Source code for sfepy.tests.test_poly_spaces

```"""
Test continuity of polynomial basis and its gradients along an edge on
:math:`y` line (2D) or on a face in :math:`x`-:math:`y` plane (3D) between two
elements aligned with the coordinate system, stack one on top of the other. The
evaluation occurs in several points shifted by a very small amount from the
boundary between the elements into the top and the bottom element.

For H1 space, the basis should be continuous. The components of its gradient
parallel to the edge/face should be continuous as well, while the perpendicular
component should have the same absolute value, but different sign in the top
and the bottom element.

All connectivity permutations of the two elements are tested.

The serendipity basis implementation is a pure python proof-of-concept. Its
order in continuity tests is limited to 2 on 3_8 elements to decrease the tests
run time.
"""
from itertools import product
import numpy as nm
import pytest

from sfepy.base.base import assert_
import sfepy.base.testing as tst

rsels = {
'2_3' : 'vertices in (y > -0.1) & (y < 0.1)',
'2_4' : 'vertices in (y > 0.9) & (y < 1.1)',
'3_4' : 'vertices in (z > -0.1) & (z < 0.1)',
'3_8' : 'vertices in (z > 0.9) & (z < 1.1)',
}

eps = 1e-5

shifts = {
'2_3' : nm.array([[0.0, 0.0], [0.0, eps]], dtype=nm.float64),
'2_4' : nm.array([[0.0, 1.0], [0.0, eps]], dtype=nm.float64),
'3_4' : nm.array([[0.0, 0.0, 0.0], [0.0, 0.0, eps]], dtype=nm.float64),
'3_8' : nm.array([[0.0, 0.0, 1.0], [0.0, 0.0, eps]], dtype=nm.float64),
}

from sfepy.discrete.fem import Mesh

coors0, ngroups0, conns0, mat_ids0, desc0 = mesh0._get_io_data()
im = nm.arange(4, 8)
cperms = [[0, 1, 2, 3],
[0, 2, 1, 3],
[0, 1, 3, 2]]
meshes = []
for ip, cperm in enumerate(cperms):
tr = nm.arange(12)
tr[im] = tr[im[cperm]]

coors = coors0.copy()
coors[im] = coors0[im[cperm]]
conn = conns0[0].copy()
conn = tr[conn]

mesh = Mesh.from_data(mesh0.name + str(ip), coors, ngroups0,
[conn], mat_ids0, desc0)
meshes.append(mesh)

return meshes

def _get_possible_oris(geom):
import sfepy.discrete.fem.facets as facets

if geom in ('2_3', '2_4'):
oris = facets.ori_line_to_iter.keys()

elif geom == '3_4':
oris = facets.ori_triangle_to_iter.keys()

elif geom == '3_8':
oris = facets._quad_ori_groups.keys() # Not ori_square_to_iter!

else:
oris = []

return set(oris)

def _gen_common_data(orders, gels):
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, FEDomain, Field
from sfepy.discrete.common.global_interp import get_ref_coors

bases = ([ii for ii in combine([['2_4', '3_8'],
['lagrange', 'serendipity', 'bernstein',
'lobatto', 'sem']])]
+ [ii for ii in combine([['2_3', '3_4'],
['lagrange', 'bernstein']])])
for geom, poly_space_basis in bases:
order = orders[geom]
if (geom == '3_8') and (poly_space_basis == 'serendipity'):
order = 2

tst.report('geometry: %s, base: %s, order: %d'
% (geom, poly_space_basis, order))

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)
if (geom == '3_8'):

else:
meshes = [mesh0]

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:, :])

all_oris = _get_possible_oris(geom)
