def test_write_read_meshes(self):
"""
Try to write and then read all supported formats.
"""
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.meshio import (supported_formats,
supported_capabilities)
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir
+ '/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
oks = []
for suffix, format_ in six.iteritems(supported_formats):
if isinstance(format_, tuple):
continue
if 'w' not in supported_capabilities[format_]: continue
filename = op.join(self.options.out_dir, 'test_mesh_wr' + suffix)
self.report('%s format: %s' % (suffix, filename))
mesh0.write(filename, io='auto')
mesh1 = Mesh.from_file(filename)
oks.extend(self._compare_meshes(mesh0, mesh1))
return sum(oks) == len(oks)
def test_write_read_meshes(self):
"""
Try to write and then read all supported formats.
"""
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.meshio import (supported_formats,
supported_capabilities)
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
oks = []
for suffix, format_ in supported_formats.iteritems():
if isinstance(format_, tuple):
continue
if 'w' not in supported_capabilities[format_]: continue
filename = op.join(self.options.out_dir, 'test_mesh_wr' + suffix)
self.report('%s format: %s' % (suffix, filename))
mesh0.write(filename, io='auto')
mesh1 = Mesh.from_file(filename)
oks.extend(self._compare_meshes(mesh0, mesh1))
return sum(oks) == len(oks)
def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh.from_file(data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh.from_file(data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh.from_file(data_dir + '/meshes/3d/block.mesh')
m2 = Mesh.from_file(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 = FEDomain('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 = FEDomain('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 test_interpolation_two_meshes(self):
from sfepy import data_dir
from sfepy.discrete import Variables
from sfepy.discrete.fem import Mesh, FEDomain, Field
m1 = Mesh.from_file(data_dir + '/meshes/3d/block.mesh')
m2 = Mesh.from_file(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 = FEDomain('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 = FEDomain('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 test_write_read_meshes(self):
"""
Try to write and then read all supported formats.
"""
import numpy as nm
from sfepy.discrete.fem import Mesh
from sfepy.discrete.fem.meshio import supported_formats
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
mesh0.cmesh.vertex_groups[:] =\
nm.random.randint(1, 10, size=mesh0.cmesh.n_coor)
mesh0.cmesh.cell_groups[:] =\
nm.random.randint(1, 10, size=mesh0.cmesh.n_el)
oks = []
for name, (cls, suffix, flag) in six.iteritems(supported_formats):
if 'w' not in flag: continue
suffix = suffix[0] # only the first of possible suffixes
filename = op.join(self.options.out_dir, 'test_mesh_wr' + suffix)
self.report('%s format: %s' % (suffix, filename))
try:
mesh0.write(filename, io='auto')
except RuntimeError:
if cls == 'meshio':
import traceback
self.report('-> cannot write "%s" format into "%s",'
' skipping' % (name, filename))
tb = traceback.format_exc()
self.report('reason:\n', tb)
continue
else:
raise
else:
mesh1 = Mesh.from_file(filename)
ok = self._compare_meshes(mesh0, mesh1, flag)
self.report('->', sum(ok) == len(ok))
oks.extend(ok)
return sum(oks) == len(oks)
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, FEDomain
if level > 0:
mesh = Mesh.from_file(filename)
domain = FEDomain(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)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.print_help()
sys.exit(1)
mesh_dir = args[0]
mesh_files = []
for (dirpath, dirnames, filenames) in os.walk(mesh_dir):
for ii in filenames:
_, ext = os.path.splitext(ii)
if ext.lower() in ['.mesh', '.vtk']:
mesh_files.append(dirpath + os.path.sep + ii)
for ii in mesh_files:
base, ext = os.path.splitext(ii)
fname_out = base + '.png'
if ext == '.mesh':
fname_in = 'aux.vtk'
mesh = Mesh.from_file(ii)
mesh.write(fname_in, io='auto')
else:
fname_in = ii
print('writing %s...' % fname_out)
gen_shot(fname_in, fname_out)
def test_read_meshes(self):
"""Try to read all listed meshes."""
