def run_test(): #meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh')) meshfile = "../data/amr-quad.mesh" mesh = mfem.Mesh(meshfile, 1, 1) dim = mesh.Dimension() sdim = mesh.SpaceDimension() fec = mfem.H1_FECollection(1, dim) fespace = mfem.FiniteElementSpace(mesh, fec, 1) print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize())) c = mfem.ConstantCoefficient(1.0) gf = mfem.GridFunction(fespace) gf.ProjectCoefficient(c) print("write mesh to STDOUT") mesh.Print(mfem.STDOUT) print("creat VTK file to file") mesh.PrintVTK('mesh.vtk', 1) print("creat VTK to STDOUT") mesh.PrintVTK(mfem.STDOUT, 1) print("save GridFunction to file") gf.Save('out_test_gridfunc.gf') gf.SaveVTK(mfem.wFILE('out_test_gridfunc1.vtk'), 'data', 1) print("save GridFunction to file in VTK format") gf.SaveVTK('out_test_gridfunc2.vtk', 'data', 1) print("Gridfunction to STDOUT") gf.Save(mfem.STDOUT) o = io.StringIO() count = gf.Save(o) count2 = gf.SaveVTK(o, 'data', 1) print("length of data ", count, count2) print('result: ', o.getvalue())
def run_test(): meshfile = expanduser(join(mfem_path, 'data', 'beam-tri.mesh')) mesh = mfem.Mesh(meshfile, 1, 1) fec = mfem.H1_FECollection(1, 1) fespace = mfem.FiniteElementSpace(mesh, fec) fespace.Save()
def run_test(): #meshfile =expanduser(join(mfem_path, 'data', 'beam-tri.mesh')) meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh')) mesh = mfem.Mesh(meshfile, 1, 1) dim = mesh.Dimension() sdim = mesh.SpaceDimension() fec = mfem.H1_FECollection(1, dim) fespace = mfem.FiniteElementSpace(mesh, fec, 1) print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize())) c = mfem.ConstantCoefficient(1.0) gf = mfem.GridFunction(fespace) gf.ProjectCoefficient(c) gf.Save('out_test_gridfunc.gf')
mesh.SetCurvature(2) mesh.EnsureNCMesh() for l in range(ref_levels): mesh.UniformRefinement() # 5. Define a parallel mesh by partitioning the serial mesh. Once the # parallel mesh is defined, the serial mesh can be deleted. pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) del mesh ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max()) ess_bdr.Assign(1) # 6. Define a finite element space on the mesh. The polynomial order is one # (linear) by default, but this can be changed on the command line. fec = mfem.H1_FECollection(order, dim) fespace = mfem.ParFiniteElementSpace(pmesh, fec) # 7. As in Example 1p, we set up bilinear and linear forms corresponding to # the Laplace problem -\Delta u = 1. We don't assemble the discrete # problem yet, this will be done in the inner loop. a = mfem.ParBilinearForm(fespace) b = mfem.ParLinearForm(fespace) one = mfem.ConstantCoefficient(1.0) bdr = BdrCoefficient() rhs = RhsCoefficient() integ = mfem.DiffusionIntegrator(one) a.AddDomainIntegrator(integ) b.AddDomainIntegrator(mfem.DomainLFIntegrator(rhs))
# degree may depend on the spatial dimension of the domain, the type of # the mesh and the trial space order. trial_order = order trace_order = order - 1 test_order = order # reduced order, full order is (order + dim - 1) if (dim == 2 and (order % 2 == 0 or (pmesh.MeshGenerator() & 2 and order > 1))): test_order = test_order + 1 if (test_order < trial_order): if myid == 0: print( "Warning, test space not enriched enough to handle primal trial space" ) x0_fec = mfem.H1_FECollection(trial_order, dim) xhat_fec = mfem.RT_Trace_FECollection(trace_order, dim) test_fec = mfem.L2_FECollection(test_order, dim) x0_space = mfem.ParFiniteElementSpace(pmesh, x0_fec) xhat_space = mfem.ParFiniteElementSpace(pmesh, xhat_fec) test_space = mfem.ParFiniteElementSpace(pmesh, test_fec) glob_true_s0 = x0_space.GlobalTrueVSize() glob_true_s1 = xhat_space.GlobalTrueVSize() glob_true_s_test = test_space.GlobalTrueVSize() if