コード例 #1
0
def solve_problem(mesh_filename, options, comm):
    order_u = options.order_u
    order_p = options.order_p

    rank, size = comm.Get_rank(), comm.Get_size()

    output('rank', rank, 'of', size)

    mesh = Mesh.from_file(mesh_filename)

    if rank == 0:
        cell_tasks = pl.partition_mesh(mesh, size, use_metis=options.metis,
                                       verbose=True)

    else:
        cell_tasks = None

    domain = FEDomain('domain', mesh)
    omega = domain.create_region('Omega', 'all')
    field1 = Field.from_args('fu', nm.float64, mesh.dim, omega,
                             approx_order=order_u)
    field2 = Field.from_args('fp', nm.float64, 1, omega,
                             approx_order=order_p)
    fields = [field1, field2]

    output('distributing fields...')
    tt = time.clock()

    lfds, gfds = pl.distribute_fields_dofs(fields, cell_tasks,
                                           is_overlap=True,
                                           use_expand_dofs=True,
                                           comm=comm, verbose=True)

    output('...done in', time.clock() - tt)

    output('creating local problem...')
    tt = time.clock()

    cells = lfds[0].cells

    omega_gi = Region.from_cells(cells, domain)
    omega_gi.finalize()
    omega_gi.update_shape()

    pb = create_local_problem(omega_gi, [order_u, order_p])

    variables = pb.get_variables()

    state = State(variables)
    state.fill(0.0)
    state.apply_ebc()

    output('...done in', time.clock() - tt)


    output('allocating global system...')
    tt = time.clock()

    sizes, drange, pdofs = pl.setup_composite_dofs(lfds, fields, variables,
                                                   verbose=True)
    pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a, sizes, pdofs, drange,
                                              is_overlap=True, comm=comm,
                                              verbose=True)

    output('...done in', time.clock() - tt)

    output('creating solver...')
    tt = time.clock()

    conf = Struct(method='bcgsl', precond='jacobi', sub_precond=None,
                  i_max=10000, eps_a=1e-50, eps_r=1e-6, eps_d=1e4,
                  verbose=True)
    status = {}
    ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

    field_ranges = {}
    for ii, variable in enumerate(variables.iter_state(ordered=True)):
        field_ranges[variable.name] = lfds[ii].petsc_dofs_range

    ls.set_field_split(field_ranges, comm=comm)

    ev = PETScParallelEvaluator(pb, pdofs, drange, True,
                                psol, comm, verbose=True)

    nls_status = {}
    conf = Struct(method='newtonls',
                  i_max=5, eps_a=0, eps_r=1e-5, eps_s=0.0,
                  verbose=True)
    nls = PETScNonlinearSolver(conf, pmtx=pmtx, prhs=prhs, comm=comm,
                               fun=ev.eval_residual,
                               fun_grad=ev.eval_tangent_matrix,
                               lin_solver=ls, status=nls_status)

    output('...done in', time.clock() - tt)

    output('solving...')
    tt = time.clock()

    state = pb.create_state()
    state.apply_ebc()

    ev.psol_i[...] = state()
    ev.gather(psol, ev.psol_i)

    psol = nls(psol)

    ev.scatter(ev.psol_i, psol)
    sol0_i = ev.psol_i[...]

    output('...done in', time.clock() - tt)

    output('saving solution...')
    tt = time.clock()

    state.set_full(sol0_i)
    out = state.create_output_dict()

    filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)
    pb.domain.mesh.write(filename, io='auto', out=out)

    gather_to_zero = pl.create_gather_to_zero(psol)

    psol_full = gather_to_zero(psol)

    if comm.rank == 0:
        sol = psol_full[...].copy()

        u = FieldVariable('u', 'parameter', field1,
                          primary_var_name='(set-to-None)')
        remap = gfds[0].id_map
        ug = sol[remap]

        p = FieldVariable('p', 'parameter', field2,
                          primary_var_name='(set-to-None)')
        remap = gfds[1].id_map
        pg = sol[remap]

