def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.fem import Mesh, Domain, H1NodalVolumeField, Variables
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 = H1NodalVolumeField('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 = H1NodalVolumeField('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 do_interpolation(m2, m1, data, field_name, force=False):
"""Interpolate data from m1 to m2. """
from sfepy.fem import Domain, H1NodalVolumeField, Variables
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 = H1NodalVolumeField('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 = H1NodalVolumeField('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_refine_3_8(self):
mesh = Mesh('3_8', data_dir + '/meshes/elements/3_8_1.mesh')
domain = refine(Domain('domain', mesh), self.options.out_dir, 1)
ok = compare_mesh('3_8', domain.mesh.coors, domain.mesh.conns[0])
return ok
def from_conf(conf, options):
import sfepy
from sfepy.fem import Mesh, Domain, H1NodalVolumeField
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 = H1NodalVolumeField('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 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.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 main():
parser = OptionParser(usage=usage, version="%prog")
options, args = parser.parse_args()
if (len(args) == 1):
mesh_filename = args[0];
else:
parser.print_help(),
return
mesh = Mesh('mesh', mesh_filename)
print mesh
domain = Domain('domain', mesh)
print domain
reg = domain.create_region('Surface',
'nodes of surface',
{'can_cells' : True})
dual_mesh = DualMesh(reg)
dual_mesh.save('dual_mesh.mesh',)
dual_mesh.save_axes('axes.vtk',)
print dual_mesh
def test_refine_hexa(self):
mesh = Mesh('mesh_hexa',
data_dir + '/meshes/various_formats/abaqus_hex.inp')
domain = Domain('domain', mesh)
refine(domain, self.options.out_dir)
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 = H1NodalVolumeField('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.fem import Mesh, Domain, Integral
from sfepy.fem.poly_spaces import PolySpace
from sfepy.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 test_invariance_qp(self):
from sfepy import data_dir
from sfepy.fem import (Mesh, Domain, H1NodalVolumeField, Variables,
Integral)
from sfepy.terms import Term
from sfepy.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 = H1NodalVolumeField('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.fem.projections import make_l2_projection
source = FieldVariable('us', 'unknown', self.field, 1)
coors = self.field.get_coor()
vals = nm.sin(2.0 * nm.pi * coors[:, 0] * coors[:, 1])
source.data_from_any(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 = H1NodalVolumeField('bilinear',
nm.float64,
'scalar',
omega,
approx_order=1)
target = FieldVariable('ut', 'unknown', field, 1)
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 from_conf(conf, options):
from sfepy import data_dir
from sfepy.fem import Mesh, Domain, Functions
mesh = Mesh('test mesh',
data_dir + '/meshes/various_formats/abaqus_tet.inp')
domain = Domain('test domain', mesh)
conf_functions = {
'get_nodes': (get_nodes, ),
'get_elements': (get_elements, ),
}
functions = Functions.from_conf(transform_functions(conf_functions))
test = Test(conf=conf,
options=options,
domain=domain,
functions=functions)
return test
def from_conf(conf, options):
from sfepy.fem import Mesh, Domain, Integral
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', 'nodes of surface')
domains.append(domain)
integrals = {'Omega' : Integral('iv', kind='v', order=3),
'Gamma' : Integral('is', kind='s', order=3)}
test = Test(domains=domains, integrals=integrals,
conf=conf, options=options)
return test
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 import data_dir
from sfepy.fem import Mesh, Domain, Functions
mesh = Mesh('test mesh',
data_dir + '/meshes/various_formats/abaqus_tet.inp')
mesh.nodal_bcs['set0'] = [0, 7]
domain = Domain('test domain', mesh)
conf_functions = {
'get_vertices': (get_vertices, ),
'get_cells': (get_cells, ),
}
functions = Functions.from_conf(transform_functions(conf_functions))
test = Test(conf=conf,
options=options,
domain=domain,
functions=functions)
return test
def from_conf(conf, options):
from sfepy.fem import Mesh, Domain, Integral
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')
options, args = parser.parse_args()
