def refine_mesh(filename, level): """ Uniformly refine `level`-times a mesh given by `filename`. The refined mesh is saved to a file with name constructed from base name of `filename` and `level`-times appended `'_r'` suffix. Parameters ---------- filename : str The mesh file name. level : int The refinement level. """ import os from sfepy.base.base import output from sfepy.discrete.fem import Mesh, Domain if level > 0: mesh = Mesh.from_file(filename) domain = Domain(mesh.name, mesh) for ii in range(level): output('refine %d...' % ii) domain = domain.refine() output('... %d nodes %d elements' % (domain.shape.n_nod, domain.shape.n_el)) suffix = os.path.splitext(filename)[1] filename = domain.name + suffix domain.mesh.write(filename, io='auto') return filename
def from_conf(conf, options): import sfepy from sfepy.discrete.fem import Mesh, Domain, Field mesh = Mesh.from_file('meshes/2d/rectangle_tri.mesh', prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) dim = domain.shape.dim min_x, max_x = domain.get_mesh_bounding_box()[:,0] eps = 1e-8 * (max_x - min_x) omega = domain.create_region('Omega', 'all') gamma1 = domain.create_region('Gamma1', 'vertices in x < %.10f' % (min_x + eps), 'facet') gamma2 = domain.create_region('Gamma2', 'vertices in x > %.10f' % (max_x - eps), 'facet') field = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=2) test = Test(conf=conf, options=options, dim=dim, omega=omega, gamma1=gamma1, gamma2=gamma2, field=field) return test
def main(): from sfepy import data_dir parser = OptionParser(usage=usage, version="%prog") parser.add_option("-s", "--show", action="store_true", dest="show", default=False, help=help["show"]) options, args = parser.parse_args() mesh = Mesh.from_file(data_dir + "/meshes/2d/rectangle_tri.mesh") domain = Domain("domain", mesh) min_x, max_x = domain.get_mesh_bounding_box()[:, 0] eps = 1e-8 * (max_x - min_x) omega = domain.create_region("Omega", "all") gamma1 = domain.create_region("Gamma1", "vertices in x < %.10f" % (min_x + eps), "facet") gamma2 = domain.create_region("Gamma2", "vertices in x > %.10f" % (max_x - eps), "facet") field = Field.from_args("fu", nm.float64, "vector", omega, approx_order=2) u = FieldVariable("u", "unknown", field) v = FieldVariable("v", "test", field, primary_var_name="u") m = Material("m", lam=1.0, mu=1.0) f = Material("f", val=[[0.02], [0.01]]) integral = Integral("i", order=3) t1 = Term.new("dw_lin_elastic_iso(m.lam, m.mu, v, u)", integral, omega, m=m, v=v, u=u) t2 = Term.new("dw_volume_lvf(f.val, v)", integral, omega, f=f, v=v) eq = Equation("balance", t1 + t2) eqs = Equations([eq]) fix_u = EssentialBC("fix_u", gamma1, {"u.all": 0.0}) bc_fun = Function("shift_u_fun", shift_u_fun, extra_args={"shift": 0.01}) shift_u = EssentialBC("shift_u", gamma2, {"u.0": bc_fun}) ls = ScipyDirect({}) nls_status = IndexedStruct() nls = Newton({}, lin_solver=ls, status=nls_status) pb = Problem("elasticity", equations=eqs, nls=nls, ls=ls) pb.save_regions_as_groups("regions") pb.time_update(ebcs=Conditions([fix_u, shift_u])) vec = pb.solve() print nls_status pb.save_state("linear_elasticity.vtk", vec) if options.show: view = Viewer("linear_elasticity.vtk") view(vector_mode="warp_norm", rel_scaling=2, is_scalar_bar=True, is_wireframe=True)