myid == 0: print('\n'.join([ "nNumber of Unknowns", " Trial space, X0 : " + str(glob_true_s0) + " (order " + str(trial_order) + ")",
mesh.AddTriangle(tri_e[j], j + 1) mesh.FinalizeTriMesh(1, 1, True) else: quad_v = [[-1, -1, -1], [+1, -1, -1], [+1, +1, -1], [-1, +1, -1], [-1, -1, +1], [+1, -1, +1], [+1, +1, +1], [-1, +1, +1]] quad_e = [[3, 2, 1, 0], [0, 1, 5, 4], [1, 2, 6, 5], [2, 3, 7, 6], [3, 0, 4, 7], [4, 5, 6, 7]] for j in range(Nvert): mesh.AddVertex(quad_v[j]) for j in range(Nelem): mesh.AddQuad(quad_e[j], j + 1) mesh.FinalizeQuadMesh(1, 1, True) # Set the space for the high-order mesh nodes. fec = mfem.H1_FECollection(order, mesh.Dimension()) nodal_fes = mfem.FiniteElementSpace(mesh, fec, mesh.SpaceDimension()) mesh.SetNodalFESpace(nodal_fes) def SnapNodes(mesh): nodes = mesh.GetNodes() node = mfem.Vector(mesh.SpaceDimension()) for i in np.arange(nodes.FESpace().GetNDofs()): for d in np.arange(mesh.SpaceDimension()): node[d] = nodes[nodes.FESpace().DofToVDof(i, d)] node /= node.Norml2() for d in range(mesh.SpaceDimension()): nodes[nodes.FESpace().DofToVDof(i, d)] = node[d]
# we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is # a command-line parameter. for lev in range(ser_ref_levels): 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. pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) del mesh for x in range(par_ref_levels): pmesh.UniformRefinement() # 7. Define the vector finite element space representing the current and the # initial temperature, u_ref. fe_coll = mfem.H1_FECollection(order, dim) fespace = mfem.ParFiniteElementSpace(pmesh, fe_coll) fe_size = fespace.GlobalTrueVSize() if myid == 0: print("Number of temperature unknowns: " + str(fe_size)) u_gf = mfem.ParGridFunction(fespace) # 8. Set the initial conditions for u. All boundaries are considered # natural. u_0 = InitialTemperature() u_gf.ProjectCoefficient(u_0) u = mfem.Vector() u_gf.GetTrueDofs(u) # 9. Initialize the conduction operator and the visualization.
def run(order = 1, static_cond = False, meshfile = def_meshfile, visualization = False, use_strumpack = False): mesh = mfem.Mesh(meshfile, 1,1) dim = mesh.Dimension() ref_levels = int(np.floor(np.log(10000./mesh.GetNE())/np.log(2.)/dim)) for x in range(ref_levels): mesh.UniformRefinement(); mesh.ReorientTetMesh(); pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) del mesh par_ref_levels = 2 for l in range(par_ref_levels): pmesh.UniformRefinement(); if order > 0: fec = mfem.H1_FECollection(order, dim) elif mesh.GetNodes(): fec = mesh.GetNodes().OwnFEC() print( "Using isoparametric FEs: " + str(fec.Name())); else: order = 1 fec = mfem.H1_FECollection(order, dim) fespace =mfem.ParFiniteElementSpace(pmesh, fec) fe_size = fespace.GlobalTrueVSize() if (myid == 0): print('Number of finite element unknowns: '+ str(fe_size)) ess_tdof_list = mfem.intArray() if pmesh.bdr_attributes.Size()>0: ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max()) ess_bdr.Assign(1) fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) # the basis functions in the finite element fespace. b = mfem.ParLinearForm(fespace) one = mfem.ConstantCoefficient(1.0) b.AddDomainIntegrator(mfem.DomainLFIntegrator(one)) b.Assemble(); x = mfem.ParGridFunction(fespace); x.Assign(0.0) a = mfem.ParBilinearForm(fespace); a.AddDomainIntegrator(mfem.DiffusionIntegrator(one)) if static_cond: a.EnableStaticCondensation() a.Assemble(); A = mfem.HypreParMatrix() B = mfem.Vector() X = mfem.Vector() a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) if (myid == 0): print("Size of linear system: " + str(x.Size())) print("Size of linear system: " + str(A.GetGlobalNumRows())) if use_strumpack: import mfem.par.strumpack