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 refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = FEDomain('d', mesh1)
domain1r = domain1.refine()
mesh1r = domain1r.mesh
n_cell = region1.shape.n_cell
n_sub = 4 if mesh0.cmesh.tdim == 2 else 8
sub_cells = nm.empty((n_cell, n_sub + 1), dtype=nm.uint32)
sub_cells[:, 0] = region1.cells
sub_cells[:, 1] = region1.cells
aux = nm.arange((n_sub - 1) * n_cell, dtype=nm.uint32)
sub_cells[:, 2:] = mesh0.n_el + aux.reshape((n_cell, -1))
coors0, vgs0, conns0, mat_ids0, descs0 = mesh0._get_io_data()
coors, vgs, _conns, _mat_ids, descs = mesh1r._get_io_data()
# Preserve vertex groups of non-refined cells.
vgs[:len(vgs0)] = vgs0
def _interleave_refined(c0, c1):
if c1.ndim == 1:
c0 = c0[:, None]
c1 = c1[:, None]
n_row, n_col = c1.shape
n_new = region0.shape.n_cell + n_row
out = nm.empty((n_new, n_col), dtype=c0.dtype)
out[region0.cells] = c0[region0.cells]
out[region1.cells] = c1[::n_sub]
aux = c1.reshape((-1, n_col * n_sub))
out[mesh0.n_el:] = aux[:, n_col:].reshape((-1, n_col))
return out
conn = _interleave_refined(conns0[0], _conns[0])
mat_id = _interleave_refined(mat_ids0[0], _mat_ids[0]).squeeze()
mesh = Mesh.from_data('a', coors, vgs, [conn], [mat_id], descs)
domain = FEDomain('d', mesh)
return domain, sub_cells
def refine_region(domain0, region0, region1):
"""
Coarse cell sub_cells[ii, 0] in mesh0 is split into sub_cells[ii, 1:] in
mesh1.
The new fine cells are interleaved among the original coarse cells so that
the indices of the coarse cells do not change.
The cell groups are preserved. The vertex groups are preserved only in the
coarse (non-refined) cells.
"""
if region1 is None:
return domain0, None
mesh0 = domain0.mesh
mesh1 = Mesh.from_region(region1, mesh0)
domain1 = FEDomain('d', mesh1)
domain1r = domain1.refine()
mesh1r = domain1r.mesh
n_cell = region1.shape.n_cell
n_sub = 4 if mesh0.cmesh.tdim == 2 else 8
sub_cells = nm.empty((n_cell, n_sub + 1), dtype=nm.uint32)
sub_cells[:, 0] = region1.cells
sub_cells[:, 1] = region1.cells
aux = nm.arange((n_sub - 1) * n_cell, dtype=nm.uint32)
sub_cells[:, 2:] = mesh0.n_el + aux.reshape((n_cell, -1))
coors0, vgs0, conns0, mat_ids0, descs0 = mesh0._get_io_data()
coors, vgs, _conns, _mat_ids, descs = mesh1r._get_io_data()