oris = set()

for (ir, pr), (ic, pc), (im, mesh0) in product(
enumerate(perms), enumerate(perms), enumerate(meshes),
):
tst.report('im: %d, ir: %d, ic: %d' % (im, ir, ic))
tst.report('pr: %s, pc: %s' % (pr, pc))

mesh = mesh0.copy()
conn = mesh.cmesh.get_conn(mesh0.cmesh.tdim, 0).indices
conn = conn.reshape((mesh0.n_el, -1))
conn[0, :] = conn[0, pr]
conn[1, :] = conn[1, pc]

conn2 = mesh.get_conn(gel.name)
assert_((conn == conn2).all())

cache = Struct(mesh=mesh)

domain = FEDomain('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_basis=poly_space_basis)
fis = region.get_facet_indices()
conn = mesh.cmesh.get_conn_as_graph(region.dim,
region.dim - 1)
_oris = mesh.cmesh.facet_oris[conn.indptr[fis[:, 0]]
+ fis[:, 1]]
oris |= set(_oris)
if oris == all_oris:
break

var = FieldVariable('u', 'unknown', field)
tst.report('# dofs: %d' % var.n_dof)

vec = nm.empty(var.n_dof, dtype=var.dtype)

ps = field.poly_space

dofs = field.get_dofs_in_region(region, 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_basis, qp_weights, mesh, im, ir, ic,
field, ps, rrc, rcells[0], crc, ccells[0],
vec, edofs, fdofs)

[docs]
@pytest.fixture(scope='module')
def gels():
from sfepy.discrete.fem.geometry_element import GeometryElement

gels = {}
for key in ['2_3', '2_4', '3_4', '3_8']:
gel = GeometryElement(key)
gel.create_surface_facet()
gels[key] = gel

return gels

[docs]
def test_partition_of_unity(gels):
from sfepy.linalg import combine
from sfepy.discrete import Integral, PolySpace

ok = True
orders = {'2_3' : 5, '2_4' : 5, '3_4' : 5, '3_8' : 5}
bases = (
[ii for ii in combine([['2_4', '3_8'],
['lagrange', 'serendipity', 'bernstein', 'sem']]
)]
+ [ii for ii in combine([['2_3', '3_4'],
['lagrange', 'bernstein']])]
)

for geom, poly_space_basis in bases:
max_order = orders[geom]
for order in range(max_order + 1):
if (poly_space_basis == 'serendipity') and not (0 < order < 4):
continue
if (poly_space_basis == 'sem') and not (0 < order):
continue
tst.report('geometry: %s, base: %s, order: %d'
% (geom, poly_space_basis, order))

integral = Integral('i', order=2 * order)
coors, _ = integral.get_qp(geom)

ps = PolySpace.any_from_args('ps', gels[geom], order,
basis=poly_space_basis)
vals = ps.eval_basis(coors)
_ok = nm.allclose(vals.sum(axis=-1), 1, atol=1e-14, rtol=0.0)
tst.report('partition of unity:', _ok)
ok = ok and _ok

assert_(ok)

[docs]
@pytest.mark.slow
def test_continuity(gels):
ok = True
orders = {'2_3' : 3, '2_4' : 3, '3_4' : 4, '3_8' : 3}

for (geom, poly_space_basis, qp_weights, mesh, im, ir, ic,
field, ps, rrc, rcell, crc, ccell, vec,
edofs, fdofs) in _gen_common_data(orders, gels):

if poly_space_basis in ('lagrange', 'serendipity', 'bernstein', 'sem'):
rbf = ps.eval_basis(rrc)
cbf = ps.eval_basis(crc)

else:
rbf = ps.eval_basis(rrc, ori=field.ori[:1])
cbf = ps.eval_basis(crc, ori=field.ori[1:])

dofs = nm.r_[edofs, fdofs]

res = nm.zeros((2, dofs.shape[0]), dtype=nm.int32)
res[0, :] = dofs
for ii, ip in enumerate(dofs):
vec.fill(0.0)
vec[ip] = 1.0

evec = vec[field.econn]

rvals = nm.dot(rbf, evec[rcell])
cvals = nm.dot(cbf, evec[ccell])