from sfepy.discrete.fem import Mesh
conf_dir = op.dirname(__file__)
meshes = {}
for ii, filename in enumerate(filename_meshes):
self.report("%d. mesh: %s" % (ii + 1, filename))
mesh = Mesh.from_file(filename, prefix_dir=conf_dir)
assert_(mesh.dim == (mesh.coors.shape[1]))
assert_(mesh.n_nod == (mesh.coors.shape[0]))
assert_(mesh.n_nod == (mesh.ngroups.shape[0]))
assert_(mesh.n_el == sum(mesh.n_els))
for ig, conn in enumerate(mesh.conns):
assert_(conn.shape[0] == len(mesh.mat_ids[ig]))
assert_(conn.shape[0] == mesh.n_els[ig])
assert_(conn.shape[1] == mesh.n_e_ps[ig])
self.report("read ok")
meshes[filename] = mesh
self.meshes = meshes
return True
def main():
parser = OptionParser(usage=usage)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.print_help()
sys.exit(1)
mesh_dir = args[0]
mesh_files = []
for (dirpath, dirnames, filenames) in os.walk(mesh_dir):
for ii in filenames:
_, ext = os.path.splitext(ii)
if ext.lower() in ['.mesh', '.vtk']:
mesh_files.append(dirpath + os.path.sep + ii)
for ii in mesh_files:
base, ext = os.path.splitext(ii)
fname_out = base + '.png'
if ext == '.mesh':
fname_in = 'aux.vtk'
mesh = Mesh.from_file(ii)
mesh.write(fname_in, io='auto')
else:
fname_in = ii
print('writing %s...' % fname_out)
gen_shot(fname_in, fname_out)
def test_refine_3_8(self):
mesh = Mesh.from_file(data_dir + '/meshes/elements/3_8_1.mesh')
domain = refine(FEDomain('domain', mesh), self.options.out_dir, 1)
ok = compare_mesh('3_8', domain.mesh.coors, domain.mesh.get_conn('3_8'))
return ok
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('mesh_dir')
options = parser.parse_args()
mesh_dir = options.mesh_dir
mesh_files = []
for (dirpath, dirnames, filenames) in os.walk(mesh_dir):
for ii in filenames:
_, ext = os.path.splitext(ii)
if ext.lower() in ['.mesh', '.vtk']:
mesh_files.append(dirpath + os.path.sep + ii)
for ii in mesh_files:
base, ext = os.path.splitext(ii)
fname_out = base + '.png'
if ext == '.mesh':
fname_in = 'aux.vtk'
mesh = Mesh.from_file(ii)
mesh.write(fname_in, io='auto')
else:
fname_in = ii
print(('writing %s...' % fname_out))
gen_shot(fname_in, fname_out)
def test_rcm(self):
from sfepy import data_dir
from sfepy.linalg import rcm, permute_in_place, save_sparse_txt
from sfepy.discrete.fem import Mesh
filename = data_dir + '/meshes/2d/special/square_triquad.mesh'
self.report('testing reversed Cuthill-McKee permutation')
conf_dir = op.dirname(__file__)
mesh = Mesh.from_file(filename, prefix_dir=conf_dir)
graph = mesh.create_conn_graph()
graph0 = graph.copy()
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_orig'),
graph, fmt='%d %d %d\n')
perm = rcm(graph)
permute_in_place(graph, perm)
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_rcm'),
graph, fmt='%d %d %d\n')
assert_((graph0.indptr != graph.indptr).any())
assert_((graph0.indices != graph.indices).any())
permute_in_place(graph, perm, inverse=True)
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_rcm_inv'),
graph, fmt='%d %d %d\n')
assert_((graph0.indptr == graph.indptr).all())
assert_((graph0.indices == graph.indices).all())
return True
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('mesh_dir')
options = parser.parse_args()
mesh_dir = options.mesh_dir
mesh_files = []
for (dirpath, dirnames, filenames) in os.walk(mesh_dir):
for ii in filenames:
_, ext = os.path.splitext(ii)
if ext.lower() in ['.mesh', '.vtk']:
mesh_files.append(dirpath + os.path.sep + ii)
for ii in mesh_files:
base, ext = os.path.splitext(ii)
fname_out = base + '.png'
if ext == '.mesh':
fname_in = 'aux.vtk'
mesh = Mesh.from_file(ii)
mesh.write(fname_in, io='auto')
else:
fname_in = ii
print(('writing %s...' % fname_out))
gen_shot(fname_in, fname_out)
def main():
parser = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('--eps', action='store', dest='eps',
default=1e-12, help=helps['eps'])
parser.add_argument('-o', '--filename-out',
action='store', dest='filename_out',
default=None, help=helps['filename-out'])
parser.add_argument('filename')
options = parser.parse_args()
filename = options.filename
mesh = Mesh.from_file(filename)
mesh_out = extract_edges(mesh, eps=float(options.eps))
mesh_out = merge_lines(mesh_out)
filename_out = options.filename_out
if filename_out is None:
filename_out = edit_filename(filename, prefix='edge_', new_ext='.vtk')
output('Outline mesh - vertices: %d, edges: %d, output filename: %s'
% (mesh_out[0].shape[0], mesh_out[2][0].shape[0], filename_out))
# hack to write '3_2' elements - edges
io = VTKMeshIO(None)
aux_mesh = Struct()
aux_mesh._get_io_data = lambda: mesh_out
aux_mesh.n_el = mesh_out[2][0].shape[0]
io.write(filename_out, aux_mesh)
def test_read_meshes(self):
"""Try to read all listed meshes."""
from sfepy.discrete.fem import Mesh
ok = True
conf_dir = op.dirname(__file__)
self.meshes = {}
for ii, filename in enumerate(filename_meshes):
self.report('%d. mesh: %s' % (ii + 1, filename))
try:
mesh = Mesh.from_file(filename, prefix_dir=conf_dir)
except Exception as exc:
self.report(exc)
self.report('read failed!')
