def get_gen_block_mesh_hook(dims,
shape,
centre,
mat_id=0,
name='block',
coors=None,
verbose=True):
"""
Parameters
----------
dims : array of 2 or 3 floats
Dimensions of the block.
shape : array of 2 or 3 ints
Shape (counts of nodes in x, y, z) of the block mesh.
centre : array of 2 or 3 floats
Centre of the block.
mat_id : int, optional
The material id of all elements.
name : string
Mesh name.
verbose : bool
If True, show progress of the mesh generation.
Returns
-------
mio : UserMeshIO instance
"""
def mesh_hook(mesh, mode):
"""
Generate the 1D mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims,
shape,
centre,
mat_id=mat_id,
name=name,
coors=coors,
verbose=verbose)
return mesh
elif mode == 'write':
pass
mio = UserMeshIO(mesh_hook)
return mio
def get_gen_1D_mesh_hook(XS, XE, n_nod):
"""
Parameters
----------
XS : float
leftmost coordinate
XE : float
rightmost coordinate
n_nod : int
number of nodes, number of cells is then n_nod - 1
Returns
-------
mio : UserMeshIO instance
"""
def mesh_hook(mesh, mode):
"""
Generate the 1D mesh.
"""
if mode == 'read':
coors = nm.linspace(XS, XE, n_nod).reshape((n_nod, 1))
conn = nm.arange(n_nod, dtype=nm.int32) \
.repeat(2)[1:-1].reshape((-1, 2))
mat_ids = nm.zeros(n_nod - 1, dtype=nm.int32)
descs = ['1_2']
mesh = Mesh.from_data('uniform_1D{}'.format(n_nod), coors, None,
[conn], [mat_ids], descs)
return mesh
elif mode == 'write':
pass
mio = UserMeshIO(mesh_hook)
return mio
def mesh_hook(mesh, mode):
"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims,
shape, [0, 0],
name='user_block',
verbose=False)
return mesh
elif mode == 'write':
pass
filename_mesh = UserMeshIO(mesh_hook)
regions = {
'Omega': 'all',
'Gamma': ('vertices of surface', 'facet'),
}
fields = {
'temperature': ('real', 1, 'Omega', 1),
}
variables = {
't': ('unknown field', 'temperature', 0),
's': ('test field', 'temperature', 't'),
}
def define(K=8.333,
mu_nh=3.846,
mu_mr=1.923,
kappa=1.923,
lam=5.769,
mu=3.846):
"""Define the problem to solve."""
from sfepy.discrete.fem.meshio import UserMeshIO
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.mechanics.matcoefs import stiffness_from_lame
def mesh_hook(mesh, mode):
"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh([2, 2, 3], [2, 2, 4], [0, 0, 1.5],
name='el3',
verbose=False)
return mesh
elif mode == 'write':
pass
filename_mesh = UserMeshIO(mesh_hook)
options = {
'nls': 'newton',
'ls': 'ls',
'ts': 'ts',
'save_times': 'all',
}
functions = {
'linear_pressure': (linear_pressure, ),
'empty': (lambda ts, coor, mode, region, ig: None,
),
}
fields = {
'displacement': ('real', 3, 'Omega', 1),
}
# Coefficients are chosen so that the tangent stiffness is the same for all
# material for zero strains.
materials = {
'solid': (
{
'K': K, # bulk modulus
'mu_nh': mu_nh, # shear modulus of neoHookean term
'mu_mr': mu_mr, # shear modulus of Mooney-Rivlin term
'kappa': kappa, # second modulus of Mooney-Rivlin term
# elasticity for LE term
'D': stiffness_from_lame(dim=3, lam=lam, mu=mu),
}, ),
'load':
'empty',
}
variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
}
regions = {
'Omega': 'all',
'Bottom': ('vertices in (z < 0.1)', 'facet'),
'Top': ('vertices in (z > 2.9)', 'facet'),
}
ebcs = {
'fixb': ('Bottom', {
'u.all': 0.0
}),
'fixt': ('Top', {
'u.[0,1]': 0.0
}),
}
integrals = {
'i': 1,
'isurf': 2,
}
equations = {
'linear':
"""dw_lin_elastic.i.Omega(solid.D, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
'neo-Hookean':
"""dw_tl_he_neohook.i.Omega(solid.mu_nh, v, u)
+ dw_tl_bulk_penalty.i.Omega(solid.K, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
'Mooney-Rivlin':
"""dw_tl_he_neohook.i.Omega(solid.mu_mr, v, u)
+ dw_tl_he_mooney_rivlin.i.Omega(solid.kappa, v, u)
+ dw_tl_bulk_penalty.i.Omega(solid.K, v, u)
= dw_surface_ltr.isurf.Top(load.val, v)""",
}
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 5,
'eps_a': 1e-10,
'eps_r': 1.0,
}),
'ts': (
'ts.simple',
{
't0': 0,
't1': 1,
'time_interval': None,
'n_step': 26, # has precedence over time_interval!