as strmpk Arow = strmpk.STRUMPACKRowLocMatrix(A) args = ["--sp_hss_min_sep_size", "128", "--sp_enable_hss"] strumpack = strmpk.STRUMPACKSolver(args, MPI.COMM_WORLD) strumpack.SetPrintFactorStatistics(True) strumpack.SetPrintSolveStatistics(False) strumpack.SetKrylovSolver(strmpk.KrylovSolver_DIRECT); strumpack.SetReorderingStrategy(strmpk.ReorderingStrategy_METIS) strumpack.SetMC64Job(strmpk.MC64Job_NONE) # strumpack.SetSymmetricPattern(True) strumpack.SetOperator(Arow) strumpack.SetFromCommandLine() strumpack.Mult(B, X); else: amg = mfem.HypreBoomerAMG(A) cg = mfem.CGSolver(MPI.COMM_WORLD) cg.SetRelTol(1e-12) cg.SetMaxIter(200) cg.SetPrintLevel(1) cg.SetPreconditioner(amg) cg.SetOperator(A) cg.Mult(B, X); a.RecoverFEMSolution(X, b, x) smyid = '{:0>6d}'.format(myid) mesh_name = "mesh."+smyid sol_name = "sol."+smyid pmesh.Print(mesh_name, 8) x.Save(sol_name, 8)
def ex19_main(args): ser_ref_levels = args.refine_serial par_ref_levels = args.refine_parallel order = args.order visualization = args.visualization mu = args.shear_modulus newton_rel_tol = args.relative_tolerance newton_abs_tol = args.absolute_tolerance newton_iter = args.newton_iterations if myid == 0: parser.print_options(args) meshfile = expanduser(join(path, 'data', args.mesh)) mesh = mfem.Mesh(meshfile, 1, 1) dim = mesh.Dimension() for lev in range(ser_ref_levels): mesh.UniformRefinement() pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) del mesh for lev in range(par_ref_levels): pmesh.UniformRefinement() # 4. Define the shear modulus for the incompressible Neo-Hookean material c_mu = mfem.ConstantCoefficient(mu) # 5. Define the finite element spaces for displacement and pressure # (Taylor-Hood elements). By default, the displacement (u/x) is a second # order vector field, while the pressure (p) is a linear scalar function. quad_coll = mfem.H1_FECollection(order, dim) lin_coll = mfem.H1_FECollection(order - 1, dim) R_space = mfem.ParFiniteElementSpace(pmesh, quad_coll, dim, mfem.Ordering.byVDIM) W_space = mfem.ParFiniteElementSpace(pmesh, lin_coll) spaces = [R_space, W_space] glob_R_size = R_space.GlobalTrueVSize() glob_W_size = W_space.GlobalTrueVSize() # 6. Define the Dirichlet conditions (set to boundary attribute 1 and 2) ess_bdr_u = mfem.intArray(R_space.GetMesh().bdr_attributes.Max()) ess_bdr_p = mfem.intArray(W_space.GetMesh().bdr_attributes.Max()) ess_bdr_u.Assign(0) ess_bdr_u[0] = 1 ess_bdr_u[1] = 1 ess_bdr_p.Assign(0) ess_bdr = [ess_bdr_u, ess_bdr_p] if myid == 0: print("***********************************************************") print("dim(u) = " + str(glob_R_size)) print("dim(p) = " + str(glob_W_size)) print("dim(u+p) = " + str(glob_R_size + glob_W_size)) print("***********************************************************") block_offsets = intArray([0, R_space.TrueVSize(), W_space.TrueVSize()]) block_offsets.PartialSum() xp = mfem.BlockVector(block_offsets) # 9. Define grid functions for the current configuration, reference # configuration, final deformation, and pressure x_gf = mfem.ParGridFunction(R_space) x_ref = mfem.ParGridFunction(R_space) x_def = mfem.ParGridFunction(R_space) p_gf = mfem.ParGridFunction(W_space) #x_gf.MakeRef(R_space, xp.GetBlock(0), 0) #p_gf.MakeRef(W_space, xp.GetBlock(1), 0) deform = InitialDeformation(dim) refconfig = ReferenceConfiguration(dim) x_gf.ProjectCoefficient(deform) x_ref.ProjectCoefficient(refconfig) p_gf.Assign(0.0) # 12. Set up the block solution vectors x_gf.GetTrueDofs(xp.GetBlock(0)) p_gf.GetTrueDofs(xp.GetBlock(1)) # 13. Initialize the incompressible neo-Hookean operator oper = RubberOperator(spaces, ess_bdr, block_offsets, newton_rel_tol, newton_abs_tol, newton_iter, mu) # 14. Solve the Newton system