if len(args) == 1:
filename = args[0]
else:
parser.print_help(),
return
mesh = Mesh.from_file(filename)
output('Mesh:')
output(' dimension: %d, vertices: %d, elements: %d' %
(mesh.dim, mesh.n_nod, mesh.n_el))
domain = Domain('domain', mesh)
output(domain.cmesh)
domain.cmesh.cprint(1)
dim = domain.cmesh.dim
ax = pc.plot_wireframe(None, domain.cmesh)
ax = pc.plot_entities(ax, domain.cmesh, 0, 'k')
ax = pc.label_global_entities(ax, domain.cmesh, 0, 'k', 12)
ax = pc.label_local_entities(ax, domain.cmesh, 0, 'k', 8)
ax = pc.plot_entities(ax, domain.cmesh, 1, 'b')
ax = pc.label_global_entities(ax, domain.cmesh, 1, 'b', 12)
ax = pc.label_local_entities(ax, domain.cmesh, 1, 'b', 8)
if dim == 3:
ax = pc.plot_entities(ax, domain.cmesh, 2, 'g')
ax = pc.label_global_entities(ax, domain.cmesh, 2, 'g', 12)
ax = pc.label_local_entities(ax, domain.cmesh, 2, 'g', 8)
ax = pc.plot_entities(ax, domain.cmesh, dim, 'r')
ax = pc.label_global_entities(ax, domain.cmesh, dim, 'r', 12)
pc.plt.show()
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',
'nodes in x < %.10f' % (min_x + eps))
gamma2 = domain.create_region('Gamma2',
'nodes in x > %.10f' % (max_x - eps))
field = H1NodalVolumeField('fu',
nm.float64,
'vector',
omega,
approx_order=2)
u = FieldVariable('u', 'unknown', field, mesh.dim)
v = FieldVariable('v', 'test', field, mesh.dim, 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 = ProblemDefinition('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 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.fem import Domain
from sfepy.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 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, 1)
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 _gen_common_data(orders, gels, report):
import sfepy
from sfepy.base.base import Struct
from sfepy.linalg import combine
from sfepy.fem import Mesh, Domain, Field, FieldVariable, Integral
from sfepy.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, 1)
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 main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=True,
help="save surface mesh [default: %default]")
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()
domain.setup_facets(create_edges=False)
lst, surf_faces = domain.surface_faces()
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)
## import sfepy.base.plotutils as plu
## plu.spy( gr_s )
## plu.pylab.show()
n_comp, comps = surface_components(gr_s, surf_faces)
# print '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 %d\n' % (row[0], row[1], row[2], row[3]))
if (filename_out != '-'):
file_out.close()
def smooth_mesh(mesh, n_iter=4, lam=0.6307, mu=-0.6347,
weights=None, bconstr=True,
volume_corr=False):
"""
FE mesh smoothing.
Based on:
[1] Steven K. Boyd, Ralph Muller, Smooth surface meshing for automated
finite element model generation from 3D image data, Journal of
Biomechanics, Volume 39, Issue 7, 2006, Pages 1287-1295,
ISSN 0021-9290, 10.1016/j.jbiomech.2005.03.006.
(http://www.sciencedirect.com/science/article/pii/S0021929005001442)
Parameters
----------
mesh : mesh
FE mesh.
n_iter : integer, optional
Number of iteration steps.
lam : float, optional
Smoothing factor, see [1].
mu : float, optional
Unshrinking factor, see [1].
weights : array, optional
Edge weights, see [1].
bconstr: logical, optional
Boundary constraints, if True only surface smoothing performed.
volume_corr: logical, optional
Correct volume after smoothing process.
Returns
-------
coors : array
Coordinates of mesh nodes.
"""
def laplacian(coors, weights):
n_nod = coors.shape[0]
displ = (weights - sps.identity(n_nod)) * coors
return displ
def taubin(coors0, weights, lam, mu, n_iter):
coors = coors0.copy()
for ii in range(n_iter):
displ = laplacian(coors, weights)
if nm.mod(ii, 2) == 0:
coors += lam * displ
else:
coors += mu * displ
return coors
def get_volume(el, nd):
from sfepy.linalg.utils import dets_fast
dim = nd.shape[1]
nnd = el.shape[1]
etype = '%d_%d' % (dim, nnd)
if etype == '2_4' or etype == '3_8':
el = elems_q2t(el)
nel = el.shape[0]
#bc = nm.zeros((dim, ), dtype=nm.double)
mul = 1.0 / factorial(dim)
if dim == 3:
mul *= -1.0
mtx = nm.ones((nel, dim + 1, dim + 1), dtype=nm.double)
mtx[:,:,:-1] = nd[el,:]
vols = mul * dets_fast(mtx.copy())
vol = vols.sum()
bc = nm.dot(vols, mtx.sum(1)[:,:-1] / nnd)
bc /= vol
return vol, bc
import time
output('smoothing...')