# Preserve vertex groups of non-refined cells.
vgs[:len(vgs0)] = vgs0
def _interleave_refined(c0, c1):
if c1.ndim == 1:
c0 = c0[:, None]
c1 = c1[:, None]
n_row, n_col = c1.shape
n_new = region0.shape.n_cell + n_row
out = nm.empty((n_new, n_col), dtype=c0.dtype)
out[region0.cells] = c0[region0.cells]
out[region1.cells] = c1[::n_sub]
aux = c1.reshape((-1, n_col * n_sub))
out[mesh0.n_el:] = aux[:, n_col:].reshape((-1, n_col))
return out
conn = _interleave_refined(conns0[0], _conns[0])
mat_id = _interleave_refined(mat_ids0[0], _mat_ids[0]).squeeze()
mesh = Mesh.from_data('a', coors, vgs, [conn], [mat_id], descs)
domain = FEDomain('d', mesh)
return domain, sub_cells
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-s',
'--scale',
metavar='scale',
action='store',
dest='scale',
default=None,
help=helps['scale'])
parser.add_argument('-c',
'--center',
metavar='center',
action='store',
dest='center',
default=None,
help=helps['center'])
parser.add_argument('-r',
'--refine',
metavar='level',
action='store',
type=int,
dest='refine',
default=0,
help=helps['refine'])
parser.add_argument('-f',
'--format',
metavar='format',
action='store',
type=str,
dest='format',
default=None,
help=helps['format'])
parser.add_argument('-l',
'--list',
action='store_true',
dest='list',
help=helps['list'])
parser.add_argument('-m',
'--merge',
action='store_true',
dest='merge',
help=helps['merge'])
parser.add_argument('-t',
'--tri-tetra',
action='store_true',
dest='tri_tetra',
help=helps['tri-tetra'])
parser.add_argument('-2',
'--2d',
action='store_true',
dest='force_2d',
help=helps['2d'])
parser.add_argument('--save-per-mat',
action='store_true',
dest='save_per_mat',
help=helps['save-per-mat'])
parser.add_argument('--remesh',
metavar='options',
action='store',
dest='remesh',
default=None,
help=helps['remesh'])
parser.add_argument('filename_in')
parser.add_argument('filename_out')
options = parser.parse_args()
if options.list:
output('Supported readable mesh formats:')
output('--------------------------------')
output_mesh_formats('r')
output('')
output('Supported writable mesh formats:')
output('--------------------------------')
output_mesh_formats('w')
sys.exit(0)
scale = _parse_val_or_vec(options.scale, 'scale', parser)
center = _parse_val_or_vec(options.center, 'center', parser)
filename_in = options.filename_in
filename_out = options.filename_out
if options.remesh:
import tempfile
import shlex
import subprocess
dirname = tempfile.mkdtemp()
is_surface = options.remesh.startswith('q')
if is_surface:
mesh = Mesh.from_file(filename_in)
domain = FEDomain(mesh.name, mesh)
region = domain.create_region('surf', 'vertices of surface',
'facet')
surf_mesh = Mesh.from_region(region,
mesh,
localize=True,
is_surface=True)
filename = op.join(dirname, 'surf.mesh')
surf_mesh.write(filename, io='auto')
else:
import shutil
shutil.copy(filename_in, dirname)
filename = op.join(dirname, op.basename(filename_in))
qopts = ''.join(options.remesh.split()) # Remove spaces.
command = 'tetgen -BFENkACp%s %s' % (qopts, filename)
args = shlex.split(command)
subprocess.call(args)
root, ext = op.splitext(filename)
mesh = Mesh.from_file(root + '.1.vtk')
remove_files(dirname)
else:
mesh = Mesh.from_file(filename_in)
if options.force_2d:
data = list(mesh._get_io_data())
data[0] = data[0][:, :2]
mesh = Mesh.from_data(mesh.name, *data)
if scale is not None:
if len(scale) == 1:
tr = nm.eye(mesh.dim, dtype=nm.float64) * scale
elif len(scale) == mesh.dim:
tr = nm.diag(scale)
else:
raise ValueError('bad scale! (%s)' % scale)
mesh.transform_coors(tr)
if center is not None:
cc = 0.5 * mesh.get_bounding_box().sum(0)
shift = center - cc
tr = nm.c_[nm.eye(mesh.dim, dtype=nm.float64), shift[:, None]]
mesh.transform_coors(tr)
if options.refine > 0:
domain = FEDomain(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
if options.tri_tetra > 0:
mesh = triangulate(mesh, verbose=True)
if options.merge:
desc = mesh.descs[0]
coor, ngroups, conns = fix_double_nodes(mesh.coors,
mesh.cmesh.vertex_groups,
mesh.get_conn(desc))
mesh = Mesh.from_data(mesh.name + '_merged', coor, ngroups, [conns],
[mesh.cmesh.cell_groups], [desc])
if options.save_per_mat:
desc = mesh.descs[0]
conns, cgroups = mesh.get_conn(desc), mesh.cmesh.cell_groups
coors, ngroups = mesh.coors, mesh.cmesh.vertex_groups
mat_ids = nm.unique(cgroups)
for mat_id in mat_ids:
idxs = nm.where(cgroups == mat_id)[0]
imesh = Mesh.from_data(mesh.name + '_matid_%d' % mat_id, coors,
ngroups, [conns[idxs]], [cgroups[idxs]],
[desc])
fbase, fext = op.splitext(filename_out)
ifilename_out = '%s_matid_%d%s' % (fbase, mat_id, fext)
io = MeshIO.for_format(ifilename_out,
format=options.format,
writable=True)
output('writing %s...' % ifilename_out)
imesh.write(ifilename_out, io=io)
output('...done')
io = MeshIO.for_format(filename_out, format=options.format, writable=True)
cell_types = ', '.join(supported_cell_types[io.format])
output('writing [%s] %s...' % (cell_types, filename_out))
mesh.write(filename_out, io=io)
output('...done')
def create_local_problem(omega_gi, orders):