ok = False
continue
try:
assert_(mesh.dim == (mesh.coors.shape[1]))
assert_(mesh.n_nod == (mesh.coors.shape[0]))
assert_(mesh.n_nod == (mesh.cmesh.vertex_groups.shape[0]))
assert_(mesh.n_el == mesh.cmesh.num[mesh.cmesh.tdim])
except ValueError as exc:
self.report(exc)
self.report('read assertion failed!')
ok = False
continue
self.report('read ok')
self.meshes[filename] = mesh
return ok
def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', help=helps['filename'])
parser.add_argument('-d', '--detailed',
action='store_true', dest='detailed',
default=False, help=helps['detailed'])
options = parser.parse_args()
mesh = Mesh.from_file(options.filename)
output(mesh.cmesh)
output('element types:', mesh.descs)
output('nodal BCs:', sorted(mesh.nodal_bcs.keys()))
bbox = mesh.get_bounding_box()
output('bounding box: %s'
% ', '.join('%s: [%s, %s]' % (name, bbox[0, ii], bbox[1, ii])
for ii, name in enumerate('xyz'[:mesh.dim])))
output('centre:', mesh.coors.mean(0))
if not options.detailed: return
from sfepy.discrete.fem.geometry_element import create_geometry_elements
gels = create_geometry_elements()
mesh.cmesh.set_local_entities(gels)
mesh.cmesh.setup_entities()
for dim in range(1, mesh.cmesh.tdim + 1):
volumes = mesh.cmesh.get_volumes(dim)
output('volumes of %d %dD entities: min: %s mean: %s max: %s'
% (mesh.cmesh.num[dim],
dim, volumes.min(), volumes.mean(), volumes.max()))
def prepare_variable(filename, n_components):
from sfepy.discrete import FieldVariable
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh = Mesh.from_file(filename)
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]))
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
field = Field.from_args('field',
nm.float64,
n_components,
omega,
approx_order=2)
u = FieldVariable('u',
'parameter',
field,
primary_var_name='(set-to-None)')
u.set_from_mesh_vertices(data * nm.arange(1, n_components + 1)[None, :])
return u
def from_conf(conf, options):
from sfepy.discrete import FieldVariable, Variables, Problem
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh = Mesh.from_file(data_dir + '/meshes/2d/square_unit_tri.mesh')
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
domain.create_region('Left', 'vertices in (x < -0.499)', 'facet')
domain.create_region(
'LeftStrip', 'vertices in (x < -0.499)'
' & (y > -0.199) & (y < 0.199)', 'facet')
domain.create_region('LeftFix', 'r.Left -v r.LeftStrip', 'facet')
domain.create_region('Right', 'vertices in (x > 0.499)', 'facet')
domain.create_region(
'RightStrip', 'vertices in (x > 0.499)'
' & (y > -0.199) & (y < 0.199)', 'facet')
domain.create_region('RightFix', 'r.Right -v r.RightStrip', 'facet')
fu = Field.from_args('fu', nm.float64, 'vector', omega, approx_order=2)
u = FieldVariable('u', 'unknown', fu)
fp = Field.from_args('fp', nm.float64, 'scalar', omega, approx_order=2)
p = FieldVariable('p', 'unknown', fp)
pb = Problem('test', domain=domain, fields=[fu, fp], auto_conf=False)
test = Test(problem=pb,
variables=Variables([u, p]),
conf=conf,
options=options)
return test
def from_conf(conf, options):
from sfepy.discrete import Integral
from sfepy.discrete.fem import Mesh, FEDomain
domains = []
for filename in filename_meshes:
mesh = Mesh.from_file(filename)
domain = FEDomain('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)
qp_coors, qp_weights = integral.get_qp('3_8')
custom_integral = Integral('i',
coors=qp_coors,
weights=qp_weights,
order='custom')
test = Test(domains=domains,
integral=integral,
custom_integral=custom_integral,
conf=conf,
options=options)
return test
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 test_spbox_2d(self):
"""
Check position of a given vertex in the deformed mesh.
"""
mesh = Mesh.from_file(data_dir + '/meshes/2d/square_tri1.mesh')
spb = SplineBox([[-1, 1], [-1, 0.6]], mesh.coors, nsg=[2,1])
spb.move_control_point(1, [0.1, -0.2])
spb.move_control_point(2, [0.2, -0.3])
spb.move_control_point(3, [0.0, -0.1])
pt0 = mesh.coors[175,:].copy()
mesh.cmesh.coors[:] = spb.evaluate()
pt1 = mesh.coors[175,:]
expected_distance = 0.165892726387
actual_distance = nm.linalg.norm(pt0 - pt1)
ok = nm.fabs(actual_distance - expected_distance)\
/ expected_distance < tolerance
if not ok:
self.report('expected distance:')
self.report(expected_distance)
self.report('actual distance:')
self.report(actual_distance)
return ok
def test_spbox_2d(self):
"""
Check position of a given vertex in the deformed mesh.