        if (((order_u == 1) and (order_p == 1))
            or (options.linearization == 'strip')):
            out = u.create_output(ug)
            out.update(p.create_output(pg))
            filename = os.path.join(options.output_dir, 'sol.h5')
            mesh.write(filename, io='auto', out=out)

        else:
            out = u.create_output(ug, linearization=Struct(kind='adaptive',
                                                           min_level=0,
                                                           max_level=order_u,
                                                           eps=1e-3))

            filename = os.path.join(options.output_dir, 'sol_u.h5')
            out['u'].mesh.write(filename, io='auto', out=out)

            out = p.create_output(pg, linearization=Struct(kind='adaptive',
                                                           min_level=0,
                                                           max_level=order_p,
                                                           eps=1e-3))

            filename = os.path.join(options.output_dir, 'sol_p.h5')
            out['p'].mesh.write(filename, io='auto', out=out)

    output('...done in', time.clock() - tt)
コード例 #2
0
def solve_problem(mesh_filename, options, comm):
    order = options.order

    rank, size = comm.Get_rank(), comm.Get_size()

    output('rank', rank, 'of', size)

    mesh = Mesh.from_file(mesh_filename)

    if rank == 0:
        cell_tasks = pl.partition_mesh(mesh, size, use_metis=options.metis,
                                       verbose=True)

    else:
        cell_tasks = None

    domain = FEDomain('domain', mesh)
    omega = domain.create_region('Omega', 'all')
    field = Field.from_args('fu', nm.float64, 1, omega, approx_order=order)

    output('distributing field %s...' % field.name)
    tt = time.clock()

    lfds, gfds = pl.distribute_fields_dofs([field], cell_tasks,
                                             is_overlap=True, comm=comm,
                                             verbose=True)
    lfd = lfds[0]

    output('...done in', time.clock() - tt)

    if rank == 0:
        dof_maps = gfds[0].dof_maps
        id_map = gfds[0].id_map

        if options.verify:
            verify_save_dof_maps(field, cell_tasks,
                                 dof_maps, id_map, options, verbose=True)

        if options.plot:
            ppd.plot_partitioning([None, None], field, cell_tasks, gfds[0],
                                  options.output_dir, size)

    output('creating local problem...')
    tt = time.clock()

    omega_gi = Region.from_cells(lfd.cells, field.domain)
    omega_gi.finalize()
    omega_gi.update_shape()

    pb = create_local_problem(omega_gi, order)

    output('...done in', time.clock() - tt)

    variables = pb.get_variables()
    eqs = pb.equations

    u_i = variables['u_i']
    field_i = u_i.field

    if options.plot:
        ppd.plot_local_dofs([None, None], field, field_i, omega_gi,
                            options.output_dir, rank)

    output('allocating global system...')
    tt = time.clock()

    sizes, drange = pl.get_sizes(lfd.petsc_dofs_range, field.n_nod, 1)
    output('sizes:', sizes)
    output('drange:', drange)

    pdofs = pl.get_local_ordering(field_i, lfd.petsc_dofs_conn)

    output('pdofs:', pdofs)

    pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a, sizes, pdofs, drange,
                                              is_overlap=True, comm=comm,
                                              verbose=True)

    output('...done in', time.clock() - tt)

    output('evaluating local problem...')
    tt = time.clock()

    state = State(variables)
    state.fill(0.0)
    state.apply_ebc()

    rhs_i = eqs.eval_residuals(state())
    # This must be after pl.create_petsc_system() call!
    mtx_i = eqs.eval_tangent_matrices(state(), pb.mtx_a)

    output('...done in', time.clock() - tt)

    output('assembling global system...')
    tt = time.clock()

    pl.apply_ebc_to_matrix(mtx_i, u_i.eq_map.eq_ebc)
    pl.assemble_rhs_to_petsc(prhs, rhs_i, pdofs, drange, is_overlap=True,
                             comm=comm, verbose=True)
    pl.assemble_mtx_to_petsc(pmtx, mtx_i, pdofs, drange, is_overlap=True,
                             comm=comm, verbose=True)

    output('...done in', time.clock() - tt)

    output('creating solver...')
    tt = time.clock()

