   int myid = mpi.WorldRank();
+
+   // 2. Parse command-line options.
+   const char *mesh_file = "../data/star.mesh";
+   int order = 1;
+   bool static_cond = false;
+   bool pa = false;
+   const char *device_config = "cpu";
+   bool visualization = true;
+   bool algebraic_ceed = false;
+
+   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(&pa, "-pa", "--partial-assembly", "-no-pa",
+                  "--no-partial-assembly", "Enable Partial Assembly.");
+   args.AddOption(&device_config, "-d", "--device",
+                  "Device configuration string, see Device::Configure().");
+#ifdef MFEM_USE_CEED
+   args.AddOption(&algebraic_ceed, "-a", "--algebraic",
+                  "-no-a", "--no-algebraic",
+                  "Use algebraic Ceed solver");
+#endif
+   args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
+                  "--no-visualization",
+                  "Enable or disable GLVis visualization.");
+   args.Parse();
+   if (!args.Good())
+   {
+      if (myid == 0)
+      {
+         args.PrintUsage(cout);
+      }
+      return 1;
+   }
+   if (myid == 0)
+   {
+      args.PrintOptions(cout);
+   }
+
+   // 3. Enable hardware devices such as GPUs, and programming models such as
+   //    CUDA, OCCA, RAJA and OpenMP based on command line options.
+   Device device(device_config);
+   if (myid == 0) { device.Print(); }
+
+   // 4. Read the (serial) mesh from the given mesh file on all processors.  We
+   //    can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
+   //    and volume meshes with the same code.
+   Mesh mesh(mesh_file, 1, 1);
+   int dim = mesh.Dimension();
+
+   // 5. Refine the serial mesh on all processors 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 10,000 elements.
+   {
+      int ref_levels =
+         (int)floor(log(10000./mesh.GetNE())/log(2.)/dim);
+      for (int l = 0; l < ref_levels; l++)
+      {
+         mesh.UniformRefinement();
+      }
+   }
+
+   // 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
+   //    this mesh further in parallel to increase the resolution. Once the
+   //    parallel mesh is defined, the serial mesh can be deleted.
+   ParMesh pmesh(MPI_COMM_WORLD, mesh);
+   mesh.Clear();
+   {
+      int par_ref_levels = 2;
+      for (int l = 0; l < par_ref_levels; l++)
+      {
+         pmesh.UniformRefinement();
+      }
+   }
+
+   // 7. 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;
+   bool delete_fec;
+   if (order > 0)
+   {
+      fec = new H1_FECollection(order, dim);
+      delete_fec = true;
+   }
+   else if (pmesh.GetNodes())
+   {
+      fec = pmesh.GetNodes()->OwnFEC();
+      delete_fec = false;
+      if (myid == 0)
+      {
+         cout << "Using isoparametric FEs: " << fec->Name() << endl;
+      }
+   }
+   else
+   {
+      fec = new H1_FECollection(order = 1, dim);
+      delete_fec = true;
+   }
+   ParFiniteElementSpace fespace(&pmesh, fec);
+   HYPRE_BigInt size = fespace.GlobalTrueVSize();
+   if (myid == 0)
+   {
+      cout << "Number of finite element unknowns: " << size << endl;
+   }
+
+   // 8. 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);
+   }
+
+   // 9. 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(&fespace);
+   ConstantCoefficient one(1.0);
+   b.AddDomainIntegrator(new DomainLFIntegrator(one));
+   b.Assemble();
+
+   // 10. 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;
+
+   ParVectorOperator vo(MPI_COMM_WORLD, myid, fespace.TrueVSize(), dim + 1);
+   {
+      for (int d=0; d <= dim; d++)
+      {
+         ParLinearForm bd(&fespace);
+         CoordCoefficient dCoef(d - 1);
+         bd.AddDomainIntegrator(new DomainLFIntegrator(dCoef));
+         bd.Assemble();
+
+         Vector *dv = new Vector(fespace.TrueVSize());
+         bd.ParallelAssemble(*dv);
+
+         vo.SetVector(d, dv, 1.0, true);
+      }
+   }
+
+   // 11. 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(&fespace);
+   if (pa) { a.SetAssemblyLevel(AssemblyLevel::PARTIAL); }
+   a.AddDomainIntegrator(new DiffusionIntegrator(one));
+
+   // 12. 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();
+
+   OperatorPtr A;
+   Vector B, X;
+   a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
+
+   // 13. Solve the linear system A X = B.
+   //     * With full assembly, use the BoomerAMG preconditioner from hypre.
+   //     * With partial assembly, use Jacobi smoothing, for now.
+   Solver *prec = NULL;
+   if (pa)
+   {
+      if (UsesTensorBasis(fespace))
+      {
+         if (algebraic_ceed)
+         {
+            prec = new ceed::AlgebraicSolver(a, ess_tdof_list);
+         }
+         else
+         {
+            prec = new OperatorJacobiSmoother(a, ess_tdof_list);
+         }
+      }
+   }
+   else
+   {
+      prec = new HypreBoomerAMG;
+   }
+   CGSolver cg(MPI_COMM_WORLD);
+   cg.SetRelTol(1e-12);
+   cg.SetMaxIter(2000);
+   cg.SetPrintLevel(1);
+   if (prec) { cg.SetPreconditioner(*prec); }
+   cg.SetOperator(*A);
+   cg.Mult(B, X);
+   delete prec;
+
+   {
+      Vector com((myid == 0) ? dim+1 : 0);
+      vo.Mult(X, com);
+
+      if (myid == 0)
+      {
+         cout << "Mass: " << com[0] << endl;
+         cout << "Center of mass: (";
+         for (int d=1; d<=dim; d++)
+         {
+            cout << com[d]/com[0];
+            if (d < dim) { cout << " ,"; }
+         }
+         cout << ")" << endl;
+      }
+   }
+
+   // 14. Recover the parallel grid function corresponding to X. This is the
+   //     local finite element solution on each processor.
+   a.RecoverFEMSolution(X, b, x);
+
+   // 15. 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);
+   }
+
+   // 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 << "parallel " << num_procs << " " << myid << "\n";
+      sol_sock.precision(8);
+      sol_sock << "solution\n" << pmesh << x << flush;
+   }
+
+   // 17. Free the used memory.
+   if (delete_fec)
+   {
+      delete fec;
+   }
+
+   return 0;
+}