tt = time.clock()
if weights is None:
n_nod = mesh.n_nod
domain = Domain('mesh', mesh)
cmesh = domain.cmesh
# initiate all vertices as inner - hierarchy = 2
node_group = nm.ones((n_nod,), dtype=nm.int16) * 2
# boundary vertices - set hierarchy = 4
if bconstr:
# get "vertices of surface"
facets = cmesh.get_surface_facets()
f_verts = cmesh.get_incident(0, facets, cmesh.dim - 1)
node_group[f_verts] = 4
# generate costs matrix
e_verts = cmesh.get_conn(1, 0).indices
fc1, fc2 = e_verts[0::2], e_verts[1::2]
idxs = nm.where(node_group[fc2] >= node_group[fc1])
rows1 = fc1[idxs]
cols1 = fc2[idxs]
idxs = nm.where(node_group[fc1] >= node_group[fc2])
rows2 = fc2[idxs]
cols2 = fc1[idxs]
crows = nm.concatenate((rows1, rows2))
ccols = nm.concatenate((cols1, cols2))
costs = sps.coo_matrix((nm.ones_like(crows), (crows, ccols)),
shape=(n_nod, n_nod),
dtype=nm.double)
# generate weights matrix
idxs = range(n_nod)
aux = sps.coo_matrix((1.0 / nm.asarray(costs.sum(1)).squeeze(),
(idxs, idxs)),
shape=(n_nod, n_nod),
dtype=nm.double)
#aux.setdiag(1.0 / costs.sum(1))
weights = (aux.tocsc() * costs.tocsc()).tocsr()
coors = taubin(mesh.coors, weights, lam, mu, n_iter)
output('...done in %.2f s' % (time.clock() - tt))
if volume_corr:
output('rescaling...')
volume0, bc = get_volume(mesh.conns[0], mesh.coors)
volume, _ = get_volume(mesh.conns[0], coors)
scale = volume0 / volume
output('scale factor: %.2f' % scale)
coors = (coors - bc) * scale + bc
output('...done in %.2f s' % (time.clock() - tt))
return coors
def smooth_mesh(mesh,
n_iter=4,
lam=0.6307,
mu=-0.6347,
weights=None,
bconstr=True,
volume_corr=False):
"""
FE mesh smoothing.
Based on:
[1] Steven K. Boyd, Ralph Muller, Smooth surface meshing for automated
finite element model generation from 3D image data, Journal of
Biomechanics, Volume 39, Issue 7, 2006, Pages 1287-1295,
ISSN 0021-9290, 10.1016/j.jbiomech.2005.03.006.
(http://www.sciencedirect.com/science/article/pii/S0021929005001442)
Parameters
----------
mesh : mesh
FE mesh.
n_iter : integer, optional
Number of iteration steps.
lam : float, optional
Smoothing factor, see [1].
mu : float, optional
Unshrinking factor, see [1].
weights : array, optional
Edge weights, see [1].
bconstr: logical, optional
Boundary constraints, if True only surface smoothing performed.
volume_corr: logical, optional
Correct volume after smoothing process.
Returns
-------
coors : array
Coordinates of mesh nodes.