"""
mesh = Mesh.from_file(data_dir + '/meshes/2d/square_tri1.mesh')
spb = SplineBox([[-1, 1], [-1, 0.6]], mesh.coors, nsg=[2, 1])
spb.move_control_point(1, [0.1, -0.2])
spb.move_control_point(2, [0.2, -0.3])
spb.move_control_point(3, [0.0, -0.1])
pt0 = mesh.coors[175, :].copy()
mesh.cmesh.coors[:] = spb.evaluate()
pt1 = mesh.coors[175, :]
expected_distance = 0.165892726387
actual_distance = nm.linalg.norm(pt0 - pt1)
ok = nm.fabs(actual_distance - expected_distance)\
/ expected_distance < tolerance
if not ok:
self.report('expected distance:')
self.report(expected_distance)
self.report('actual distance:')
self.report(actual_distance)
return ok
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, FEDomain
if level > 0:
mesh = Mesh.from_file(filename)
domain = FEDomain(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 = ArgumentParser(description=__doc__)
parser.add_argument('--version', action='version', version='%(prog)s')
parser.add_argument('filename')
options = parser.parse_args()
filename = options.filename
mesh = Mesh.from_file(filename)
output('Mesh:')
output(' dimension: %d, vertices: %d, elements: %d'
% (mesh.dim, mesh.n_nod, mesh.n_el))
domain = FEDomain('domain', mesh)
output(domain.cmesh)
domain.cmesh.cprint(1)
dim = domain.cmesh.dim
entities_opts = [
{'color' : 'k', 'label_global' : 12, 'label_local' : 8},
{'color' : 'b', 'label_global' : 12, 'label_local' : 8},
{'color' : 'g', 'label_global' : 12, 'label_local' : 8},
{'color' : 'r', 'label_global' : 12},
]
if dim == 2: entities_opts.pop(2)
pc.plot_cmesh(None, domain.cmesh,
wireframe_opts = {'color' : 'k'},
entities_opts=entities_opts)
plt.show()
def from_conf(conf, options):
import sfepy
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh = Mesh.from_file('meshes/2d/rectangle_tri.mesh',
prefix_dir=sfepy.data_dir)
domain = FEDomain('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 test_rcm(self):
from sfepy import data_dir
from sfepy.linalg import rcm, permute_in_place, save_sparse_txt
from sfepy.discrete.fem import Mesh
filename = data_dir + '/meshes/2d/special/square_triquad.mesh'
self.report('testing reversed Cuthill-McKee permutation')
conf_dir = op.dirname(__file__)
mesh = Mesh.from_file(filename, prefix_dir=conf_dir)
graph = mesh.create_conn_graph()
graph0 = graph.copy()
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_orig'),
graph, fmt='%d %d %d\n')
perm = rcm(graph)
permute_in_place(graph, perm)
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_rcm'),
graph, fmt='%d %d %d\n')
assert_((graph0.indptr != graph.indptr).any())
assert_((graph0.indices != graph.indices).any())
permute_in_place(graph, perm, inverse=True)
save_sparse_txt(op.join(self.options.out_dir, 'test_rcm_graph_rcm_inv'),
graph, fmt='%d %d %d\n')
assert_((graph0.indptr == graph.indptr).all())
assert_((graph0.indices == graph.indices).all())
return True
def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', help=helps['filename'])
parser.add_argument('-d', '--detailed',
action='store_true', dest='detailed',
default=False, help=helps['detailed'])
options = parser.parse_args()
mesh = Mesh.from_file(options.filename)
output(mesh.cmesh)
output('element types:', mesh.descs)
output('nodal BCs:', sorted(mesh.nodal_bcs.keys()))
bbox = mesh.get_bounding_box()
output('bounding box:\n%s'
% '\n'.join('%s: [%14.7e, %14.7e]' % (name, bbox[0, ii], bbox[1, ii])
for ii, name in enumerate('xyz'[:mesh.dim])))
output('centre: [%s]'
% ', '.join('%14.7e' % ii for ii in 0.5 * (bbox[0] + bbox[1])))
output('coordinates mean: [%s]'
% ', '.join('%14.7e' % ii for ii in mesh.coors.mean(0)))
if not options.detailed: return
domain = FEDomain(mesh.name, mesh)
for dim in range(1, mesh.cmesh.tdim + 1):
volumes = mesh.cmesh.get_volumes(dim)
output('volumes of %d %dD entities:\nmin: %.7e mean: %.7e median:'
' %.7e max: %.7e'
% (mesh.cmesh.num[dim], dim, volumes.min(), volumes.mean(),
nm.median(volumes), volumes.max()))
euler = lambda mesh: nm.dot(mesh.cmesh.num, [1, -1, 1, -1])
ec = euler(mesh)
output('Euler characteristic:', ec)
graph = mesh.create_conn_graph(verbose=False)
n_comp, _ = graph_components(graph.shape[0], graph.indptr, graph.indices)
output('number of connected components:', n_comp)
if mesh.dim > 1:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
FEDomain(surf_mesh.name, surf_mesh) # Calls CMesh.setup_entities().