"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
order_u, order_p = orders
mesh = omega_gi.domain.mesh
# All tasks have the whole mesh.
bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)
min_y, max_y = bbox[:, 1]
eps_y = 1e-8 * (max_y - min_y)
mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)
domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')
gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f)'
% (min_x + eps_x),
'facet', allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f)'
% (max_x - eps_x),
'facet', allow_empty=True)
gamma3_i = domain_i.create_region('Gamma3',
'vertices in (y < %.10f)'
% (min_y + eps_y),
'facet', allow_empty=True)
field1_i = Field.from_args('fu', nm.float64, mesh.dim, omega_i,
approx_order=order_u)
field2_i = Field.from_args('fp', nm.float64, 1, omega_i,
approx_order=order_p)
output('field 1: number of local DOFs:', field1_i.n_nod)
output('field 2: number of local DOFs:', field2_i.n_nod)
u_i = FieldVariable('u_i', 'unknown', field1_i, order=0)
v_i = FieldVariable('v_i', 'test', field1_i, primary_var_name='u_i')
p_i = FieldVariable('p_i', 'unknown', field2_i, order=1)
q_i = FieldVariable('q_i', 'test', field2_i, primary_var_name='p_i')
if mesh.dim == 2:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.092]])
else:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.132],
[0.092], [0.092], [0.092]])
mat = Material('m', D=stiffness_from_lame(mesh.dim, lam=10, mu=5),
k=1, alpha=alpha)
integral = Integral('i', order=2*(max(order_u, order_p)))
t11 = Term.new('dw_lin_elastic(m.D, v_i, u_i)',
integral, omega_i, m=mat, v_i=v_i, u_i=u_i)
t12 = Term.new('dw_biot(m.alpha, v_i, p_i)',
integral, omega_i, m=mat, v_i=v_i, p_i=p_i)
t21 = Term.new('dw_biot(m.alpha, u_i, q_i)',
integral, omega_i, m=mat, u_i=u_i, q_i=q_i)
t22 = Term.new('dw_laplace(m.k, q_i, p_i)',
integral, omega_i, m=mat, q_i=q_i, p_i=p_i)
eq1 = Equation('eq1', t11 - t12)
eq2 = Equation('eq1', t21 + t22)
eqs = Equations([eq1, eq2])
ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all' : 0.0})
ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.0' : 0.05})
def bc_fun(ts, coors, **kwargs):
val = 0.3 * nm.sin(4 * nm.pi * (coors[:, 0] - min_x) / (max_x - min_x))
return val
fun = Function('bc_fun', bc_fun)
ebc3 = EssentialBC('ebc3', gamma3_i, {'p_i.all' : fun})
pb = Problem('problem_i', equations=eqs, active_only=False)
pb.time_update(ebcs=Conditions([ebc1, ebc2, ebc3]))
pb.update_materials()
return pb
def create_local_problem(omega_gi, orders):