linalg/vector_operator.cpp

@@ -0,0 +1,80 @@
+// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#include "vector_operator.hpp"
+
+namespace mfem
+{
+
+#ifdef MFEM_USE_MPI
+
+ParVectorOperator::ParVectorOperator(MPI_Comm comm,
+                                     int myid,
+                                     int local_vec_size,
+                                     int num_vecs)
+   : Operator((myid == 0) ? num_vecs : 0, local_vec_size),
+     comm(comm),
+     myid(myid),
+     vecs(num_vecs),
+     coefs(num_vecs),
+     owns(num_vecs)
+{
+   vecs = NULL;
+   coefs = 1.0;
+   owns = false;
+}
+
+ParVectorOperator::~ParVectorOperator()
+{
+   for (int i=0; i < vecs.Size(); i++)
+   {
+      if (owns[i]) { delete vecs[i]; }
+      vecs[i] = NULL;
+   }
+}
+
+void ParVectorOperator::SetVector(int idx, Vector *vec,
+                                  double c, bool own_vec)
+{
+   MFEM_VERIFY(idx >= 0 && idx < vecs.Size(),
+               "ParVectorOperator: Index out of range");
+
+   vecs[idx] = vec;
+   coefs[idx] = c;
+   owns[idx] = own_vec;
+}
+
+void ParVectorOperator::Mult(const Vector &x, Vector &y) const
+{
+   for (int i=0; i<vecs.Size(); i++)
+   {
+      double vo = coefs[i] * (*vecs[i] * x);
+      double vi = 0.0;
+      MPI_Reduce(&vo, &vi, 1, MPI_DOUBLE, MPI_SUM, 0, comm);
+      if (myid == 0) { y[i] = vi; }
+   }
+}
+
+/// Action of the transpose operator: `y=A^t(x)`.
+void ParVectorOperator::MultTranspose(const Vector &x, Vector &y) const
+{
+   y = 0.0;
+   for (int i=0; i<vecs.Size(); i++)
+   {
+      double xi = (myid == 0) ? x[i] : 0.0;
+      MPI_Bcast(&xi, 1, MPI_DOUBLE, 0, comm);
+      y.Add(xi * coefs[i], *vecs[i]);
+   }
+}
+
+}
+
+#endif // MFEM_USE_MPI

linalg/vector_operator.hpp

@@ -0,0 +1,55 @@
+// Copyright (c) 2010-2021, Lawrence Livermore National Security, LLC. Produced
+// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
+// LICENSE and NOTICE for details. LLNL-CODE-806117.
+//
+// This file is part of the MFEM library. For more information and source code
+// availability visit https://mfem.org.
+//
+// MFEM is free software; you can redistribute it and/or modify it under the
+// terms of the BSD-3 license. We welcome feedback and contributions, see file
+// CONTRIBUTING.md for details.
+
+#ifndef MFEM_VECTOR_OPERATOR
+#define MFEM_VECTOR_OPERATOR
+
+#include "operator.hpp"
+#include "vector.hpp"
+
+namespace mfem
+{
+
+#ifdef MFEM_USE_MPI
+
+class ParVectorOperator : public Operator
+{
+private:
+   MPI_Comm comm;
+   int myid;
+
+   Array<Vector*> vecs;
+   Array<double> coefs;
+   Array<bool> owns;
+
+public:
+   ParVectorOperator(MPI_Comm comm,
+                     int myid,
+                     int local_vec_size,
+                     int num_vecs);
+
+   ~ParVectorOperator();
+
+   void SetVector(int idx, Vector *vec,
+                  double c = 1.0, bool own_vec = false);
+
+   /// Operator application: `y=A(x)`.
+   void Mult(const Vector &x, Vector &y) const;
+
+   /// Action of the transpose operator: `y=A^t(x)`.
+   void MultTranspose(const Vector &x, Vector &y) const;
+};
+
+#endif // MFEM_USE_MPI
+
+} // namespace mfem
+
+#endif // MFEM_VECTOR_OPERATOR