sec = euler(surf_mesh)
output('surface Euler characteristic:', sec)
if mesh.dim == 3:
output('surface genus:', (2.0 - sec) / 2.0)
surf_graph = surf_mesh.create_conn_graph(verbose=False)
n_comp, _ = graph_components(surf_graph.shape[0],
surf_graph.indptr, surf_graph.indices)
output('number of connected surface components:', n_comp)
def test_entity_volumes(self):
import sfepy
from sfepy.discrete.fem import Mesh, FEDomain
from sfepy.discrete.common import Field
from sfepy.discrete import Integral
mesh = Mesh.from_file('meshes/3d/special/cross3d.mesh',
prefix_dir=sfepy.data_dir)
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
gamma = domain.create_region('Gamma', 'vertices of surface', 'facet')
top = domain.create_region('Top', 'cell 2')
vfield = Field.from_args('v', nm.float64, 'scalar', omega,
approx_order=1)
sfield = Field.from_args('s', nm.float64, 'scalar', gamma,
approx_order=1)
integral = Integral('i', order=3)
vgeo, _ = vfield.get_mapping(omega, integral, 'volume')
domain.create_surface_group(gamma)
sgeo, _ = sfield.get_mapping(gamma, integral, 'surface')
evols = mesh.cmesh.get_volumes(1)
fvols = mesh.cmesh.get_volumes(2) # Approximate for non-planar faces.
cvols = mesh.cmesh.get_volumes(3)
ok = True
_ok = abs(cvols.sum() - vgeo.volume.sum()) < 1e-15
self.report('total cell volume: %s (ok: %s)' % (cvols.sum(), _ok))
ok = _ok and ok
top_evols = nm.array([ 1. , 1. ,
1. , 1. ,
0.7211102550927979, 0.7211102550927979,
0.7211102550927979, 0.7211102550927979,
1.16619037896906 , 1.16619037896906 ,
1.16619037896906 , 1.16619037896906 ])
_ok = nm.allclose(top_evols, evols[top.edges], rtol=0.0, atol=1e-15)
self.report('total top cell edge length: %s (ok: %s)'
% (evols[top.edges].sum(), _ok))
ok = _ok and ok
i1 = [5, 6, 8, 9]
i2 = nm.setdiff1d(nm.arange(len(gamma.faces)), i1)
aux = fvols[gamma.faces] - sgeo.volume.ravel()
_ok = nm.allclose(aux[i1], 0.10560208437556773, rtol=0.0, atol=1e-15)
ok = _ok and ok
self.report('non-planar faces diff: %s (ok: %s)' % (aux[i1], _ok))
_ok = (nm.abs(aux[i2]) < 1e-15).all()
self.report('max. planar faces diff: %s (ok: %s)'
% (nm.abs(aux[i2]).max(), _ok))
ok = _ok and ok
return ok
def solveLaplaceEquationTetrahedral(mesh, meshVTK, boundaryPoints,
boundaryConditions):
"""
mesh: path to a 3D mesh / sfepy mesh
"""
if isinstance(mesh, str):
mesh = Mesh.from_file(mesh)
#Set domains
domain = FEDomain('domain', mesh)
omega = domain.create_region('Omega', 'all')
boundary = domain.create_region(
'gamma',
'vertex %s' % ','.join(map(str, range(meshVTK.GetNumberOfPoints()))),
'facet')
#set fields
field = Field.from_args('fu', np.float64, 1, omega, approx_order=1)
u = FieldVariable('u', 'unknown', field)
v = FieldVariable('v', 'test', field, primary_var_name='u')
m = Material('m', val=[1.])
#Define element integrals
integral = Integral('i', order=3)
#Equations defining
t1 = Term.new('dw_laplace( v, u )', integral, omega, v=v, u=u)
eq = Equation('balance', t1)
eqs = Equations([eq])
heatBoundary = boundaryConditions
points = boundaryPoints
#Boundary conditions
c = ClosestPointStupid(points, heatBoundary, meshVTK)
def u_fun(ts, coors, bc=None, problem=None, c=c):
c.distances = []
v = np.zeros(len(coors))
for i, p in enumerate(coors):
v[i] = c.interpolate(p)
#c.findClosestPoint(p)
return v
bc_fun = Function('u_fun', u_fun)
fix1 = EssentialBC('fix_u', boundary, {'u.all': bc_fun})
#Solve problem
ls = ScipyDirect({})
nls = Newton({}, lin_solver=ls)
pb = Problem('heat', equations=eqs)
pb.set_bcs(ebcs=Conditions([fix1]))
pb.set_solver(nls)
state = pb.solve(verbose=False, save_results=False)
u = state.get_parts()['u']
return u
def test_refine_hexa(self):
filename = data_dir + '/meshes/various_formats/abaqus_hex.inp'
mesh = Mesh.from_file(filename)
domain = FEDomain('domain', mesh)
refine(domain, self.options.out_dir)
return True
def test_refine_3_8(self):
mesh = Mesh.from_file(data_dir + '/meshes/elements/3_8_1.mesh')
domain = refine(FEDomain('domain', mesh), self.options.out_dir, 1)
ok = compare_mesh('3_8', domain.mesh.coors,
domain.mesh.get_conn('3_8'))
return ok
def test_refine_hexa(self):
filename = data_dir + '/meshes/various_formats/abaqus_hex.inp'
mesh = Mesh.from_file(filename)
domain = FEDomain('domain', mesh)
refine(domain, self.options.out_dir)
return True
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_normals(self):
"""
Check orientations of surface normals on the reference elements.