_ok = nm.allclose(rvals, cvals, atol=1e-14, rtol=0.0)
res[1, ii] = _ok
if not _ok:
bads.append([geom, poly_space_basis, im, ir, ic, ip])

ok = ok and _ok

tst.report('results (dofs, status: 1 ok, 0 failure):\n%s' % res)

if not ok:
tst.report('%d in total!' % len(bads))
tst.report('continuity errors occurred in these spaces:\n',

assert_(ok)

[docs]
@pytest.mark.slow
from sfepy.discrete.fem.mappings import FEMapping

ok = True
orders = {'2_3' : 3, '2_4' : 3, '3_4' : 4, '3_8' : 3}

for (geom, poly_space_basis, qp_weights, mesh, im, ir, ic,
field, ps, rrc, rcell, crc, ccell, vec,
edofs, fdofs) in _gen_common_data(orders, gels):
gel = gels[geom]
conn = mesh.get_conn(gel.name)

geo_ps = field.gel.poly_space
rmapping = FEMapping(mesh.coors, conn[rcell:rcell+1],
poly_space=geo_ps)
rori = field.ori[:1] if field.ori is not None else None
rvg = rmapping.get_mapping(rrc, qp_weights, poly_space=ps, ori=rori)
rbfg = rvg.bfg

cmapping = FEMapping(mesh.coors, conn[ccell:ccell+1],
poly_space=geo_ps)
cori = field.ori[1:] if field.ori is not None else None
cvg = cmapping.get_mapping(crc, qp_weights, poly_space=ps, ori=cori)
cbfg = cvg.bfg

dofs = nm.r_[edofs, fdofs]

res = nm.zeros((2, dofs.shape[0]), dtype=nm.int32)
res[0, :] = dofs
for ii, ip in enumerate(dofs):
vec.fill(0.0)
vec[ip] = 1.0

evec = vec[field.econn]

rvals = nm.dot(rbfg, evec[rcell])[0]
cvals = nm.dot(cbfg, evec[ccell])[0]

okx = nm.allclose(rvals[:, 0], cvals[:, 0],
atol=1e-12, rtol=0.0)
if gel.dim == 2:
oky = nm.allclose(rvals[:, 1], -cvals[:, 1],
atol=1e-12, rtol=0.0)
_ok = okx and oky

else:
oky = nm.allclose(rvals[:, 1], cvals[:, 1],
atol=1e-12, rtol=0.0)
okz = nm.allclose(rvals[:, 2], -cvals[:, 2],
atol=1e-12, rtol=0.0)
_ok = okx and oky and okz

res[1, ii] = _ok
if not _ok:
bads.append([geom, poly_space_basis, im, ir, ic, ip])

ok = ok and _ok

tst.report('results (dofs, status: 1 ok, 0 failure):\n%s' % res)

if not ok:
tst.report('%d in total!' % len(bads))
tst.report('gradient continuity errors occurred in these'

assert_(ok)

[docs]
def test_hessians(gels):
"""
Test the second partial derivatives of basis functions using finite
differences.
"""
from sfepy.linalg import combine
from sfepy.discrete import Integral, PolySpace

ok = True
orders = {'2_3' : 3, '2_4' : 3, '3_4' : 4, '3_8' : 3}
bases = ([ii for ii in combine([['2_3', '2_4', '3_4', '3_8'],
['lagrange']])])

for geom, poly_space_basis in bases:
tst.report('geometry: %s, base: %s' % (geom, poly_space_basis))
order = orders[geom]

integral = Integral('i', order=order)
coors, _ = integral.get_qp(geom)

ps = PolySpace.any_from_args('ps', gels[geom], order,
basis=poly_space_basis)

dim = coors.shape[1]
h1 = nm.zeros((coors.shape[0], dim, dim, ps.n_nod), nm.float64)
eps = 1e-8
for ir in range(dim):
cc = coors.copy()

cc[:, ir] -= eps
aux0 = ps.eval_basis(cc, diff=1)

cc[:, ir] += 2 * eps
aux1 = ps.eval_basis(cc, diff=1)

h1[:, :, ir, :] = 0.5 * (aux1 - aux0) / eps

h2 = ps.eval_basis(coors, diff=2)

_ok = nm.allclose(h1, h2, rtol=0, atol=50*eps)
tst.report('hessians: error: %.2e ok: %s'
% (nm.abs(h1 - h2).max(), _ok))
ok = ok and _ok

assert_(ok)

```