def test_interpolation_two_meshes(self): from sfepy import data_dir from sfepy.discrete import Variables from sfepy.discrete.fem import Mesh, Domain, Field m1 = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh') m2 = Mesh('target mesh', data_dir + '/meshes/3d/cube_medium_tetra.mesh') m2.coors *= 2.0 bbox = m1.get_bounding_box() dd = bbox[1,:] - bbox[0,:] data = nm.sin(4.0 * nm.pi * m1.coors[:,0:1] / dd[0]) \ * nm.cos(4.0 * nm.pi * m1.coors[:,1:2] / dd[1]) variables1 = { 'u' : ('unknown field', 'scalar_tp', 0), 'v' : ('test field', 'scalar_tp', 'u'), } variables2 = { 'u' : ('unknown field', 'scalar_si', 0), 'v' : ('test field', 'scalar_si', 'u'), } d1 = Domain('d1', m1) omega1 = d1.create_region('Omega', 'all') field1 = Field.from_args('scalar_tp', nm.float64, (1,1), omega1, approx_order=1) ff1 = {field1.name : field1} d2 = Domain('d2', m2) omega2 = d2.create_region('Omega', 'all') field2 = Field.from_args('scalar_si', nm.float64, (1,1), omega2, approx_order=0) ff2 = {field2.name : field2} vv1 = Variables.from_conf(transform_variables(variables1), ff1) u1 = vv1['u'] u1.set_from_mesh_vertices(data) vv2 = Variables.from_conf(transform_variables(variables2), ff2) u2 = vv2['u'] # Performs interpolation, if other field differs from self.field # or, in particular, is defined on a different mesh. u2.set_from_other(u1, strategy='interpolation', close_limit=0.1) fname = in_dir(self.options.out_dir) u1.save_as_mesh(fname('test_mesh_interp_block_scalar.vtk')) u2.save_as_mesh(fname('test_mesh_interp_cube_scalar.vtk')) return True
def from_conf(conf, options): mesh = Mesh.from_file('meshes/2d/square_unit_tri.mesh', prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') field = Field.from_args('linear', nm.float64, 'scalar', omega, approx_order=1) test = Test(conf=conf, options=options, omega=omega, field=field) return test
def test_normals(self): """ Check orientations of surface normals on the reference elements. """ import sfepy from sfepy.discrete import Integral from sfepy.discrete.fem import Mesh, Domain from sfepy.discrete.fem.poly_spaces import PolySpace from sfepy.discrete.fem.mappings import SurfaceMapping from sfepy.linalg import normalize_vectors ok = True for geom in ['2_3', '2_4', '3_4', '3_8']: mesh = Mesh.from_file('meshes/elements/%s_1.mesh' % geom, prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) surface = domain.create_region('Surface', 'vertices of surface', 'facet') domain.create_surface_group(surface) sd = domain.surface_groups[0][surface.name] coors = domain.get_mesh_coors() gel = domain.geom_els[geom].surface_facet ps = PolySpace.any_from_args('aux', gel, 1) mapping = SurfaceMapping(coors, sd.get_connectivity(), ps) integral = Integral('i', order=1) vals, weights = integral.get_qp(gel.name) # Evaluate just in the first quadrature point... geo = mapping.get_mapping(vals[:1], weights[:1]) expected = expected_normals[geom].copy() normalize_vectors(expected) _ok = nm.allclose(expected, geo.normal[:, 0, :, 0], rtol=0.0, atol=1e-14) self.report('%s: %s' % (geom, _ok)) if not _ok: self.report('expected:') self.report(expected) self.report('actual:') self.report(geo.normal[:, 0, :, 0]) ok = ok and _ok return ok