    conf = Struct(method='cg', precond='gamg', sub_precond=None,
                  i_max=10000, eps_a=1e-50, eps_r=1e-5, eps_d=1e4, verbose=True)
    status = {}
    ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

    output('...done in', time.clock() - tt)

    output('solving...')
    tt = time.clock()

    psol = ls(prhs, psol, conf)

    psol_i = pl.create_local_petsc_vector(pdofs)
    gather, scatter = pl.create_gather_scatter(pdofs, psol_i, psol, comm=comm)

    scatter(psol_i, psol)

    sol0_i = state() - psol_i[...]
    psol_i[...] = sol0_i

    gather(psol, psol_i)

    output('...done in', time.clock() - tt)

    output('saving solution...')
    tt = time.clock()

    u_i.set_data(sol0_i)
    out = u_i.create_output()

    filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)
    pb.domain.mesh.write(filename, io='auto', out=out)

    gather_to_zero = pl.create_gather_to_zero(psol)

    psol_full = gather_to_zero(psol)

    if comm.rank == 0:
        sol = psol_full[...].copy()[id_map]

        u = FieldVariable('u', 'parameter', field,
                          primary_var_name='(set-to-None)')

        filename = os.path.join(options.output_dir, 'sol.h5')
        if (order == 1) or (options.linearization == 'strip'):
            out = u.create_output(sol)
            mesh.write(filename, io='auto', out=out)

        else:
            out = u.create_output(sol, linearization=Struct(kind='adaptive',
                                                            min_level=0,
                                                            max_level=order,
                                                            eps=1e-3))

            out['u'].mesh.write(filename, io='auto', out=out)

    output('...done in', time.clock() - tt)

    if options.show:
        ppd.pc.plt.show()
コード例 #3
0
def solve_problem(mesh_filename, options, comm):
    order_u = options.order_u
    order_p = options.order_p

    rank, size = comm.Get_rank(), comm.Get_size()

    output('rank', rank, 'of', size)

    mesh = Mesh.from_file(mesh_filename)

    if rank == 0:
        cell_tasks = pl.partition_mesh(mesh,
                                       size,
                                       use_metis=options.metis,
                                       verbose=True)

    else:
        cell_tasks = None

    domain = FEDomain('domain', mesh)
    omega = domain.create_region('Omega', 'all')
    field1 = Field.from_args('fu',
                             nm.float64,
                             mesh.dim,
                             omega,
                             approx_order=order_u)
    field2 = Field.from_args('fp', nm.float64, 1, omega, approx_order=order_p)
    fields = [field1, field2]

    output('distributing fields...')
    tt = time.clock()

    lfds, gfds = pl.distribute_fields_dofs(fields,
                                           cell_tasks,
                                           is_overlap=True,
                                           use_expand_dofs=True,
                                           comm=comm,
                                           verbose=True)

    output('...done in', time.clock() - tt)

    output('creating local problem...')
    tt = time.clock()

    cells = lfds[0].cells

    omega_gi = Region.from_cells(cells, domain)
    omega_gi.finalize()
    omega_gi.update_shape()

    pb = create_local_problem(omega_gi, [order_u, order_p])

    variables = pb.get_variables()

    state = State(variables)
    state.fill(0.0)
    state.apply_ebc()

    output('...done in', time.clock() - tt)

    output('allocating global system...')
    tt = time.clock()

    sizes, drange, pdofs = pl.setup_composite_dofs(lfds,
                                                   fields,
                                                   variables,
                                                   verbose=True)
    pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a,
                                              sizes,
                                              pdofs,
                                              drange,
                                              is_overlap=True,
                                              comm=comm,
                                              verbose=True)

    output('...done in', time.clock() - tt)

    output('creating solver...')
    tt = time.clock()

    conf = Struct(method='bcgsl',
                  precond='jacobi',
                  sub_precond=None,
                  i_max=10000,
                  eps_a=1e-50,
                  eps_r=1e-6,
                  eps_d=1e4,
                  verbose=True)
    status = {}
    ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

    field_ranges = {}
    for ii, variable in enumerate(variables.iter_state(ordered=True)):
        field_ranges[variable.name] = lfds[ii].petsc_dofs_range