oper.Solve(xp) # 15. Distribute the shared degrees of freedom x_gf.Distribute(xp.GetBlock(0)) p_gf.Distribute(xp.GetBlock(1)) # 16. Compute the final deformation mfem.subtract_vector(x_gf, x_ref, x_def) # 17. Visualize the results if requested if (visualization): vis_u = mfem.socketstream("localhost", 19916) visualize(vis_u, pmesh, x_gf, x_def, "Deformation", True) MPI.COMM_WORLD.Barrier() vis_p = mfem.socketstream("localhost", 19916) visualize(vis_p, pmesh, x_gf, p_gf, "Deformation", True) # 14. Save the displaced mesh, the final deformation, and the pressure nodes = x_gf owns_nodes = 0 nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes) smyid = '.' + '{:0>6d}'.format(myid) pmesh.PrintToFile('deformed.mesh' + smyid, 8) p_gf.SaveToFile('pressure.sol' + smyid, 8) x_def.SaveToFile("deformation.sol" + smyid, 8)
def run_test(): #meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh')) meshfile = "../data/amr-quad.mesh" mesh = mfem.Mesh(meshfile, 1, 1) dim = mesh.Dimension() sdim = mesh.SpaceDimension() fec = mfem.H1_FECollection(1, dim) fespace = mfem.FiniteElementSpace(mesh, fec, 1) print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize())) c = mfem.ConstantCoefficient(1.0) gf = mfem.GridFunction(fespace) gf.ProjectCoefficient(c) odata = gf.GetDataArray().copy() gf.Save("out_test_gz.gf") gf2 = mfem.GridFunction(mesh, "out_test_gz.gf") odata2 = gf2.GetDataArray().copy() check(odata, odata2, "text file does not agree with original") gf.Save("out_test_gz.gz") gf2.Assign(0.0) gf2 = mfem.GridFunction(mesh, "out_test_gz.gz") odata2 = gf2.GetDataArray().copy() check(odata, odata2, ".gz file does not agree with original") gf.Print("out_test_gz.dat") gf2.Assign(0.0) gf2.Load("out_test_gz.dat", gf.Size()) odata2 = gf2.GetDataArray().copy() check(odata, odata2, ".dat file does not agree with original") gf.Print("out_test_gz.dat.gz") gf2.Assign(0.0) gf2.Load("out_test_gz.dat.gz", gf.Size()) odata2 = gf2.GetDataArray().copy() check(odata, odata2, ".dat file does not agree with original (gz)") import gzip import io gf.Print("out_test_gz.dat2.gz") with gzip.open("out_test_gz.dat2.gz", 'rt') as f: sio = io.StringIO(f.read()) gf3 = mfem.GridFunction(fespace) gf3.Load(sio, gf.Size()) odata3 = gf3.GetDataArray().copy() check(odata, odata3, ".dat file does not agree with original(gz-io)") c = mfem.ConstantCoefficient(2.0) gf.ProjectCoefficient(c) odata = gf.GetDataArray().copy() o = io.StringIO() gf.Print(o) gf2.Load(o, gf.Size()) odata2 = gf2.GetDataArray().copy() check(odata, odata2, "StringIO does not agree with original") print("GridFunction .gf, .gz .dat and StringIO agree with original") mesh2 = mfem.Mesh() mesh.Print("out_test_gz.mesh") mesh2.Load("out_test_gz.mesh") check_mesh(mesh, mesh2, ".mesh does not agree with original") mesh2 = mfem.Mesh() mesh.Print("out_test_gz.mesh.gz") mesh2.Load("out_test_gz.mesh.gz") check_mesh(mesh, mesh2, ".mesh.gz does not agree with original") mesh3 = mfem.Mesh() mesh.PrintGZ("out_test_gz3.mesh") mesh3.Load("out_test_gz3.mesh") check_mesh(mesh, mesh3, ".mesh (w/o .gz exntension) does not agree with original") o = io.StringIO() mesh2 = mfem.Mesh() mesh.Print(o) mesh2.Load(o) check_mesh(mesh, mesh2, ".mesh.gz does not agree with original") print("Mesh .mesh, .mesh.gz and StringIO agree with original") print("PASSED")