def do_interpolation(m2, m1, data, field_name, force=False): """Interpolate data from m1 to m2. """ from sfepy.discrete import Variables from sfepy.discrete.fem import Domain, Field fields = { 'scalar_si' : ((1,1), 'Omega', 2), 'vector_si' : ((3,1), 'Omega', 2), 'scalar_tp' : ((1,1), 'Omega', 1), 'vector_tp' : ((3,1), 'Omega', 1), } d1 = Domain('d1', m1) omega1 = d1.create_region('Omega', 'all') f = fields[field_name] field1 = Field.from_args('f', nm.float64, f[0], d1.regions[f[1]], approx_order=f[2]) ff = {field1.name : field1} vv = Variables.from_conf(transform_variables(variables), ff) u1 = vv['u'] u1.set_from_mesh_vertices(data) d2 = Domain('d2', m2) omega2 = d2.create_region('Omega', 'all') field2 = Field.from_args('f', nm.float64, f[0], d2.regions[f[1]], approx_order=f[2]) ff2 = {field2.name : field2} vv2 = Variables.from_conf(transform_variables(variables), ff2) u2 = vv2['u'] if not force: # Performs interpolation, if other field differs from self.field # or, in particular, is defined on a different mesh. u2.set_from_other(u1, strategy='interpolation', close_limit=0.5) else: coors = u2.field.get_coor() vals = u1.evaluate_at(coors, close_limit=0.5) u2.set_data(vals) return u1, u2
def test_invariance_qp(self): from sfepy import data_dir from sfepy.discrete import Variables, Integral from sfepy.discrete.fem import Mesh, Domain, Field from sfepy.terms import Term from sfepy.discrete.fem.mappings import get_physical_qps mesh = Mesh('source mesh', data_dir + '/meshes/3d/block.mesh') bbox = mesh.get_bounding_box() dd = bbox[1,:] - bbox[0,:] data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / dd[0]) \ * nm.cos(4.0 * nm.pi * mesh.coors[:,1:2] / dd[1]) variables = { 'u' : ('unknown field', 'scalar_tp', 0), 'v' : ('test field', 'scalar_tp', 'u'), } domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') field = Field.from_args('scalar_tp', nm.float64, 1, omega, approx_order=1) ff = {field.name : field} vv = Variables.from_conf(transform_variables(variables), ff) u = vv['u'] u.set_from_mesh_vertices(data) integral = Integral('i', order=2) term = Term.new('ev_volume_integrate(u)', integral, omega, u=u) term.setup() val1, _ = term.evaluate(mode='qp') val1 = val1.ravel() qps = get_physical_qps(omega, integral) coors = qps.get_merged_values() val2 = u.evaluate_at(coors).ravel() self.report('max. difference:', nm.abs(val1 - val2).max()) ok = nm.allclose(val1, val2, rtol=0.0, atol=1e-12) self.report('invariance in qp: %s' % ok) return ok
def test_projection_tri_quad(self): from sfepy.discrete.projections import make_l2_projection source = FieldVariable('us', 'unknown', self.field) coors = self.field.get_coor() vals = nm.sin(2.0 * nm.pi * coors[:,0] * coors[:,1]) source.set_data(vals) name = op.join(self.options.out_dir, 'test_projection_tri_quad_source.vtk') source.save_as_mesh(name) mesh = Mesh.from_file('meshes/2d/square_quad.mesh', prefix_dir=sfepy.data_dir) domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') field = Field.from_args('bilinear', nm.float64, 'scalar', omega, approx_order=1) target = FieldVariable('ut', 'unknown', field) make_l2_projection(target, source) name = op.join(self.options.out_dir, 'test_projection_tri_quad_target.vtk') target.save_as_mesh(name) bbox = self.field.domain.get_mesh_bounding_box() x = nm.linspace(bbox[0, 0] + 0.001, bbox[1, 0] - 0.001, 20) y = nm.linspace(bbox[0, 1] + 0.001, bbox[1, 1] - 0.001, 20) xx, yy = nm.meshgrid(x, y) test_coors = nm.c_[xx.ravel(), yy.ravel()].copy() vec1 = source.evaluate_at(test_coors) vec2 = target.evaluate_at(test_coors) ok = (nm.abs(vec1 - vec2) < 0.01).all() return ok