"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
order_u, order_p = orders
mesh = omega_gi.domain.mesh
# All tasks have the whole mesh.
bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)
min_y, max_y = bbox[:, 1]
eps_y = 1e-8 * (max_y - min_y)
mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)
domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')
gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f)'
% (min_x + eps_x),
'facet', allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f)'
% (max_x - eps_x),
'facet', allow_empty=True)
gamma3_i = domain_i.create_region('Gamma3',
'vertices in (y < %.10f)'
% (min_y + eps_y),
'facet', allow_empty=True)
field1_i = Field.from_args('fu', nm.float64, mesh.dim, omega_i,
approx_order=order_u)
field2_i = Field.from_args('fp', nm.float64, 1, omega_i,
approx_order=order_p)
output('field 1: number of local DOFs:', field1_i.n_nod)
output('field 2: number of local DOFs:', field2_i.n_nod)
u_i = FieldVariable('u_i', 'unknown', field1_i, order=0)
v_i = FieldVariable('v_i', 'test', field1_i, primary_var_name='u_i')
p_i = FieldVariable('p_i', 'unknown', field2_i, order=1)
q_i = FieldVariable('q_i', 'test', field2_i, primary_var_name='p_i')
if mesh.dim == 2:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.092]])
else:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.132],
[0.092], [0.092], [0.092]])
mat = Material('m', D=stiffness_from_lame(mesh.dim, lam=10, mu=5),
k=1, alpha=alpha)
integral = Integral('i', order=2*(max(order_u, order_p)))
t11 = Term.new('dw_lin_elastic(m.D, v_i, u_i)',
integral, omega_i, m=mat, v_i=v_i, u_i=u_i)
t12 = Term.new('dw_biot(m.alpha, v_i, p_i)',
integral, omega_i, m=mat, v_i=v_i, p_i=p_i)
t21 = Term.new('dw_biot(m.alpha, u_i, q_i)',
integral, omega_i, m=mat, u_i=u_i, q_i=q_i)
t22 = Term.new('dw_laplace(m.k, q_i, p_i)',
integral, omega_i, m=mat, q_i=q_i, p_i=p_i)
eq1 = Equation('eq1', t11 - t12)
eq2 = Equation('eq1', t21 + t22)
eqs = Equations([eq1, eq2])
ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all' : 0.0})
ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.0' : 0.05})
def bc_fun(ts, coors, **kwargs):
val = 0.3 * nm.sin(4 * nm.pi * (coors[:, 0] - min_x) / (max_x - min_x))
return val
fun = Function('bc_fun', bc_fun)
ebc3 = EssentialBC('ebc3', gamma3_i, {'p_i.all' : fun})
pb = Problem('problem_i', equations=eqs, active_only=False)
pb.time_update(ebcs=Conditions([ebc1, ebc2, ebc3]))
pb.update_materials()
return pb
def create_local_problem(omega_gi, order):
"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
mesh = omega_gi.domain.mesh
# All tasks have the whole mesh.
bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)
mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)
domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')
gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f)'
% (min_x + eps_x),
'facet', allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f)'
% (max_x - eps_x),
'facet', allow_empty=True)
field_i = Field.from_args('fu', nm.float64, 1, omega_i,
approx_order=order)
output('number of local field DOFs:', field_i.n_nod)
u_i = FieldVariable('u_i', 'unknown', field_i)
v_i = FieldVariable('v_i', 'test', field_i, primary_var_name='u_i')
integral = Integral('i', order=2*order)
mat = Material('m', lam=10, mu=5)
t1 = Term.new('dw_laplace(m.lam, v_i, u_i)',
integral, omega_i, m=mat, v_i=v_i, u_i=u_i)
def _get_load(coors):
val = nm.ones_like(coors[:, 0])
for coor in coors.T:
val *= nm.sin(4 * nm.pi * coor)
return val
def get_load(ts, coors, mode=None, **kwargs):
if mode == 'qp':
return {'val' : _get_load(coors).reshape(coors.shape[0], 1, 1)}
load = Material('load', function=Function('get_load', get_load))
t2 = Term.new('dw_volume_lvf(load.val, v_i)',
integral, omega_i, load=load, v_i=v_i)
eq = Equation('balance', t1 - 100 * t2)
eqs = Equations([eq])
ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all' : 0.0})
ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.all' : 0.1})
pb = Problem('problem_i', equations=eqs, active_only=False)
pb.time_update(ebcs=Conditions([ebc1, ebc2]))
pb.update_materials()
return pb
def create_local_problem(omega_gi, order):