    ls.set_field_split(field_ranges, comm=comm)

    ev = PETScParallelEvaluator(pb,
                                pdofs,
                                drange,
                                True,
                                psol,
                                comm,
                                verbose=True)

    nls_status = {}
    conf = Struct(method='newtonls',
                  i_max=5,
                  eps_a=0,
                  eps_r=1e-5,
                  eps_s=0.0,
                  verbose=True)
    nls = PETScNonlinearSolver(conf,
                               pmtx=pmtx,
                               prhs=prhs,
                               comm=comm,
                               fun=ev.eval_residual,
                               fun_grad=ev.eval_tangent_matrix,
                               lin_solver=ls,
                               status=nls_status)

    output('...done in', time.clock() - tt)

    output('solving...')
    tt = time.clock()

    state = pb.create_state()
    state.apply_ebc()

    ev.psol_i[...] = state()
    ev.gather(psol, ev.psol_i)

    psol = nls(psol)

    ev.scatter(ev.psol_i, psol)
    sol0_i = ev.psol_i[...]

    output('...done in', time.clock() - tt)

    output('saving solution...')
    tt = time.clock()

    state.set_full(sol0_i)
    out = state.create_output_dict()

    filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)
    pb.domain.mesh.write(filename, io='auto', out=out)

    gather_to_zero = pl.create_gather_to_zero(psol)

    psol_full = gather_to_zero(psol)

    if comm.rank == 0:
        sol = psol_full[...].copy()

        u = FieldVariable('u',
                          'parameter',
                          field1,
                          primary_var_name='(set-to-None)')
        remap = gfds[0].id_map
        ug = sol[remap]

        p = FieldVariable('p',
                          'parameter',
                          field2,
                          primary_var_name='(set-to-None)')
        remap = gfds[1].id_map
        pg = sol[remap]

        if (((order_u == 1) and (order_p == 1))
                or (options.linearization == 'strip')):
            out = u.create_output(ug)
            out.update(p.create_output(pg))
            filename = os.path.join(options.output_dir, 'sol.h5')
            mesh.write(filename, io='auto', out=out)

        else:
            out = u.create_output(ug,
                                  linearization=Struct(kind='adaptive',
                                                       min_level=0,
                                                       max_level=order_u,
                                                       eps=1e-3))

            filename = os.path.join(options.output_dir, 'sol_u.h5')
            out['u'].mesh.write(filename, io='auto', out=out)

            out = p.create_output(pg,
                                  linearization=Struct(kind='adaptive',
                                                       min_level=0,
                                                       max_level=order_p,
                                                       eps=1e-3))

            filename = os.path.join(options.output_dir, 'sol_p.h5')
            out['p'].mesh.write(filename, io='auto', out=out)

    output('...done in', time.clock() - tt)
コード例 #4
0
def solve_problem(mesh_filename, options, comm):
    order = options.order

    rank, size = comm.Get_rank(), comm.Get_size()

    output('rank', rank, 'of', size)

    mesh = Mesh.from_file(mesh_filename)

    if rank == 0:
        cell_tasks = pl.partition_mesh(mesh,
                                       size,
                                       use_metis=options.metis,
                                       verbose=True)

    else:
        cell_tasks = None

    domain = FEDomain('domain', mesh)
    omega = domain.create_region('Omega', 'all')
    field = Field.from_args('fu', nm.float64, 1, omega, approx_order=order)

    output('distributing field %s...' % field.name)
    tt = time.clock()

    lfds, gfds = pl.distribute_fields_dofs([field],
                                           cell_tasks,
                                           is_overlap=True,
                                           comm=comm,
                                           verbose=True)
    lfd = lfds[0]

    output('...done in', time.clock() - tt)

    if rank == 0:
        dof_maps = gfds[0].dof_maps
        id_map = gfds[0].id_map

        if options.verify:
            verify_save_dof_maps(field,
                                 cell_tasks,
                                 dof_maps,
                                 id_map,
                                 options,
                                 verbose=True)

        if options.plot:
            ppd.plot_partitioning([None, None], field, cell_tasks, gfds[0],
                                  options.output_dir, size)