def mesh_hook(mesh, mode): """ Load and refine a mesh here. """ if mode == 'read': mesh = Mesh.from_file(base_mesh) domain = Domain(mesh.name, mesh) for ii in range(3): output('refine %d...' % ii) domain = domain.refine() output('... %d nodes %d elements' % (domain.shape.n_nod, domain.shape.n_el)) domain.mesh.name = '2_4_2_refined' return domain.mesh elif mode == 'write': pass
def from_conf(conf, options): from sfepy.discrete import Integral from sfepy.discrete.fem import Mesh, Domain domains = [] for filename in filename_meshes: mesh = Mesh.from_file(filename) domain = Domain('domain_%s' % mesh.name.replace(data_dir, ''), mesh) domain.create_region('Omega', 'all') domain.create_region('Gamma', 'vertices of surface', 'facet') domains.append(domain) integral = Integral('i', order=3) test = Test(domains=domains, integral=integral, conf=conf, options=options) return test
def main(): parser = OptionParser(usage=usage, version='%prog') parser.add_option('-b', '--basis', metavar='name', action='store', dest='basis', default='lagrange', help=help['basis']) parser.add_option('-n', '--max-order', metavar='order', type=int, action='store', dest='max_order', default=10, help=help['max_order']) parser.add_option('-m', '--matrix', metavar='type', action='store', dest='matrix_type', default='laplace', help=help['matrix_type']) parser.add_option('-g', '--geometry', metavar='name', action='store', dest='geometry', default='2_4', help=help['geometry']) options, args = parser.parse_args() dim, n_ep = int(options.geometry[0]), int(options.geometry[2]) output('reference element geometry:') output(' dimension: %d, vertices: %d' % (dim, n_ep)) n_c = {'laplace' : 1, 'elasticity' : dim}[options.matrix_type] output('matrix type:', options.matrix_type) output('number of variable components:', n_c) output('polynomial space:', options.basis) output('max. order:', options.max_order) mesh = Mesh.from_file(data_dir + '/meshes/elements/%s_1.mesh' % options.geometry) domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') orders = nm.arange(1, options.max_order + 1, dtype=nm.int) conds = [] order_fix = 0 if options.geometry in ['2_4', '3_8'] else 1 for order in orders: output('order:', order, '...') field = Field.from_args('fu', nm.float64, n_c, omega, approx_order=order, space='H1', poly_space_base=options.basis) to = field.approx_order quad_order = 2 * (max(to - order_fix, 0)) output('quadrature order:', quad_order) integral = Integral('i', order=quad_order) qp, _ = integral.get_qp(options.geometry) output('number of quadrature points:', qp.shape[0]) u = FieldVariable('u', 'unknown', field) v = FieldVariable('v', 'test', field, primary_var_name='u') m = Material('m', lam=1.0, mu=1.0) if options.matrix_type == 'laplace': term = Term.new('dw_laplace(m.mu, v, u)', integral, omega, m=m, v=v, u=u) n_zero = 1 else: assert_(options.matrix_type == 'elasticity') term = Term.new('dw_lin_elastic_iso(m.lam, m.mu, v, u)', integral, omega, m=m, v=v, u=u) n_zero = (dim + 1) * dim / 2 term.setup() output('assembling...') tt = time.clock() mtx, iels = term.evaluate(mode='weak', diff_var='u') output('...done in %.2f s' % (time.clock() - tt)) mtx = mtx[0][0, 0] try: assert_(nm.max(nm.abs(mtx - mtx.T)) < 1e-10) except: from sfepy.base.base import debug; debug() output('matrix shape:', mtx.shape) eigs = eig(mtx, method='eig.sgscipy', eigenvectors=False) eigs.sort() # Zero 'true' zeros. eigs[:n_zero] = 0.0 ii = nm.where(eigs < 0.0)[0] if len(ii): output('matrix is not positive semi-definite!') ii = nm.where(eigs[n_zero:] < 1e-12)[0] if