def run(order = 1, static_cond = False, meshfile = def_meshfile, visualization = False): mesh = mfem.Mesh(meshfile, 1,1) dim = mesh.Dimension() ref_levels = int(np.floor(np.log(10000./mesh.GetNE())/np.log(2.)/dim)) for x in range(ref_levels): mesh.UniformRefinement(); mesh.ReorientTetMesh(); pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) del mesh par_ref_levels = 2 for l in range(par_ref_levels): pmesh.UniformRefinement(); if order > 0: fec = mfem.H1_FECollection(order, dim) elif mesh.GetNodes(): fec = mesh.GetNodes().OwnFEC() prinr( "Using isoparametric FEs: " + str(fec.Name())); else: order = 1 fec = mfem.H1_FECollection(order, dim) fespace =mfem.ParFiniteElementSpace(pmesh, fec) fe_size = fespace.GlobalTrueVSize() if (myid == 0): print('Number of finite element unknowns: '+ str(fe_size)) ess_tdof_list = mfem.intArray() if pmesh.bdr_attributes.Size()>0: ess_bdr = mfem.intArray(pmesh.bdr_attributes.Max()) ess_bdr.Assign(1) fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list) # the basis functions in the finite element fespace. b = mfem.ParLinearForm(fespace) one = mfem.ConstantCoefficient(1.0) b.AddDomainIntegrator(mfem.DomainLFIntegrator(one)) b.Assemble(); x = mfem.ParGridFunction(fespace); x.Assign(0.0) a = mfem.ParBilinearForm(fespace); a.AddDomainIntegrator(mfem.DiffusionIntegrator(one)) if static_cond: a.EnableStaticCondensation() a.Assemble(); A = mfem.HypreParMatrix() B = mfem.Vector() X = mfem.Vector() a.FormLinearSystem(ess_tdof_list, x, b, A, X, B) if (myid == 0): print("Size of linear system: " + str(x.Size())) print("Size of linear system: " + str(A.GetGlobalNumRows())) amg = mfem.HypreBoomerAMG(A) pcg = mfem.HyprePCG(A) pcg.SetTol(1e-12) pcg.SetMaxIter(200) pcg.SetPrintLevel(2) pcg.SetPreconditioner(amg) pcg.Mult(B, X); a.RecoverFEMSolution(X, b, x) smyid = '{:0>6d}'.format(myid) mesh_name = "mesh."+smyid sol_name = "sol."+smyid pmesh.PrintToFile(mesh_name, 8) x.SaveToFile(sol_name, 8)
def run_test(): #meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh')) mesh = mfem.Mesh(3, 3, 3, "TETRAHEDRON") mesh.ReorientTetMesh() order = 1 dim = mesh.Dimension() sdim = mesh.SpaceDimension() fec1 = mfem.H1_FECollection(order, dim) fespace1 = mfem.FiniteElementSpace(mesh, fec1, 1) fec2 = mfem.ND_FECollection(order, dim) fespace2 = mfem.FiniteElementSpace(mesh, fec2, 1) print("Element order :", order) print('Number of H1 finite element unknowns: ' + str(fespace1.GetTrueVSize())) print('Number of ND finite element unknowns: ' + str(fespace2.GetTrueVSize())) print("Checking scalar") gf = mfem.GridFunction(fespace1) c1 = mfem.NumbaFunction(s_func, sdim).GenerateCoefficient() c2 = s_coeff() gf.Assign(0.0) start = time.time() gf.ProjectCoefficient(c1) end = time.time() data1 = gf.GetDataArray().copy() print("Numba time (scalar)", end - start) gf.Assign(0.0) start = time.time() gf.ProjectCoefficient(c2) end = time.time() data2 = gf.GetDataArray().copy() print("Python time (scalar)", end - start) check(data1, data2, "scalar coefficient does not agree with original") print("Checking vector") gf = mfem.GridFunction(fespace2) c3 = mfem.VectorNumbaFunction(v_func, sdim, dim).GenerateCoefficient() c4 = v_coeff(dim) gf.Assign(0.0) start = time.time() gf.ProjectCoefficient(c3) end = time.time() data1 = gf.GetDataArray().copy() print("Numba time (vector)", end - start) gf.Assign(0.0) start = time.time() gf.ProjectCoefficient(c4) end = time.time() data2 = gf.GetDataArray().copy() print("Python time (vector)", end - start) check(data1, data2, "vector coefficient does not agree with original") print("Checking matrix") a1 = mfem.BilinearForm(fespace2) a2 = mfem.BilinearForm(fespace2) c4 = mfem.MatrixNumbaFunction(m_func, sdim, dim).GenerateCoefficient() c5 = m_coeff(dim) a1.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c4)) a2.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c5)) start = time.time() a1.Assemble() end = time.time() a1.Finalize() M1 = a1.SpMat() print("Numba time (matrix)", end - start) start = time.time() a2.Assemble() end = time.time() a2.Finalize() M2 = a2.SpMat() print("Python time (matrix)", end - start) #from mfem.commmon.sparse_utils import sparsemat_to_scipycsr #csr1 = sparsemat_to_scipycsr(M1, float) #csr2 = sparsemat_to_scipycsr(M2, float) check(M1.GetDataArray(), M2.GetDataArray(), "matrix coefficient does not agree with original") check(M1.GetIArray(), M2.GetIArray(), "matrix coefficient does not agree with original") check(M1.GetJArray(), M2.GetJArray(), "matrix coefficient does not agree with original") print("PASSED")