    output('creating local problem...')
    tt = time.clock()

    omega_gi = Region.from_cells(lfd.cells, field.domain)
    omega_gi.finalize()
    omega_gi.update_shape()

    pb = create_local_problem(omega_gi, order)

    output('...done in', time.clock() - tt)

    variables = pb.get_variables()
    eqs = pb.equations

    u_i = variables['u_i']
    field_i = u_i.field

    if options.plot:
        ppd.plot_local_dofs([None, None], field, field_i, omega_gi,
                            options.output_dir, rank)

    output('allocating global system...')
    tt = time.clock()

    sizes, drange = pl.get_sizes(lfd.petsc_dofs_range, field.n_nod, 1)
    output('sizes:', sizes)
    output('drange:', drange)

    pdofs = pl.get_local_ordering(field_i, lfd.petsc_dofs_conn)

    output('pdofs:', pdofs)

    pmtx, psol, prhs = pl.create_petsc_system(pb.mtx_a,
                                              sizes,
                                              pdofs,
                                              drange,
                                              is_overlap=True,
                                              comm=comm,
                                              verbose=True)

    output('...done in', time.clock() - tt)

    output('evaluating local problem...')
    tt = time.clock()

    state = State(variables)
    state.fill(0.0)
    state.apply_ebc()

    rhs_i = eqs.eval_residuals(state())
    # This must be after pl.create_petsc_system() call!
    mtx_i = eqs.eval_tangent_matrices(state(), pb.mtx_a)

    output('...done in', time.clock() - tt)

    output('assembling global system...')
    tt = time.clock()

    pl.apply_ebc_to_matrix(mtx_i, u_i.eq_map.eq_ebc)
    pl.assemble_rhs_to_petsc(prhs,
                             rhs_i,
                             pdofs,
                             drange,
                             is_overlap=True,
                             comm=comm,
                             verbose=True)
    pl.assemble_mtx_to_petsc(pmtx,
                             mtx_i,
                             pdofs,
                             drange,
                             is_overlap=True,
                             comm=comm,
                             verbose=True)

    output('...done in', time.clock() - tt)

    output('creating solver...')
    tt = time.clock()

    conf = Struct(method='cg',
                  precond='gamg',
                  sub_precond=None,
                  i_max=10000,
                  eps_a=1e-50,
                  eps_r=1e-5,
                  eps_d=1e4,
                  verbose=True)
    status = {}
    ls = PETScKrylovSolver(conf, comm=comm, mtx=pmtx, status=status)

    output('...done in', time.clock() - tt)

    output('solving...')
    tt = time.clock()

    psol = ls(prhs, psol, conf)

    psol_i = pl.create_local_petsc_vector(pdofs)
    gather, scatter = pl.create_gather_scatter(pdofs, psol_i, psol, comm=comm)

    scatter(psol_i, psol)

    sol0_i = state() - psol_i[...]
    psol_i[...] = sol0_i

    gather(psol, psol_i)

    output('...done in', time.clock() - tt)

    output('saving solution...')
    tt = time.clock()

    u_i.set_data(sol0_i)
    out = u_i.create_output()

    filename = os.path.join(options.output_dir, 'sol_%02d.h5' % comm.rank)
    pb.domain.mesh.write(filename, io='auto', out=out)

    gather_to_zero = pl.create_gather_to_zero(psol)

    psol_full = gather_to_zero(psol)

    if comm.rank == 0:
        sol = psol_full[...].copy()[id_map]

        u = FieldVariable('u',
                          'parameter',
                          field,
                          primary_var_name='(set-to-None)')

        filename = os.path.join(options.output_dir, 'sol.h5')
        if (order == 1) or (options.linearization == 'strip'):
            out = u.create_output(sol)
            mesh.write(filename, io='auto', out=out)

        else:
            out = u.create_output(sol,
                                  linearization=Struct(kind='adaptive',
                                                       min_level=0,
                                                       max_level=order,
                                                       eps=1e-3))

            out['u'].mesh.write(filename, io='auto', out=out)

    output('...done in', time.clock() - tt)

    if options.show:
        plt.show()