len(ii): output('matrix has more than %d zero eigenvalues!' % n_zero) output('smallest eigs:\n', eigs[:10]) ii = nm.where(eigs > 0.0)[0] emin, emax = eigs[ii[[0, -1]]] output('min:', emin, 'max:', emax) cond = emax / emin conds.append(cond) output('condition number:', cond) output('...done') plt.figure(1) plt.semilogy(orders, conds) plt.xticks(orders, orders) plt.xlabel('polynomial order') plt.ylabel('condition number') plt.grid() plt.figure(2) plt.loglog(orders, conds) plt.xticks(orders, orders) plt.xlabel('polynomial order') plt.ylabel('condition number') plt.grid() plt.show()
def save_basis_on_mesh(mesh, options, output_dir, lin, permutations=None, suffix=''): if permutations is not None: mesh = mesh.copy() for ig, conn in enumerate(mesh.conns): gel = GeometryElement(mesh.descs[ig]) perms = gel.get_conn_permutations()[permutations] n_el, n_ep = conn.shape offsets = nm.arange(n_el) * n_ep conn[:] = conn.take(perms + offsets[:, None]) domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') field = Field.from_args('f', nm.float64, shape=1, region=omega, approx_order=options.max_order, poly_space_base=options.basis) var = FieldVariable('u', 'unknown', field) if options.plot_dofs: import sfepy.postprocess.plot_dofs as pd group = domain.groups[0] ax = pd.plot_mesh(None, mesh.coors, mesh.conns[0], group.gel.edges) ax = pd.plot_global_dofs(ax, field.get_coor(), field.aps[0].econn) ax = pd.plot_local_dofs(ax, field.get_coor(), field.aps[0].econn) if options.dofs is not None: ax = pd.plot_nodes(ax, field.get_coor(), field.aps[0].econn, field.aps[0].interp.poly_spaces['v'].nodes, get_dofs(options.dofs, var.n_dof)) pd.plt.show() output('dofs: %d' % var.n_dof) vec = nm.empty(var.n_dof, dtype=var.dtype) n_digit, _format = get_print_info(var.n_dof, fill='0') name_template = os.path.join(output_dir, 'dof_%s%s.vtk' % (_format, suffix)) for ip in get_dofs(options.dofs, var.n_dof): output('dof %d...' % ip) vec.fill(0.0) vec[ip] = 1.0 var.set_data(vec) if options.derivative == 0: out = var.create_output(vec, linearization=lin) else: out = create_expression_output('ev_grad.ie.Elements(u)', 'u', 'f', {'f' : field}, None, Variables([var]), mode='qp', verbose=False, min_level=lin.min_level, max_level=lin.max_level, eps=lin.eps) name = name_template % ip ensure_path(name) out['u'].mesh.write(name, out=out) output('...done (%s)' % name)
def main(): parser = OptionParser(usage=usage) parser.add_option('-s', '--scale', metavar='scale', action='store', dest='scale', default=None, help=help['scale']) parser.add_option('-c', '--center', metavar='center', action='store', dest='center', default=None, help=help['center']) parser.add_option('-r', '--refine', metavar='level', action='store', type=int, dest='refine', default=0, help=help['refine']) parser.add_option('-f', '--format', metavar='format', action='store', type='string', dest='format', default=None, help=help['format']) parser.add_option('-l', '--list', action='store_true', dest='list', help=help['list']) (options, args) = parser.parse_args() if options.list: output_writable_meshes() sys.exit(0) if len(args) != 2: parser.print_help() sys.exit(1) scale = _parse_val_or_vec(options.scale, 'scale', parser) center = _parse_val_or_vec(options.center, 'center', parser) filename_in, filename_out = args mesh = Mesh.from_file(filename_in) if scale is not None: if len(scale) == 1: tr = nm.eye(mesh.dim, dtype=nm.float64) * scale