def initialize(self, inMeshObj=None, inMeshFile=None): # 2. Problem initialization self.parser = ArgParser(description='Based on MFEM Ex16p') self.parser.add_argument('-m', '--mesh', default='beam-tet.mesh', action='store', type=str, help='Mesh file to use.') self.parser.add_argument('-rs', '--refine-serial', action='store', default=1, type=int, help="Number of times to refine the mesh \ uniformly in serial") self.parser.add_argument('-rp', '--refine-parallel', action='store', default=0, type=int, help="Number of times to refine the mesh \ uniformly in parallel") self.parser.add_argument('-o', '--order', action='store', default=1, type=int, help="Finite element order (polynomial \ degree)") self.parser.add_argument( '-s', '--ode-solver', action='store', default=3, type=int, help='\n'.join([ "ODE solver: 1 - Backward Euler, 2 - SDIRK2, \ 3 - SDIRK3", "\t\t 11 - Forward Euler, \ 12 - RK2, 13 - RK3 SSP, 14 - RK4." ])) self.parser.add_argument('-t', '--t-final', action='store', default=20., type=float, help="Final time; start time is 0.") self.parser.add_argument("-dt", "--time-step", action='store', default=5e-3, type=float, help="Time step.") self.parser.add_argument("-v", "--viscosity", action='store', default=0.00, type=float, help="Viscosity coefficient.") self.parser.add_argument('-L', '--lmbda', action='store', default=1.e0, type=float, help='Lambda of Hooks law') self.parser.add_argument('-mu', '--shear-modulus', action='store', default=1.e0, type=float, help='Shear modulus for Hooks law') self.parser.add_argument('-rho', '--density', action='store', default=1.0, type=float, help='mass density') self.parser.add_argument('-vis', '--visualization', action='store_true', help='Enable GLVis visualization') self.parser.add_argument('-vs', '--visualization-steps', action='store', default=25, type=int, help="Visualize every n-th timestep.") args = self.parser.parse_args() self.ser_ref_levels = args.refine_serial self.par_ref_levels = args.refine_parallel self.order = args.order self.dt = args.time_step self.visc = args.viscosity self.t_final = args.t_final self.lmbda = args.lmbda self.mu = args.shear_modulus self.rho = args.density self.visualization = args.visualization self.ti = 1 self.vis_steps = args.visualization_steps self.ode_solver_type = args.ode_solver self.t = 0.0 self.last_step = False if self.myId == 0: self.parser.print_options(args) # 3. Reading mesh if inMeshObj is None: self.meshFile = inMeshFile if self.meshFile is None: self.meshFile = args.mesh self.mesh = mfem.Mesh(self.meshFile, 1, 1) else: self.mesh = inMeshObj self.dim = self.mesh.Dimension() print("Mesh dimension: %d" % self.dim) print("Number of vertices in the mesh: %d " % self.mesh.GetNV()) print("Number of elements in the mesh: %d " % self.mesh.GetNE()) # 4. Define the ODE solver used for time integration. # Several implicit singly diagonal implicit # Runge-Kutta (SDIRK) methods, as well as # explicit Runge-Kutta methods are available. if self.ode_solver_type == 1: self.ode_solver = BackwardEulerSolver() elif self.ode_solver_type == 2: self.ode_solver = mfem.SDIRK23Solver(2) elif self.ode_solver_type == 3: self.ode_solver = mfem.SDIRK33Solver() elif self.ode_solver_type == 11: self.ode_solver = ForwardEulerSolver() elif