"""
import sfepy
from sfepy.discrete import Integral
from sfepy.discrete.fem import Mesh, FEDomain
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 = FEDomain('domain', mesh)
surface = domain.create_region('Surface', 'vertices of surface',
'facet')
domain.create_surface_group(surface)
sd = domain.surface_groups[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 from_conf(conf, options):
mesh = Mesh.from_file('meshes/2d/square_unit_tri.mesh',
prefix_dir=sfepy.data_dir)
domain = FEDomain('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_evaluate_at(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
meshes = {
'tp': Mesh.from_file(data_dir + '/meshes/3d/block.mesh'),
}
datas = gen_datas(meshes)
fields = {
'scalar_tp': ((1, 1), 'Omega', 1),
'vector_tp': ((3, 1), 'Omega', 1),
}
ok = True
for field_name in ['scalar_tp', 'vector_tp']:
d = FEDomain('d', meshes['tp'])
d.create_region('Omega', 'all')
f = fields[field_name]
field = Field.from_args('f',
nm.complex128,
f[0],
d.regions[f[1]],
approx_order=f[2])
ff = {field.name: field}
vv = Variables.from_conf(transform_variables(variables), ff)
u = vv['u']
bbox = d.get_mesh_bounding_box()
t = nm.expand_dims(nm.linspace(0, 1, 100), 1)
coors = nm.expand_dims(bbox[1] - bbox[0], 0) * t + bbox[0]
data_r = datas[field_name]
data_i = 2. / (1 + datas[field_name])
u.set_from_mesh_vertices(data_r)
vals_r = u.evaluate_at(coors)
u.set_from_mesh_vertices(data_i)
vals_i = u.evaluate_at(coors)
u.set_from_mesh_vertices(data_r + data_i * 1j)
vals = u.evaluate_at(coors)
_ok = nm.allclose(vals_r + vals_i * 1j, vals, rtol=0.0, atol=1e-12)
_ok = _ok and nm.abs(vals).sum() > 1
self.report('evaluating complex field %s: %s' % (field_name, _ok))
ok = ok and _ok
return ok
def from_conf(conf, options):
mesh = Mesh.from_file('meshes/2d/square_unit_tri.mesh',
prefix_dir=sfepy.data_dir)
domain = FEDomain('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, FEDomain
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 = FEDomain('domain', mesh)
surface = domain.create_region('Surface', 'vertices of surface',
'facet')
domain.create_surface_group(surface)
sd = domain.surface_groups[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_evaluate_at(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.discrete import Variables
from sfepy.discrete.fem import FEDomain, Field
meshes = {
'tp' : Mesh.from_file(data_dir + '/meshes/3d/block.mesh'),
}
datas = gen_datas(meshes)
fields = {
'scalar_tp' : ((1,1), 'Omega', 1),
'vector_tp' : ((3,1), 'Omega', 1),
}
ok = True
for field_name in ['scalar_tp', 'vector_tp']:
d = FEDomain('d', meshes['tp'])
d.create_region('Omega', 'all')
f = fields[field_name]
field = Field.from_args('f', nm.complex128, f[0],
d.regions[f[1]],
approx_order=f[2])
ff = {field.name : field}
vv = Variables.from_conf(transform_variables(variables), ff)
u = vv['u']
bbox = d.get_mesh_bounding_box()
t = nm.expand_dims(nm.linspace(0, 1, 100), 1)
coors = nm.expand_dims(bbox[1] - bbox[0], 0) * t + bbox[0]
data_r = datas[field_name]
data_i = 2. / (1 + datas[field_name])
u.set_from_mesh_vertices(data_r)
vals_r = u.evaluate_at(coors)
u.set_from_mesh_vertices(data_i)
vals_i = u.evaluate_at(coors)
u.set_from_mesh_vertices(data_r + data_i * 1j)
vals = u.evaluate_at(coors)
_ok = nm.allclose(vals_r + vals_i * 1j, vals, rtol=0.0, atol=1e-12)
_ok = _ok and nm.abs(vals).sum() > 1
self.report('evaluating complex field %s: %s' % (field_name, _ok))
ok = ok and _ok
return ok
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 = FEDomain('domain', mesh)
output(domain.cmesh)
domain.cmesh.cprint(1)
dim = domain.cmesh.dim
entities_opts = [
{
'color': 'k',
'label_global': 12,
'label_local': 8
},
{
'color': 'b',
'label_global': 12,
'label_local': 8
},
{
'color': 'g',
'label_global': 12,
'label_local': 8
},
{
'color': 'r',
'label_global': 12
},
]
if dim == 2: entities_opts.pop(2)
pc.plot_cmesh(None,
domain.cmesh,
wireframe_opts={'color': 'k'},
entities_opts=entities_opts)
plt.show()
def test_invariance(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
meshes = {
'tp' : Mesh.from_file(data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh.from_file(data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
ok = True