elif len(scale) == mesh.dim: tr = nm.diag(scale) else: raise ValueError('bad scale! (%s)' % scale) mesh.transform_coors(tr) if center is not None: cc = 0.5 * mesh.get_bounding_box().sum(0) shift = center - cc tr = nm.c_[nm.eye(mesh.dim, dtype=nm.float64), shift[:, None]] mesh.transform_coors(tr) if options.refine > 0: domain = Domain(mesh.name, mesh) output('initial mesh: %d nodes %d elements' % (domain.shape.n_nod, domain.shape.n_el)) for ii in range(options.refine): output('refine %d...' % ii) domain = domain.refine() output('... %d nodes %d elements' % (domain.shape.n_nod, domain.shape.n_el)) mesh = domain.mesh io = MeshIO.for_format(filename_out, format=options.format, writable=True) cell_types = ', '.join(supported_cell_types[io.format]) output('writing [%s] %s...' % (cell_types, filename_out)) mesh.write(filename_out, io=io) output('...done')
def _gen_common_data(orders, gels, report): import sfepy from sfepy.base.base import Struct from sfepy.linalg import combine from sfepy.discrete import FieldVariable, Integral from sfepy.discrete.fem import Mesh, Domain, Field from sfepy.discrete.fem.global_interp import get_ref_coors bases = ([ii for ii in combine([['2_4', '3_8'], ['lagrange', 'lobatto']])] + [ii for ii in combine([['2_3', '3_4'], ['lagrange']])]) for geom, poly_space_base in bases: report('geometry: %s, base: %s' % (geom, poly_space_base)) order = orders[geom] integral = Integral('i', order=order) aux = '' if geom in ['2_4', '3_8'] else 'z' mesh0 = Mesh.from_file('meshes/elements/%s_2%s.mesh' % (geom, aux), prefix_dir=sfepy.data_dir) gel = gels[geom] perms = gel.get_conn_permutations() qps, qp_weights = integral.get_qp(gel.surface_facet.name) zz = nm.zeros_like(qps[:, :1]) qps = nm.hstack(([qps] + [zz])) shift = shifts[geom] rcoors = nm.ascontiguousarray(qps + shift[:1, :] - shift[1:, :]) ccoors = nm.ascontiguousarray(qps + shift[:1, :] + shift[1:, :]) for ir, pr in enumerate(perms): for ic, pc in enumerate(perms): report('ir: %d, ic: %d' % (ir, ic)) report('pr: %s, pc: %s' % (pr, pc)) mesh = mesh0.copy() conn = mesh.conns[0] conn[0, :] = conn[0, pr] conn[1, :] = conn[1, pc] cache = Struct(mesh=mesh) domain = Domain('domain', mesh) omega = domain.create_region('Omega', 'all') region = domain.create_region('Facet', rsels[geom], 'facet') field = Field.from_args('f', nm.float64, shape=1, region=omega, approx_order=order, poly_space_base=poly_space_base) var = FieldVariable('u', 'unknown', field) report('# dofs: %d' % var.n_dof) vec = nm.empty(var.n_dof, dtype=var.dtype) ap = field.aps[0] ps = ap.interp.poly_spaces['v'] dofs = field.get_dofs_in_region_group(region, 0, merge=False) edofs, fdofs = nm.unique(dofs[1]), nm.unique(dofs[2]) rrc, rcells, rstatus = get_ref_coors(field, rcoors, cache=cache) crc, ccells, cstatus = get_ref_coors(field, ccoors, cache=cache) assert_((rstatus == 0).all() and (cstatus == 0).all()) yield (geom, poly_space_base, qp_weights, mesh, ir, ic, ap, ps, rrc, rcells[0, 1], crc, ccells[0, 1], vec, edofs, fdofs)