self.ode_solver_type == 12: self.ode_solver = mfem.RK2Solver(0.5) elif self.ode_solver_type == 13: self.ode_solver = mfem.RK3SSPSolver() elif self.ode_solver_type == 14: self.ode_solver = mfem.RK4Solver() elif self.ode_solver_type == 22: self.ode_solver = mfem.ImplicitMidpointSolver() elif self.ode_solver_type == 23: self.ode_solver = mfem.SDIRK23Solver() elif self.ode_solver_type == 24: self.ode_solver = mfem.SDIRK34Solver() else: print("Unknown ODE solver type: " + str(self.ode_solver_type)) exit # 5. Refine the mesh in serial to increase the # resolution. In this example we do # 'ser_ref_levels' of uniform refinement, where # 'ser_ref_levels' is a command-line parameter. for lev in range(self.ser_ref_levels): self.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. self.pmesh = mfem.ParMesh(MPI.COMM_WORLD, self.mesh) for lev in range(self.par_ref_levels): self.pmesh.UniformRefinement() # 7. Define the vector finite element space # representing the current and the # initial temperature, u_ref. self.fe_coll = mfem.H1_FECollection(self.order, self.dim) self.fespace = mfem.ParFiniteElementSpace(self.pmesh, self.fe_coll, self.dim) self.fe_size = self.fespace.GlobalTrueVSize() if self.myId == 0: print("FE Number of unknowns: " + str(self.fe_size)) true_size = self.fespace.TrueVSize() self.true_offset = mfem.intArray(3) self.true_offset[0] = 0 self.true_offset[1] = true_size self.true_offset[2] = 2 * true_size self.vx = mfem.BlockVector(self.true_offset) self.v_gf = mfem.ParGridFunction(self.fespace) self.v_gfbnd = mfem.ParGridFunction(self.fespace) self.x_gf = mfem.ParGridFunction(self.fespace) self.x_gfbnd = mfem.ParGridFunction(self.fespace) self.x_ref = mfem.ParGridFunction(self.fespace) self.pmesh.GetNodes(self.x_ref) # 8. Set the initial conditions for u. #self.velo = InitialVelocity(self.dim) self.velo = velBCs(self.dim) #self.deform = InitialDeformation(self.dim) self.deform = defBCs(self.dim) self.v_gf.ProjectCoefficient(self.velo) self.v_gfbnd.ProjectCoefficient(self.velo) self.x_gf.ProjectCoefficient(self.deform) self.x_gfbnd.ProjectCoefficient(self.deform) #self.v_gf.GetTrueDofs(self.vx.GetBlock(0)); #self.x_gf.GetTrueDofs(self.vx.GetBlock(1)); # setup boundary-conditions self.xess_bdr = mfem.intArray( self.fespace.GetMesh().bdr_attributes.Max()) self.xess_bdr.Assign(0) self.xess_bdr[0] = 1 self.xess_bdr[1] = 1 self.xess_tdof_list = intArray() self.fespace.GetEssentialTrueDofs(self.xess_bdr, self.xess_tdof_list) #print('True x essential BCs are') #self.xess_tdof_list.Print() self.vess_bdr = mfem.intArray( self.fespace.GetMesh().bdr_attributes.Max()) self.vess_bdr.Assign(0) self.vess_bdr[0] = 1 self.vess_bdr[1] = 1 self.vess_tdof_list = intArray() self.fespace.GetEssentialTrueDofs(self.vess_bdr, self.vess_tdof_list) #print('True v essential BCs are') #self.vess_tdof_list.Print() # 9. Initialize the stiffness operator self.oper = StiffnessOperator(self.fespace, self.lmbda, self.mu, self.rho, self.visc, self.vess_tdof_list, self.vess_bdr, self.xess_tdof_list, self.xess_bdr, self.v_gfbnd, self.x_gfbnd, self.deform, self.velo, self.vx) # 10. Setting up file output self.smyid = '{:0>2d}'.format(self.myId) # initializing ode solver self.ode_solver.Init(self.oper)