"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
mesh = omega_gi.domain.mesh
# All tasks have the whole mesh.
bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)
mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)
domain_i = FEDomain('domain_i', mesh_i)
omega_i = domain_i.create_region('Omega', 'all')
gamma1_i = domain_i.create_region('Gamma1',
'vertices in (x < %.10f)' %
(min_x + eps_x),
'facet',
allow_empty=True)
gamma2_i = domain_i.create_region('Gamma2',
'vertices in (x > %.10f)' %
(max_x - eps_x),
'facet',
allow_empty=True)
field_i = Field.from_args('fu', nm.float64, 1, omega_i, approx_order=order)
output('number of local field DOFs:', field_i.n_nod)
u_i = FieldVariable('u_i', 'unknown', field_i)
v_i = FieldVariable('v_i', 'test', field_i, primary_var_name='u_i')
integral = Integral('i', order=2 * order)
mat = Material('m', lam=10, mu=5)
t1 = Term.new('dw_laplace(m.lam, v_i, u_i)',
integral,
omega_i,
m=mat,
v_i=v_i,
u_i=u_i)
def _get_load(coors):
val = nm.ones_like(coors[:, 0])
for coor in coors.T:
val *= nm.sin(4 * nm.pi * coor)
return val
def get_load(ts, coors, mode=None, **kwargs):
if mode == 'qp':
return {'val': _get_load(coors).reshape(coors.shape[0], 1, 1)}
load = Material('load', function=Function('get_load', get_load))
t2 = Term.new('dw_volume_lvf(load.val, v_i)',
integral,
omega_i,
load=load,
v_i=v_i)
eq = Equation('balance', t1 - 100 * t2)
eqs = Equations([eq])
ebc1 = EssentialBC('ebc1', gamma1_i, {'u_i.all': 0.0})
ebc2 = EssentialBC('ebc2', gamma2_i, {'u_i.all': 0.1})
pb = Problem('problem_i', equations=eqs, active_only=False)
pb.time_update(ebcs=Conditions([ebc1, ebc2]))
pb.update_materials()
return pb
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('-s', '--scale', metavar='scale',
action='store', dest='scale',
default=None, help=helps['scale'])
parser.add_argument('-c', '--center', metavar='center',
action='store', dest='center',
default=None, help=helps['center'])
parser.add_argument('-r', '--refine', metavar='level',
action='store', type=int, dest='refine',
default=0, help=helps['refine'])
parser.add_argument('-f', '--format', metavar='format',
action='store', type=str, dest='format',
default=None, help=helps['format'])
parser.add_argument('-l', '--list', action='store_true',
dest='list', help=helps['list'])
parser.add_argument('-m', '--merge', action='store_true',
dest='merge', help=helps['merge'])
parser.add_argument('-t', '--tri-tetra', action='store_true',
dest='tri_tetra', help=helps['tri-tetra'])
parser.add_argument('-2', '--2d', action='store_true',
dest='force_2d', help=helps['2d'])
parser.add_argument('--save-per-mat', action='store_true',
dest='save_per_mat', help=helps['save-per-mat'])
parser.add_argument('--remesh', metavar='options',
action='store', dest='remesh',
default=None, help=helps['remesh'])
parser.add_argument('filename_in')
parser.add_argument('filename_out')
options = parser.parse_args()
if options.list:
output('Supported readable mesh formats:')
output('--------------------------------')
output_mesh_formats('r')
output('')
output('Supported writable mesh formats:')
output('--------------------------------')
output_mesh_formats('w')
sys.exit(0)
scale = _parse_val_or_vec(options.scale, 'scale', parser)
center = _parse_val_or_vec(options.center, 'center', parser)
filename_in = options.filename_in
filename_out = options.filename_out
if options.remesh:
import tempfile
import shlex
import subprocess
dirname = tempfile.mkdtemp()
is_surface = options.remesh.startswith('q')
if is_surface:
mesh = Mesh.from_file(filename_in)
domain = FEDomain(mesh.name, mesh)
region = domain.create_region('surf', 'vertices of surface',
'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
filename = op.join(dirname, 'surf.mesh')
surf_mesh.write(filename, io='auto')
else:
import shutil
shutil.copy(filename_in, dirname)
filename = op.join(dirname, op.basename(filename_in))
qopts = ''.join(options.remesh.split()) # Remove spaces.