"""
def laplacian(coors, weights):
n_nod = coors.shape[0]
displ = (weights - sps.identity(n_nod)) * coors
return displ
def taubin(coors0, weights, lam, mu, n_iter):
coors = coors0.copy()
for ii in range(n_iter):
displ = laplacian(coors, weights)
if nm.mod(ii, 2) == 0:
coors += lam * displ
else:
coors += mu * displ
return coors
def get_volume(el, nd):
dim = nd.shape[1]
nnd = el.shape[1]
etype = '%d_%d' % (dim, nnd)
if etype == '2_4' or etype == '3_8':
el = elems_q2t(el)
vol = 0.0
bc = nm.zeros((dim, ), dtype=nm.double)
mtx = nm.ones((dim + 1, dim + 1), dtype=nm.double)
mul = 1.0 / sc.factorial(dim)
if dim == 3:
mul *= -1.0
for iel in el:
mtx[:, :-1] = nd[iel, :]
ve = mul * nm.linalg.det(mtx)
vol += ve
bc += ve * mtx.sum(0)[:-1] / nnd
bc /= vol
return vol, bc
domain = Domain('mesh', mesh)
n_nod = mesh.n_nod
edges = domain.ed
if weights is None:
# initiate all vertices as inner - hierarchy = 2
node_group = nm.ones((n_nod, ), dtype=nm.int16) * 2
# boundary vertices - set hierarchy = 4
if bconstr:
# get "nodes of surface"
if domain.fa: # 3D.
fa = domain.fa
else:
fa = domain.ed
flag = fa.mark_surface_facets()
ii = nm.where(flag > 0)[0]
aux = nm.unique(fa.facets[ii])
if aux[0] == -1: # Triangular faces have -1 as 4. point.
aux = aux[1:]
node_group[aux] = 4
# generate costs matrix
costs = sps.lil_matrix((n_nod, n_nod), dtype=nm.double)
for ied in range(edges.mtx.shape[0]):
cc = edges.mtx.getrow(ied).indices[0]
n1, n2 = edges.facets[cc, :]
if node_group[n2] >= node_group[n1]:
costs[n1, n2] = 1.0
if node_group[n1] >= node_group[n2]:
costs[n2, n1] = 1.0
# generate weights matrix
aux = sps.lil_matrix((n_nod, n_nod), dtype=nm.double)
aux.setdiag(1.0 / costs.sum(1))
weights = (aux * costs).tocsr()
coors = taubin(mesh.coors, weights, lam, mu, n_iter)
if volume_corr:
volume0, bc = get_volume(mesh.conns[0], mesh.coors)
volume, _ = get_volume(mesh.conns[0], coors)
scale = volume0 / volume
coors = (coors - bc) * scale + bc
return coors
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, n_c)
v = FieldVariable('v', 'test', field, n_c, 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 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('-d',
'--derivative',
metavar='d',
type=int,
action='store',
dest='derivative',
default=0,
help=help['derivative'])
parser.add_option('-n',
'--max-order',
metavar='order',
type=int,
action='store',
dest='max_order',
default=2,
help=help['max_order'])
parser.add_option('-g',
'--geometry',
metavar='name',
action='store',
dest='geometry',
default='2_4',
help=help['geometry'])
parser.add_option('-m',
'--mesh',
metavar='mesh',
action='store',
dest='mesh',
default=None,
help=help['mesh'])
parser.add_option('',
'--permutations',
metavar='permutations',
action='store',
dest='permutations',
default=None,
help=help['permutations'])
parser.add_option('',
'--dofs',
metavar='dofs',
action='store',
dest='dofs',
default=None,
help=help['dofs'])
parser.add_option('-l',
'--lin-options',
metavar='options',
action='store',
dest='lin_options',
default='min_level=2,max_level=5,eps=1e-3',
help=help['lin_options'])
parser.add_option('',
'--plot-dofs',
action='store_true',
dest='plot_dofs',
default=False,
help=help['plot_dofs'])
options, args = parser.parse_args()
if len(args) == 1:
output_dir = args[0]
else:
parser.print_help(),
return
output('polynomial space:', options.basis)
output('max. order:', options.max_order)
lin = Struct(kind='adaptive', min_level=2, max_level=5, eps=1e-3)
for opt in options.lin_options.split(','):
key, val = opt.split('=')
setattr(lin, key, eval(val))
if options.mesh is None:
dim, n_ep = int(options.geometry[0]), int(options.geometry[2])
output('reference element geometry:')
output(' dimension: %d, vertices: %d' % (dim, n_ep))
gel = GeometryElement(options.geometry)
gps = PolySpace.any_from_args(None, gel, 1, base=options.basis)
ps = PolySpace.any_from_args(None,
gel,
options.max_order,
base=options.basis)
n_digit, _format = get_print_info(ps.n_nod, fill='0')
name_template = os.path.join(output_dir, 'bf_%s.vtk' % _format)
for ip in get_dofs(options.dofs, ps.n_nod):
output('shape function %d...' % ip)
def eval_dofs(iels, rx):
if options.derivative == 0:
bf = ps.eval_base(rx).squeeze()
rvals = bf[None, :, ip:ip + 1]
else:
bfg = ps.eval_base(rx, diff=True)
rvals = bfg[None, ..., ip]
return rvals
def eval_coors(iels, rx):
bf = gps.eval_base(rx).squeeze()
coors = nm.dot(bf, gel.coors)[None, ...]