'verbose': 1,
}),
}
return locals()
def define(order=5, basis='lagrange', min_level=0, max_level=5, eps=1e-3):
filename_mesh = UserMeshIO(mesh_hook)
# Get the mesh bounding box.
io = MeshIO.any_from_filename(base_mesh)
bbox, dim = io.read_bounding_box(ret_dim=True)
options = {
'nls': 'newton',
'ls': 'ls',
'post_process_hook': 'post_process',
'linearization': {
'kind': 'adaptive',
'min_level':
min_level, # Min. refinement level applied everywhere.
'max_level': max_level, # Max. refinement level.
'eps': eps, # Relative error tolerance.
},
}
materials = {
'coef': ({
'val': 1.0
}, ),
}
regions = {
'Omega': 'all',
}
regions.update(define_box_regions(dim, bbox[0], bbox[1], 1e-5))
fields = {
'temperature': ('real', 1, 'Omega', order, 'H1', basis),
}
variables = {
't': ('unknown field', 'temperature', 0),
's': ('test field', 'temperature', 't'),
}
amplitude = 1.0
def ebc_sin(ts, coor, **kwargs):
x0 = 0.5 * (coor[:, 1].min() + coor[:, 1].max())
val = amplitude * nm.sin((coor[:, 1] - x0) * 2. * nm.pi)
return val
ebcs = {
't1': ('Left', {
't.0': 'ebc_sin'
}),
't2': ('Right', {
't.0': -0.5
}),
't3': ('Top', {
't.0': 1.0
}),
}
functions = {
'ebc_sin': (ebc_sin, ),
}
equations = {'Temperature': """dw_laplace.10.Omega(coef.val, s, t) = 0"""}
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-10,
}),
}
return locals()
def define(dims=(3, 1, 0.5),
shape=(11, 15, 15),
u_order=1,
refine=0,
ls='ls_d',
u_inlet=None,
mode='lcbc',
term_mode='original',
backend='numpy',
optimize='optimal',
verbosity=0):
"""
Parameters
----------
dims : tuple
The block domain dimensions.
shape : tuple
The mesh resolution: increase to improve accuracy.
u_order : int
The velocity field approximation order.
refine : int
The refinement level.
ls : 'ls_d' or 'ls_i'
The pre-configured linear solver name.
u_inlet : float, optional
The x-component of the inlet velocity.
mode : 'lcbc' or 'penalty'
The alternative formulations.
term_mode : 'original' or 'einsum'
The switch to use either the original or new experimental einsum-based
terms.
backend : str
The einsum mode backend.
optimize : str
The einsum mode optimization (backend dependent).
verbosity : 0, 1, 2, 3
The verbosity level of einsum-based terms.
"""
output('dims: {}, shape: {}, u_order: {}, refine: {}, u_inlet: {}'.format(
dims, shape, u_order, refine, u_inlet))
output('linear solver: {}'.format(ls))
output('mode: {}, term_mode: {}'.format(mode, term_mode))
if term_mode == 'einsum':
output('backend: {}, optimize: {}, verbosity: {}'.format(
backend, optimize, verbosity))
assert_(mode in {'lcbc', 'penalty'})
assert_(term_mode in {'original', 'einsum'})
if u_order > 1:
assert_(mode == 'penalty', msg='set mode=penalty to use u_order > 1!')
dims = nm.array(dims, dtype=nm.float64)
shape = nm.array(shape, dtype=nm.int32)
def mesh_hook(mesh, mode):
"""
Generate the block mesh.
"""
if mode == 'read':
mesh = gen_block_mesh(dims,
shape, [0, 0, 0],
name='user_block',
verbose=False)
return mesh
elif mode == 'write':
pass
filename_mesh = UserMeshIO(mesh_hook)
regions = define_box_regions(3, 0.5 * dims)
regions.update({
'Omega':
'all',
'Edges_v': ("""(r.Near *v r.Bottom) +v
(r.Bottom *v r.Far) +v
(r.Far *v r.Top) +v
(r.Top *v r.Near)""", 'edge'),
'Gamma1_f': ('copy r.Top', 'face'),
'Gamma2_f': ('r.Near +v r.Bottom +v r.Far', 'face'),
'Gamma_f': ('r.Gamma1_f +v r.Gamma2_f', 'face'),
'Gamma_v': ('r.Gamma_f -v r.Edges_v', 'face'),
'Inlet_f': ('r.Left -v r.Gamma_f', 'face'),
})
fields = {
'velocity': ('real', 3, 'Omega', u_order),
'pressure': ('real', 1, 'Omega', 1),
}
def get_u_d(ts, coors, region=None):
"""
Given stator velocity.