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
data = datas[field_name]
u1, u2 = do_interpolation(m1, m1, data, field_name, force=True)
self.report('max. difference:', nm.abs(u1() - u2()).max())
_ok = nm.allclose(u1(), u2(), rtol=0.0, atol=1e-12)
self.report('invariance for %s field: %s' % (field_name, _ok))
ok = ok and _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 = FEDomain('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 test_invariance_qp(self):
from sfepy import data_dir
from sfepy.discrete import Variables, Integral
from sfepy.discrete.fem import Mesh, FEDomain, Field
from sfepy.terms import Term
from sfepy.discrete.common.mappings import get_physical_qps
mesh = Mesh.from_file(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 = FEDomain('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.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 prepare_variable(filename, n_components):
from sfepy.discrete import FieldVariable
from sfepy.discrete.fem import Mesh, FEDomain, Field
mesh = Mesh.from_file(filename)
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])
domain = FEDomain("domain", mesh)
omega = domain.create_region("Omega", "all")
field = Field.from_args("field", nm.float64, n_components, omega, approx_order=2)
u = FieldVariable("u", "parameter", field, primary_var_name="(set-to-None)")
u.set_from_mesh_vertices(data * nm.arange(1, n_components + 1)[None, :])
return u
def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', help=helps['filename'])
options = parser.parse_args()
mesh = Mesh.from_file(options.filename)
output(mesh.cmesh)
output('element types:', mesh.descs)
output('nodal BCs:', mesh.nodal_bcs)
bbox = mesh.get_bounding_box()
output('bounding box: %s'
% ', '.join('%s: [%s, %s]' % (name, bbox[0, ii], bbox[1, ii])
for ii, name in enumerate('xyz'[:mesh.dim])))
output('centre:', mesh.coors.mean(0))
def main():
parser = ArgumentParser(description=__doc__.rstrip(),
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('filename', help=helps['filename'])
options = parser.parse_args()
mesh = Mesh.from_file(options.filename)
output(mesh.cmesh)
output('element types:', mesh.descs)
output('nodal BCs:', mesh.nodal_bcs)
bbox = mesh.get_bounding_box()
output('bounding box: %s'
% ', '.join('%s: [%s, %s]' % (name, bbox[0, ii], bbox[1, ii])
for ii, name in enumerate('xyz'[:mesh.dim])))
output('centre:', mesh.coors.mean(0))
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 = FEDomain('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 extendScalarField(tetraMeshPath,
meshVTK=None,
threshold=None,
meshNameType='_withScalarField',
recompute=False):
"""
Given two meshes, one superficial and another tetrahedral, extends all the scalar fields in the superficial mesh to the superficial using Laplace equation (Heat equation)
TODO: vectorise the sfepy problem for speedup!
"""
writePath = appendBeforeFileType(tetraMeshPath,
meshNameType).replace('.1', '')
if recompute or not os.path.exists(writePath):
mesh = Mesh.from_file(tetraMeshPath)
#horrible way, but could not write fields on ply files...
if isinstance(meshVTK, str):
meshVTK = utilities.read_poly(meshVTK)
#Poly
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(tetraMeshPath)
reader.Update()
v = reader.GetOutput()
for i in range(meshVTK.GetPointData().GetNumberOfArrays()):
heatBoundary = numpy_support.vtk_to_numpy(
meshVTK.GetPointData().GetArray(i))
points = utilities.vtk_to_numpy(meshVTK, flatten=False)
u = solveLaplaceEquationTetrahedral(mesh, meshVTK, points,
heatBoundary)
array = numpy_support.numpy_to_vtk(u)
array.SetName(meshVTK.GetPointData().GetArray(i).GetName())
v.GetPointData().AddArray(array)
#Write poly
utilities.writeUnstructuredGridVTK(writePath, v)
else:
v = utilities.readUnstructuredGridVTK(writePath)
#Do the split
if threshold is not None:
return writePath, computeVolumes(v, threshold, path=writePath)
else:
return writePath
def from_conf(conf, options):
from sfepy.discrete import Integral
from sfepy.discrete.fem import Mesh, FEDomain
domains = []
for filename in filename_meshes:
mesh = Mesh.from_file(filename)
domain = FEDomain('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 test_spregion2d(self):
"""
Check position of a given vertex in the deformed mesh.