return coors
(level, coors, conn, vdofs,
mat_ids) = create_output(eval_dofs,
eval_coors,
1,
ps,
min_level=lin.min_level,
max_level=lin.max_level,
eps=lin.eps)
out = {
'bf':
Struct(name='output_data',
mode='vertex',
data=vdofs,
var_name='bf',
dofs=None)
}
mesh = Mesh.from_data('bf_mesh', coors, None, [conn], [mat_ids],
[options.geometry])
name = name_template % ip
mesh.write(name, out=out)
output('...done (%s)' % name)
else:
mesh = Mesh.from_file(options.mesh)
output('mesh geometry:')
output(' dimension: %d, vertices: %d, elements: %d' %
(mesh.dim, mesh.n_nod, mesh.n_el))
domain = Domain('domain', mesh)
if options.permutations:
permutations = [int(ii) for ii in options.permutations.split(',')]
output('using connectivity permutations:', permutations)
for group in domain.iter_groups():
perms = group.gel.get_conn_permutations()[permutations]
offsets = nm.arange(group.shape.n_el) * group.shape.n_ep
group.conn[:] = group.conn.take(perms + offsets[:, None])
domain.setup_facets()
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, 1)
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.vtk' % _format)
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
out['u'].mesh.write(name, out=out)
output('...done (%s)' % name)
def smooth_mesh(mesh,
n_iter=4,
lam=0.6307,
mu=-0.6347,
weights=None,
bconstr=True,
volume_corr=False):
"""
FE mesh smoothing.
Based on:
[1] Steven K. Boyd, Ralph Muller, Smooth surface meshing for automated
finite element model generation from 3D image data, Journal of
Biomechanics, Volume 39, Issue 7, 2006, Pages 1287-1295,
ISSN 0021-9290, 10.1016/j.jbiomech.2005.03.006.
(http://www.sciencedirect.com/science/article/pii/S0021929005001442)
Parameters
----------
mesh : mesh
FE mesh.
n_iter : integer, optional
Number of iteration steps.
lam : float, optional
Smoothing factor, see [1].
mu : float, optional
Unshrinking factor, see [1].
weights : array, optional
Edge weights, see [1].
bconstr: logical, optional
Boundary constraints, if True only surface smoothing performed.
volume_corr: logical, optional
Correct volume after smoothing process.
Returns
-------
coors : array
Coordinates of mesh nodes.
"""
def laplacian(coors, weights):
n_nod = coors.shape[0]
displ = (weights - sps.identity(n_nod)) * coors
return displ
def taubin(coors0, weights, lam, mu, n_iter):
coors = coors0.copy()
for ii in range(n_iter):
displ = laplacian(coors, weights)
if nm.mod(ii, 2) == 0:
coors += lam * displ
else:
coors += mu * displ
return coors
def dets_fast(a):
m = a.shape[0]
n = a.shape[1]
lapack_routine = lapack_lite.dgetrf
pivots = nm.zeros((m, n), intc)
flags = nm.arange(1, n + 1).reshape(1, -1)
for i in xrange(m):
tmp = a[i]
lapack_routine(n, n, tmp, n, pivots[i], 0)
sign = 1. - 2. * (nm.add.reduce(pivots != flags, axis=1) % 2)
idx = nm.arange(n)
d = a[:, idx, idx]
absd = nm.absolute(d)
sign *= nm.multiply.reduce(d / absd, axis=1)
nm.log(absd, absd)
logdet = nm.add.reduce(absd, axis=-1)
return sign * nm.exp(logdet)
def get_volume(el, nd):
dim = nd.shape[1]
nnd = el.shape[1]
etype = '%d_%d' % (dim, nnd)
if etype == '2_4' or etype == '3_8':
el = elems_q2t(el)
nel = el.shape[0]
#bc = nm.zeros((dim, ), dtype=nm.double)
mul = 1.0 / factorial(dim)
if dim == 3:
mul *= -1.0
mtx = nm.ones((nel, dim + 1, dim + 1), dtype=nm.double)
mtx[:, :, :-1] = nd[el, :]
vols = mul * dets_fast(mtx.copy()) # copy() ???