def test_linearization(self): from sfepy.base.base import Struct from sfepy.discrete.fem import Mesh, Domain, Field from sfepy import data_dir geometries = ["2_3", "2_4", "3_4", "3_8"] approx_orders = [1, 2] funs = [nm.cos, nm.sin, lambda x: x] ok = True for geometry in geometries: name = os.path.join(data_dir, "meshes/elements/%s_1.mesh" % geometry) mesh = Mesh.from_file(name) domain = Domain("", mesh) domain = domain.refine() domain.mesh.write(self.join("linearizer-%s-0.mesh" % geometry)) omega = domain.create_region("Omega", "all") for approx_order in approx_orders: for dpn in [1, mesh.dim]: self.report("geometry: %s, approx. order: %d, dpn: %d" % (geometry, approx_order, dpn)) field = Field.from_args("fu", nm.float64, dpn, omega, approx_order=approx_order) cc = field.get_coor() dofs = nm.zeros((field.n_nod, dpn), dtype=nm.float64) for ic in range(dpn): dofs[:, ic] = funs[ic](3 * (cc[:, 0] * cc[:, 1])) vmesh, vdofs, levels = field.linearize(dofs, min_level=0, max_level=3, eps=1e-2) level = levels[0] if approx_order == 1: _ok = level == 0 else: _ok = level > 0 self.report("max. refinement level: %d: %s" % (level, _ok)) ok = ok and _ok rdofs = nm.zeros((vmesh.n_nod, dpn), dtype=nm.float64) cc = vmesh.coors for ic in range(dpn): rdofs[:, ic] = funs[ic](3 * (cc[:, 0] * cc[:, 1])) _ok = nm.allclose(rdofs, vdofs, rtol=0.0, atol=0.03) self.report("interpolation: %s" % _ok) ok = ok and _ok out = {"u": Struct(name="output_data", mode="vertex", data=vdofs, var_name="u", dofs=None)} name = self.join("linearizer-%s-%d-%d" % (geometry, approx_order, dpn)) vmesh.write(name + ".mesh") vmesh.write(name + ".vtk", out=out) return ok
def main(): parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__) parser.add_option("-m", "--mesh", action="store_true", dest="save_mesh", default=False, help="save surface mesh") parser.add_option("-n", "--no-surface", action="store_true", dest="no_surface", default=False, help="do not output surface [default: %default]") (options, args) = parser.parse_args() if (len(args) == 2): filename_in = args[0]; filename_out = args[1]; else: parser.print_help(), return if (filename_in == '-'): file_in = sys.stdin else: file_in = open(filename_in, "r"); mesh = Mesh.from_file(filename_in) if (filename_in != '-'): file_in.close() domain = Domain('domain', mesh) domain.setup_groups() if domain.has_faces(): domain.fix_element_orientation() lst, surf_faces = get_surface_faces(domain) surf_mesh = Mesh.from_surface(surf_faces, mesh) if options.save_mesh: aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh') surf_mesh.write(aux, io='auto') if options.no_surface: return gr_s = surface_graph(surf_faces, mesh.n_nod) n_comp, comps = surface_components(gr_s, surf_faces) output('number of surface components:', n_comp) ccs, comps = comps, nm.zeros((0,1), nm.int32) for cc in ccs: comps = nm.concatenate((comps, cc[:,nm.newaxis]), 0) out = nm.concatenate((lst, comps), 1) if (filename_out == '-'): file_out = sys.stdout else: file_out = open(filename_out, "w"); for row in out: file_out.write('%d %d %d\n' % (row[0], row[1], row[2])) if (filename_out != '-'): file_out.close()
def refine_reference(geometry, level): """ Refine reference element given by `geometry`. Notes ----- The error edges must be generated in the order of the connectivity of the previous (lower) level. """ from sfepy.discrete.fem import Domain from sfepy.discrete.fem.geometry_element import geometry_data gcoors, gconn = geometry.coors, geometry.conn if level == 0: return gcoors, gconn gd = geometry_data[geometry.name] conn = nm.array([gd.conn], dtype=nm.int32) mat_id = conn[:, 0].copy() mat_id[:] = 0 mesh = Mesh.from_data('aux', gd.coors, None, [conn], [mat_id], [geometry.name]) domain = Domain('aux', mesh) for ii in range(level): domain = domain.refine() coors = domain.mesh.coors