"""
line_l = nm.array([[-1, 1], [-1, .5], [-1, 0], [-1, -.5]])
line_r = nm.array([[0, -.2], [.1, .2], [.3, .6], [.4, 1]])
sp_l = BSpline(3, is_cyclic=False)
sp_l.approximate(line_l, ncp=4)
kn_lr = sp_l.get_knot_vector()
sp_r = BSpline(3, is_cyclic=False)
sp_r.approximate(line_r, knots=kn_lr)
line_b = nm.array([[-1, -.5], [-.8, -.6], [-.5, -.4], [-.2, -.2],
[0, -.2]])
line_t = nm.array([[.4, 1], [0, 1], [-.2, 1], [-.6, 1], [-1, 1]])
sp_b = BSpline(3, is_cyclic=False)
sp_b.approximate(line_b, ncp=5)
kn_bt = sp_b.get_knot_vector()
sp_t = BSpline(3, is_cyclic=False)
sp_t.approximate(line_t, knots=kn_bt)
mesh = Mesh.from_file(data_dir + '/meshes/2d/square_tri1.mesh')
spb = SplineRegion2D([sp_b, sp_r, sp_t, sp_l], mesh.coors)
spb.move_control_point(5, [-.2, .1])
spb.move_control_point(10, [-.3, .2])
spb.move_control_point(15, [-.1, .2])
pt0 = mesh.coors[145, :].copy()
mesh.cmesh.coors[:] = spb.evaluate()
pt1 = mesh.coors[145, :]
expected_distance = 0.0908306614584
actual_distance = nm.linalg.norm(pt0 - pt1)
ok = nm.fabs(actual_distance - expected_distance)\
/ expected_distance < tolerance
if not ok:
self.report('expected distance:')
self.report(expected_distance)
self.report('actual distance:')
self.report(actual_distance)
return ok
def from_conf( conf, options ):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh, FEDomain
from sfepy.discrete import Functions
mesh = Mesh.from_file(data_dir
+ '/meshes/various_formats/abaqus_tet.inp')
mesh.nodal_bcs['set0'] = [0, 7]
domain = FEDomain('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 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 test_spregion2d(self):
"""
Check position of a given vertex in the deformed mesh.
"""
line_l = nm.array([[-1, 1], [-1, .5], [-1, 0], [-1, -.5]])
line_r = nm.array([[0, -.2], [.1, .2], [.3, .6], [.4, 1]])
sp_l = BSpline(3, is_cyclic=False)
sp_l.approximate(line_l, ncp=4)
kn_lr = sp_l.get_knot_vector()
sp_r = BSpline(3, is_cyclic=False)
sp_r.approximate(line_r, knots=kn_lr)
line_b = nm.array([[-1, -.5], [-.8, -.6], [-.5, -.4], [-.2, -.2],
[0, -.2]])
line_t = nm.array([[.4, 1], [0, 1], [-.2, 1], [-.6, 1], [-1, 1]])
sp_b = BSpline(3, is_cyclic=False)
sp_b.approximate(line_b, ncp=5)
kn_bt = sp_b.get_knot_vector()
sp_t = BSpline(3, is_cyclic=False)
sp_t.approximate(line_t, knots=kn_bt)
mesh = Mesh.from_file(data_dir + '/meshes/2d/square_tri1.mesh')
spb = SplineRegion2D([sp_b, sp_r, sp_t, sp_l], mesh.coors)
spb.move_control_point(5, [-.2, .1])
spb.move_control_point(10, [-.3, .2])
spb.move_control_point(15, [-.1, .2])
pt0 = mesh.coors[145,:].copy()
mesh.cmesh.coors[:] = spb.evaluate()
pt1 = mesh.coors[145,:]
expected_distance = 0.0908306614584
actual_distance = nm.linalg.norm(pt0 - pt1)
ok = nm.fabs(actual_distance - expected_distance)\
/ expected_distance < tolerance
if not ok:
self.report('expected distance:')
self.report(expected_distance)
self.report('actual distance:')
self.report(actual_distance)
return ok
def test_spbox_field(self):
"""
'Field' vs. 'coors'.
"""
mesh = Mesh.from_file(data_dir + '/meshes/2d/its2D.mesh')
coors = mesh.coors.copy()
bbox = nm.vstack((nm.amin(coors, 0), nm.amax(coors, 0))).T
coors_1 = coors.copy()
alpha = coors[:, 0]
spbox = SplineBox(bbox, coors, nsg=[1, 2], field=alpha)
dv1 = spbox.evaluate_derivative(6, 1)
spbox.move_control_point(6, -0.2)
c1 = spbox.evaluate()
coors_1[:, 0] = c1[:, 0]
alpha = coors[:, 1]
spbox = SplineBox(bbox, coors, nsg=[1, 2], field=alpha)
dv2 = spbox.evaluate_derivative(6, 1)
spbox.move_control_point(6, 0.2)
c2 = spbox.evaluate()
coors_1[:, 1] = c2[:, 0]
spbox = SplineBox(bbox, coors, nsg=[1, 2])
dv = spbox.evaluate_derivative(6, [1, 1])
spbox.move_control_point(6, [-0.2, 0.2])
coors_2 = spbox.evaluate()
rel_coor_dist = nm.linalg.norm(coors_2 - coors_1)\
/ nm.linalg.norm(coors_2)
ok = rel_coor_dist < tolerance
rel_dvel_dist = nm.linalg.norm(dv - nm.hstack([dv1, dv2]))\
/ nm.linalg.norm(dv)
ok = ok and rel_dvel_dist < tolerance
if not ok:
self.report('modified coordinates do not match, relative error:')
self.report(rel_coor_dist)
self.report('derivatives do not match, relative error:')
self.report(rel_dvel_dist)
return ok
def mesh_hook(mesh, mode):
"""
Load and refine a mesh here.
"""
if mode == 'read':
mesh = Mesh.from_file(base_mesh)
domain = FEDomain(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