vol = vols.sum()
bc = nm.dot(vols, mtx.sum(1)[:, :-1] / nnd)
bc /= vol
return vol, bc
import time
output('smoothing...')
tt = time.clock()
domain = Domain('mesh', mesh)
n_nod = mesh.n_nod
edges = domain.ed
if weights is None:
# initiate all vertices as inner - hierarchy = 2
node_group = nm.ones((n_nod, ), dtype=nm.int16) * 2
# boundary vertices - set hierarchy = 4
if bconstr:
# get "nodes of surface"
if domain.fa: # 3D.
fa = domain.fa
else:
fa = domain.ed
flag = fa.mark_surface_facets()
ii = nm.where(flag > 0)[0]
aux = nm.unique(fa.facets[ii])
if aux[0] == -1: # Triangular faces have -1 as 4. point.
aux = aux[1:]
node_group[aux] = 4
# generate costs matrix
mtx_ed = edges.mtx.tocoo()
_, idxs = nm.unique(mtx_ed.row, return_index=True)
aux = edges.facets[mtx_ed.col[idxs]]
fc1 = aux[:, 0]
fc2 = aux[:, 1]
idxs = nm.where(node_group[fc2] >= node_group[fc1])
rows1 = fc1[idxs]
cols1 = fc2[idxs]
idxs = nm.where(node_group[fc1] >= node_group[fc2])
rows2 = fc2[idxs]
cols2 = fc1[idxs]
crows = nm.concatenate((rows1, rows2))
ccols = nm.concatenate((cols1, cols2))
costs = sps.coo_matrix((nm.ones_like(crows), (crows, ccols)),
shape=(n_nod, n_nod),
dtype=nm.double)
# generate weights matrix
idxs = range(n_nod)
aux = sps.coo_matrix(
(1.0 / nm.asarray(costs.sum(1)).squeeze(), (idxs, idxs)),
shape=(n_nod, n_nod),
dtype=nm.double)
#aux.setdiag(1.0 / costs.sum(1))
weights = (aux.tocsc() * costs.tocsc()).tocsr()
coors = taubin(mesh.coors, weights, lam, mu, n_iter)
output('...done in %.2f s' % (time.clock() - tt))
if volume_corr:
output('rescaling...')
volume0, bc = get_volume(mesh.conns[0], mesh.coors)
volume, _ = get_volume(mesh.conns[0], coors)
scale = volume0 / volume
output('scale factor: %.2f' % scale)
coors = (coors - bc) * scale + bc
output('...done in %.2f s' % (time.clock() - tt))
return coors
def test_linearization(self):
from sfepy.base.base import Struct
from sfepy.fem import Mesh, Domain, H1NodalVolumeField
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 = H1NodalVolumeField('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 from_conf(conf, options):
mesh = Mesh('mesh_tetra',
data_dir + '/meshes/various_formats/small3d.mesh')
domain = Domain('domain', mesh)
return Test(conf=conf, options=options, domain=domain)
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('-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 = options.scale
if scale is not None:
try:
try:
scale = float(scale)
except ValueError:
scale = [float(ii) for ii in scale.split(',')]
scale = nm.array(scale, dtype=nm.float64, ndmin=1)
except:
output('bad scale! (%s)' % scale)
parser.print_help()
sys.exit(1)
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 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)
output('writing %s...' % filename_out)
mesh.write(filename_out, io=io)
output('...done')