conn = domain.mesh.conns[0] n_el = conn.shape[0] if geometry.name == '2_3': aux_conn = conn.reshape((n_el / 4, 4, 3)) ir = [[0, 1, 2], [2, 2, 3], [3, 3, 0]] ic = [[0, 0, 0], [0, 1, 0], [0, 1, 0]] elif geometry.name == '2_4': aux_conn = conn.reshape((n_el / 4, 4, 4)) ir = [[0, 0, 1], [1, 1, 2], [2, 2, 3], [3, 3, 0], [0, 0, 2], [3, 3, 1]] ic = [[0, 1, 0], [0, 1, 0], [0, 1, 0], [0, 1, 0], [1, 2, 1], [1, 2, 1]] elif geometry.name == '3_4': aux_conn = conn.reshape((n_el / 8, 8, 4)) ir = [[0, 0, 1], [1, 1, 2], [2, 0, 0], [3, 1, 1], [3, 2, 2], [3, 0, 0]] ic = [[0, 1, 1], [1, 2, 2], [2, 2, 0], [3, 3, 1], [3, 3, 2], [3, 3, 0]] elif geometry.name == '3_8': aux_conn = conn.reshape((n_el / 8, 8, 8)) ir = [[0, 0, 1], [1, 1, 2], [2, 2, 3], [3, 0, 0], [0, 0, 2], [0, 0, 1], [0, 0, 1], [1, 1, 2], [2, 2, 3], [3, 0, 0], [0, 0, 2], [0, 0, 1], [4, 4, 5], [5, 5, 6], [6, 6, 7], [7, 4, 4], [4, 4, 6], [4, 4, 5], [0, 0, 4], [1, 1, 5], [2, 2, 6], [3, 3, 7], [0, 0, 4], [1, 1, 5], [2, 2, 6], [0, 0, 4], [0, 0, 4]] ic = [[0, 1, 0], [0, 1, 0], [0, 1, 0], [0, 3, 0], [1, 2, 1], [3, 2, 1], [4, 5, 4], [4, 5, 4], [4, 5, 4], [4, 7, 4], [5, 6, 5], [7, 6, 5], [0, 3, 0], [0, 3, 0], [0, 3, 0], [0, 1, 0], [3, 2, 3], [1, 2, 3], [0, 4, 0], [0, 4, 0], [0, 4, 0], [0, 4, 0], [1, 5, 3], [1, 5, 3], [1, 5, 3], [3, 7, 1], [2, 6, 2]] else: raise ValueError('unsupported geometry! (%s)' % geometry.name) conn = nm.array(conn, dtype=nm.int32) error_edges = aux_conn[:, ir, ic] return coors, conn, error_edges
def _solve(self, property_array): """ Solve the Sfepy problem for one sample. Args: property_array: array of shape (Nx, Ny, 2) where the last index is for Lame's parameter and shear modulus, respectively. Returns: the strain field of shape (Nx, Ny, 2) where the last index represents the x and y displacements """ shape = property_array.shape[:-1] mesh = self._get_mesh(shape) domain = Domain('domain', mesh) region_all = domain.create_region('region_all', 'all') field = Field.from_args('fu', np.float64, 'vector', region_all, approx_order=2) u = FieldVariable('u', 'unknown', field) v = FieldVariable('v', 'test', field, primary_var_name='u') m = self._get_material(property_array, domain) integral = Integral('i', order=4) t1 = Term.new('dw_lin_elastic_iso(m.lam, m.mu, v, u)', integral, region_all, m=m, v=v, u=u) eq = Equation('balance_of_forces', t1) eqs = Equations([eq]) epbcs, functions = self._get_periodicBCs(domain) ebcs = self._get_displacementBCs(domain) lcbcs = self._get_linear_combinationBCs(domain) ls = ScipyDirect({}) pb = Problem('elasticity', equations=eqs, auto_solvers=None) pb.save_regions_as_groups('regions') pb.time_update(ebcs=ebcs, epbcs=epbcs, lcbcs=lcbcs, functions=functions) ev = pb.get_evaluator() nls = Newton({}, lin_solver=ls, fun=ev.eval_residual, fun_grad=ev.eval_tangent_matrix) pb.set_solvers_instances(ls, nls) vec = pb.solve() u = vec.create_output_dict()['u'].data u_reshape = np.reshape(u, (tuple(x + 1 for x in shape) + u.shape[-1:])) dims = domain.get_mesh_bounding_box().shape[1] strain = np.squeeze( pb.evaluate( 'ev_cauchy_strain.{dim}.region_all(u)'.format(dim=dims), mode='el_avg')) strain_reshape = np.reshape(strain, (shape + strain.shape[-1:])) stress = np.squeeze( pb.evaluate( 'ev_cauchy_stress.{dim}.region_all(m.D, u)'.format(dim=dims), mode='el_avg')) stress_reshape = np.reshape(stress, (shape + stress.shape[-1:])) return strain_reshape, u_reshape, stress_reshape