command = 'tetgen -BFENkACp%s %s' % (qopts, filename)
args = shlex.split(command)
subprocess.call(args)
root, ext = op.splitext(filename)
mesh = Mesh.from_file(root + '.1.vtk')
remove_files(dirname)
else:
mesh = Mesh.from_file(filename_in)
if options.force_2d:
data = list(mesh._get_io_data())
data[0] = data[0][:, :2]
mesh = Mesh.from_data(mesh.name, *data)
if scale is not None:
if len(scale) == 1:
tr = nm.eye(mesh.dim, dtype=nm.float64) * scale
elif len(scale) == mesh.dim:
tr = nm.diag(scale)
else:
raise ValueError('bad scale! (%s)' % scale)
mesh.transform_coors(tr)
if center is not None:
cc = 0.5 * mesh.get_bounding_box().sum(0)
shift = center - cc
tr = nm.c_[nm.eye(mesh.dim, dtype=nm.float64), shift[:, None]]
mesh.transform_coors(tr)
if options.refine > 0:
domain = FEDomain(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
if options.tri_tetra > 0:
conns = None
for k, new_desc in [('3_8', '3_4'), ('2_4', '2_3')]:
if k in mesh.descs:
conns = mesh.get_conn(k)
break
if conns is not None:
nelo = conns.shape[0]
output('initial mesh: %d elements' % nelo)
new_conns = elems_q2t(conns)
nn = new_conns.shape[0] // nelo
new_cgroups = nm.repeat(mesh.cmesh.cell_groups, nn)
output('new mesh: %d elements' % new_conns.shape[0])
mesh = Mesh.from_data(mesh.name, mesh.coors,
mesh.cmesh.vertex_groups,
[new_conns], [new_cgroups], [new_desc])
if options.merge:
desc = mesh.descs[0]
coor, ngroups, conns = fix_double_nodes(mesh.coors,
mesh.cmesh.vertex_groups,
mesh.get_conn(desc), 1e-9)
mesh = Mesh.from_data(mesh.name + '_merged',
coor, ngroups,
[conns], [mesh.cmesh.cell_groups], [desc])
if options.save_per_mat:
desc = mesh.descs[0]
conns, cgroups = mesh.get_conn(desc), mesh.cmesh.cell_groups
coors, ngroups = mesh.coors, mesh.cmesh.vertex_groups
mat_ids = nm.unique(cgroups)
for mat_id in mat_ids:
idxs = nm.where(cgroups == mat_id)[0]
imesh = Mesh.from_data(mesh.name + '_matid_%d' % mat_id,
coors, ngroups,
[conns[idxs]], [cgroups[idxs]], [desc])
fbase, fext = op.splitext(filename_out)
ifilename_out = '%s_matid_%d%s' % (fbase, mat_id, fext)
io = MeshIO.for_format(ifilename_out, format=options.format,
writable=True)
output('writing %s...' % ifilename_out)
imesh.write(ifilename_out, io=io)
output('...done')
io = MeshIO.for_format(filename_out, format=options.format,
writable=True)
cell_types = ', '.join(supported_cell_types[io.format])
output('writing [%s] %s...' % (cell_types, filename_out))
mesh.write(filename_out, io=io)
output('...done')
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--version",
action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_argument("-n",
"--no-surface",
action="store_true",
dest="no_surface",
default=False,
help="do not output surface [default: %(default)s]")
parser.add_argument('filename_in', help="'-' is for stdin")
parser.add_argument('filename_out', help="'-' is for stdout")
options = parser.parse_args()
filename_in = options.filename_in
filename_out = options.filename_out
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 = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region,
mesh,
localize=True,
is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0, 1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:, nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m", "--mesh",
action="store_true", dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_option("-n", "--no-surface",
action="store_true", dest="no_surface",
default=False,
help="do not output surface [default: %default]")
(options, args) = parser.parse_args()
if (len(args) == 2):
filename_in = args[0];
filename_out = args[1];
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r");
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0,1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:,nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w");
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def post_process_hook(pb,
nd_data,
qp_data,
ccoor,
vol,
im,
tstep,
eps0,
recovery_file_tag=''):
from sfepy.discrete.fem import Mesh
elavg_data = {}
elvol = nm.sum(vol, axis=1)
sh0 = vol.shape[:2]
for k in qp_data.keys():
print(k, qp_data[k].shape, vol.shape, elvol.shape)
sh1 = qp_data[k].shape[1:]
val = qp_data[k].reshape(sh0 + sh1)
elavg_data[k] = (nm.sum(val * vol, axis=1) / elvol)[:, None, ...]