def run_test(): print("Test complex_operator module") Nvert = 6 Nelem = 8 Nbelem = 2 mesh = mfem.Mesh(2, Nvert, Nelem, 2, 3) tri_v = [[1., 0., 0.], [0., 1., 0.], [-1., 0., 0.], [0., -1., 0.], [0., 0., 1.], [0., 0., -1.]] tri_e = [[0, 1, 4], [1, 2, 4], [2, 3, 4], [3, 0, 4], [1, 0, 5], [2, 1, 5], [3, 2, 5], [0, 3, 5]] tri_l = [[1, 4], [1, 2]] for j in range(Nvert): mesh.AddVertex(tri_v[j]) for j in range(Nelem): mesh.AddTriangle(tri_e[j], 1) for j in range(Nbelem): mesh.AddBdrSegment(tri_l[j], 1) mesh.FinalizeTriMesh(1, 1, True) dim = mesh.Dimension() order = 1 fec = mfem.H1_FECollection(order, dim) if use_parallel: mesh = mfem.ParMesh(MPI.COMM_WORLD, mesh) fes = mfem.ParFiniteElementSpace(mesh, fec) a1 = mfem.ParBilinearForm(fes) a2 = mfem.ParBilinearForm(fes) else: fes = mfem.FiniteElementSpace(mesh, fec) a1 = mfem.BilinearForm(fes) a2 = mfem.BilinearForm(fes) one = mfem.ConstantCoefficient(1.0) a1.AddDomainIntegrator(mfem.DiffusionIntegrator(one)) a1.Assemble() a1.Finalize() a2.AddDomainIntegrator(mfem.DiffusionIntegrator(one)) a2.Assemble() a2.Finalize() if use_parallel: M1 = a1.ParallelAssemble() M2 = a2.ParallelAssemble() M1.Print('M1') width = fes.GetTrueVSize() #X = mfem.HypreParVector(fes) #Y = mfem.HypreParVector(fes) #X.SetSize(fes.TrueVSize()) #Y.SetSize(fes.TrueVSize()) #from mfem.common.parcsr_extra import ToScipyCoo #MM1 = ToScipyCoo(M1) #print(MM1.toarray()) #print(MM1.dot(np.ones(6))) else: M1 = a1.SpMat() M2 = a2.SpMat() M1.Print('M1') width = fes.GetVSize() #X = mfem.Vector() #Y = mfem.Vector() #X.SetSize(M1.Width()) #Y.SetSize(M1.Height()) #from mfem.common.sparse_utils import sparsemat_to_scipycsr #MM1 = sparsemat_to_scipycsr(M1, np.float) #print(MM1.toarray()) #print(MM1.dot(np.ones(6))) #X.Assign(0.0) #X[0] = 1.0 #M1.Mult(X, Y) #print(Y.GetDataArray()) Mc = mfem.ComplexOperator(M1, M2, hermitan=True) offsets = mfem.intArray([0, width, width]) offsets.PartialSum() x = mfem.BlockVector(offsets) y = mfem.BlockVector(offsets) x.GetBlock(0).Assign(0) if myid == 0: x.GetBlock(0)[0] = 1.0 x.GetBlock(1).Assign(0) if myid == 0: x.GetBlock(1)[0] = 1.0 Mc.Mult(x, y) print("x", x.GetDataArray()) print("y", y.GetDataArray()) if myid == 0: x.GetBlock(1)[0] = -1.0 x.Print() Mc.Mult(x, y) print("x", x.GetDataArray()) print("y", y.GetDataArray())
def do_integration(expr, solvars, phys, mesh, kind, attrs, order, num): from petram.helper.variables import (Variable, var_g, NativeCoefficientGenBase, CoefficientVariable) from petram.phys.coefficient import SCoeff st = parser.expr(expr) code= st.compile('<string>') names = code.co_names g = {} #print solvars.keys() for key in phys._global_ns.keys(): g[key] = phys._global_ns[key] for key in solvars.keys(): g[key] = solvars[key] l = var_g.copy() ind_vars = ','.join(phys.get_independent_variables()) if kind == 'Domain': size = max(max(mesh.attributes.ToList()), max(attrs)) else: size = max(max(mesh.bdr_attributes.ToList()), max(attrs)) arr = [0]*(size) for k in attrs: arr[k-1] = 1 flag = mfem.intArray(arr) s = SCoeff(expr, ind_vars, l, g, return_complex=False) ## note L2 does not work for boundary....:D if kind == 'Domain': fec = mfem.L2_FECollection(order, mesh.Dimension()) else: fec = mfem.H1_FECollection(order, mesh.Dimension()) fes = mfem.FiniteElementSpace(mesh, fec) one = mfem.ConstantCoefficient(1) gf = mfem.GridFunction(fes) gf.Assign(0.0) if kind == 'Domain': gf.ProjectCoefficient(mfem.RestrictedCoefficient(s, flag)) else: gf.ProjectBdrCoefficient(mfem.RestrictedCoefficient(s, flag), flag) b = mfem.LinearForm(fes) one = mfem.ConstantCoefficient(1) if kind == 'Domain': itg = mfem.DomainLFIntegrator(one) b.AddDomainIntegrator(itg) else: itg = mfem.BoundaryLFIntegrator(one) b.AddBoundaryIntegrator(itg) b.Assemble() from petram.engine import SerialEngine en = SerialEngine() ans = mfem.InnerProduct(en.x2X(gf), en.b2B(b)) if not np.isfinite(ans): print("not finite", ans, arr) print(size, mesh.bdr_attributes.ToList()) from mfem.common.chypre import LF2PyVec, PyVec2PyMat, Array2PyVec, IdentityPyMat #print(list(gf.GetDataArray())) print(len(gf.GetDataArray()), np.sum(gf.GetDataArray())) print(np.sum(list(b.GetDataArray()))) return ans