output_dir = pb.conf.options.get('output_dir', '.')
suffix = '%03d.%03d' % (im, tstep)
coors = pb.get_mesh_coors(actual=True)
coors = (coors - 0.5*(nm.max(coors, axis=0)\
- nm.min(coors, axis=0))) * eps0 + ccoor
# Y
out = {}
out['displacement'] = Struct(name='output_data',
mode='vertex',
data=nd_data['u'] * eps0,
variable='u')
out['green_strain'] = Struct(name='output_data',
mode='cell',
data=elavg_data['E'])
mesh = Mesh.from_region(pb.domain.regions['Y'], pb.domain.mesh)
mesh.coors[:] = coors
micro_name = pb.get_output_name(extra='recovered_Y_' + recovery_file_tag +
suffix)
filename = osp.join(output_dir, osp.basename(micro_name))
output(' %s' % filename)
mesh.write(filename, io='auto', out=out)
p_tab = {'Ym': 'p', 'Yc1': 'p1', 'Yc2': 'p2'}
mesh0 = pb.domain.mesh
for rname in ['Ym'] + ['Yc%d' % ch for ch in pb.conf.chs]:
reg = pb.domain.regions[rname]
cells = reg.get_cells()
out = {}
out['cauchy_stress'] = Struct(name='output_data',
mode='cell',
data=elavg_data['S'][cells])
out['velocity'] = Struct(name='output_data',
mode='cell',
data=elavg_data['w'][cells])
out['pressure'] = Struct(name='output_data',
mode='vertex',
data=nd_data[p_tab[rname]][:, None])
ac = nm.ascontiguousarray
conn = mesh0.cmesh.get_cell_conn()
cells = reg.entities[-1]
verts = reg.entities[0]
aux = nm.diff(conn.offsets)
assert nm.sum(nm.diff(aux)) == 0
conn = ac(conn.indices.reshape((mesh0.n_el, aux[0]))[cells])
remap = -nm.ones(mesh0.n_nod)
remap[verts] = nm.arange(verts.shape[0])
conn = remap[conn]
mesh = Mesh.from_data('region_%s' % rname, ac(coors[verts]),
ac(mesh0.cmesh.vertex_groups[verts]), [conn],
[ac(mesh0.cmesh.cell_groups[cells])],
[mesh0.descs[0]])
micro_name = pb.get_output_name(extra='recovered_%s_' % rname +
recovery_file_tag + suffix)
filename = osp.join(output_dir, osp.basename(micro_name))
output(' %s' % filename)
mesh.write(filename, io='auto', out=out)
def main():
parser = OptionParser(usage=usage, version="%prog " + sfepy.__version__)
parser.add_option("-m",
"--mesh",
action="store_true",
dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_option("-n",
"--no-surface",
action="store_true",
dest="no_surface",
default=False,
help="do not output surface [default: %default]")
(options, args) = parser.parse_args()
if (len(args) == 2):
filename_in = args[0]
filename_out = args[1]
else:
parser.print_help(),
return
if (filename_in == '-'):
file_in = sys.stdin
else:
file_in = open(filename_in, "r")
mesh = Mesh.from_file(filename_in)
if (filename_in != '-'):
file_in.close()
domain = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region,
mesh,
localize=True,
is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0, 1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:, nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--version", action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument("-m", "--mesh",
action="store_true", dest="save_mesh",
default=False,
help="save surface mesh")
parser.add_argument("-n", "--no-surface",
action="store_true", dest="no_surface",
default=False,
help="do not output surface [default: %(default)s]")
parser.add_argument('filename_in', help="'-' is for stdin")
parser.add_argument('filename_out', help="'-' is for stdout")
options = parser.parse_args()
filename_in = options.filename_in
filename_out = options.filename_out
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 = FEDomain('domain', mesh)
if options.save_mesh:
region = domain.create_region('surf', 'vertices of surface', 'facet')
surf_mesh = Mesh.from_region(region, mesh,
localize=True, is_surface=True)
aux = edit_filename(filename_in, prefix='surf_', new_ext='.mesh')
surf_mesh.write(aux, io='auto')
if domain.has_faces():
domain.fix_element_orientation()
lst, surf_faces = get_surface_faces(domain)
if options.no_surface:
return
gr_s = surface_graph(surf_faces, mesh.n_nod)
n_comp, comps = surface_components(gr_s, surf_faces)
output('number of surface components:', n_comp)
ccs, comps = comps, nm.zeros((0,1), nm.int32)
for cc in ccs:
comps = nm.concatenate((comps, cc[:,nm.newaxis]), 0)
out = nm.concatenate((lst, comps), 1)
if (filename_out == '-'):
file_out = sys.stdout
else:
file_out = open(filename_out, "w")
for row in out:
file_out.write('%d %d %d\n' % (row[0], row[1], row[2]))
if (filename_out != '-'):
file_out.close()
def create_local_problem(omega_gi, orders):
"""
Local problem definition using a domain corresponding to the global region
`omega_gi`.
"""
order_u, order_p = orders
mesh = omega_gi.domain.mesh
# All tasks have the whole mesh.
bbox = mesh.get_bounding_box()
min_x, max_x = bbox[:, 0]
eps_x = 1e-8 * (max_x - min_x)
min_y, max_y = bbox[:, 1]
eps_y = 1e-8 * (max_y - min_y)
mesh_i = Mesh.from_region(omega_gi, mesh, localize=True)
domain_i = FEDomain("domain_i", mesh_i)
omega_i = domain_i.create_region("Omega", "all")
gamma1_i = domain_i.create_region("Gamma1", "vertices in (x < %.10f)" % (min_x + eps_x), "facet", allow_empty=True)
gamma2_i = domain_i.create_region("Gamma2", "vertices in (x > %.10f)" % (max_x - eps_x), "facet", allow_empty=True)
gamma3_i = domain_i.create_region("Gamma3", "vertices in (y < %.10f)" % (min_y + eps_y), "facet", allow_empty=True)
field1_i = Field.from_args("fu", nm.float64, mesh.dim, omega_i, approx_order=order_u)
field2_i = Field.from_args("fp", nm.float64, 1, omega_i, approx_order=order_p)
output("field 1: number of local DOFs:", field1_i.n_nod)
output("field 2: number of local DOFs:", field2_i.n_nod)
u_i = FieldVariable("u_i", "unknown", field1_i, order=0)
v_i = FieldVariable("v_i", "test", field1_i, primary_var_name="u_i")
p_i = FieldVariable("p_i", "unknown", field2_i, order=1)
q_i = FieldVariable("q_i", "test", field2_i, primary_var_name="p_i")
if mesh.dim == 2:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.092]])
else:
alpha = 1e2 * nm.array([[0.132], [0.132], [0.132], [0.092], [0.092], [0.092]])
mat = Material("m", lam=10, mu=5, k=1, alpha=alpha)
integral = Integral("i", order=2 * (max(order_u, order_p)))
t11 = Term.new("dw_lin_elastic_iso(m.lam, m.mu, v_i, u_i)", integral, omega_i, m=mat, v_i=v_i, u_i=u_i)
t12 = Term.new("dw_biot(m.alpha, v_i, p_i)", integral, omega_i, m=mat, v_i=v_i, p_i=p_i)
t21 = Term.new("dw_biot(m.alpha, u_i, q_i)", integral, omega_i, m=mat, u_i=u_i, q_i=q_i)
t22 = Term.new("dw_laplace(m.k, q_i, p_i)", integral, omega_i, m=mat, q_i=q_i, p_i=p_i)
eq1 = Equation("eq1", t11 - t12)
eq2 = Equation("eq1", t21 + t22)
eqs = Equations([eq1, eq2])
ebc1 = EssentialBC("ebc1", gamma1_i, {"u_i.all": 0.0})
ebc2 = EssentialBC("ebc2", gamma2_i, {"u_i.0": 0.05})
def bc_fun(ts, coors, **kwargs):
val = 0.3 * nm.sin(4 * nm.pi * (coors[:, 0] - min_x) / (max_x - min_x))
return val
fun = Function("bc_fun", bc_fun)
ebc3 = EssentialBC("ebc3", gamma3_i, {"p_i.all": fun})
pb = Problem("problem_i", equations=eqs, active_only=False)
pb.time_update(ebcs=Conditions([ebc1, ebc2, ebc3]))
pb.update_materials()
return pb
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)