"""
out = nm.zeros_like(coors)
out[:] = [1.0, 1.0, 0.0]
return out
functions = {
'get_u_d': (get_u_d, ),
}
variables = {
'u': ('unknown field', 'velocity', 0),
'v': ('test field', 'velocity', 'u'),
'u_d': ('parameter field', 'velocity', {
'setter': 'get_u_d'
}),
'p': ('unknown field', 'pressure', 1),
'q': ('test field', 'pressure', 'p'),
}
materials = {
'm': ({
'nu': 1e-3,
'beta': 1e-2,
'mu': 1e-10,
}, ),
}
ebcs = {}
if u_inlet is not None:
ebcs['inlet'] = ('Inlet_f', {'u.0': u_inlet, 'u.[1, 2]': 0.0})
if mode == 'lcbc':
lcbcs = {
'walls': ('Gamma_v', {
'u.all': None
}, None, 'no_penetration', 'normals_Gamma.vtk'),
'edges': ('Edges_v', [(-0.5, 1.5)], {
'u.all': None
}, None, 'edge_direction', 'edges_Edges.vtk'),
}
if term_mode == 'original':
equations = {
'balance':
"""dw_div_grad.5.Omega(m.nu, v, u)
- dw_stokes.5.Omega(v, p)
+ dw_dot.5.Gamma1_f(m.beta, v, u)
+ dw_dot.5.Gamma2_f(m.beta, v, u)
=
+ dw_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility':
"""dw_laplace.5.Omega(m.mu, q, p)
+ dw_stokes.5.Omega(u, q) = 0""",
}
else:
equations = {
'balance':
"""de_div_grad.5.Omega(m.nu, v, u)
- de_stokes.5.Omega(v, p)
+ de_dot.5.Gamma1_f(m.beta, v, u)
+ de_dot.5.Gamma2_f(m.beta, v, u)
=
+ de_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility':
"""de_laplace.5.Omega(m.mu, q, p)
+ de_stokes.5.Omega(u, q) = 0""",
}
else:
materials['m'][0]['np_eps'] = 1e3
if term_mode == 'original':
equations = {
'balance':
"""dw_div_grad.5.Omega(m.nu, v, u)
- dw_stokes.5.Omega(v, p)
+ dw_dot.5.Gamma1_f(m.beta, v, u)
+ dw_dot.5.Gamma2_f(m.beta, v, u)
+ dw_non_penetration_p.5.Gamma1_f(m.np_eps, v, u)
+ dw_non_penetration_p.5.Gamma2_f(m.np_eps, v, u)
=
+ dw_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility':
"""dw_laplace.5.Omega(m.mu, q, p)
+ dw_stokes.5.Omega(u, q) = 0""",
}
else:
equations = {
'balance':
"""de_div_grad.5.Omega(m.nu, v, u)
- de_stokes.5.Omega(v, p)
+ de_dot.5.Gamma1_f(m.beta, v, u)
+ de_dot.5.Gamma2_f(m.beta, v, u)
+ de_non_penetration_p.5.Gamma1_f(m.np_eps, v, u)
+ de_non_penetration_p.5.Gamma2_f(m.np_eps, v, u)
=
+ de_dot.5.Gamma1_f(m.beta, v, u_d)""",
'incompressibility':
"""de_laplace.5.Omega(m.mu, q, p)
+ de_stokes.5.Omega(u, q) = 0""",
}
solvers = {
'ls_d': ('ls.auto_direct', {}),
'ls_i': (
'ls.petsc',
{
'method': 'bcgsl', # ksp_type
'precond': 'bjacobi', # pc_type
'sub_precond': 'ilu', # sub_pc_type
'eps_a': 0.0, # abstol
'eps_r': 1e-12, # rtol
'eps_d': 1e10, # Divergence tolerance.
'i_max': 200, # maxits
}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-10,
}),
}
options = {
'nls': 'newton',
'ls': ls,
'eterm': {
'verbosity': verbosity,
'backend_args': {
'backend': backend,
'optimize': optimize,
'layout': None,
},
},
'refinement_level': refine,
}
return locals()
if mode == 'read':
nodes = [[0, 0], [1, 0], [1, 1], [0, 1]]
nod_ids = [0, 0, 1, 1]
conns = [[[0, 1, 2], [0, 2, 3]]]
mat_ids = [[0, 1]]
descs = ['2_3']
mesh._set_io_data(nodes, nod_ids, conns, mat_ids, descs)
elif mode == 'write':
pass
from sfepy.discrete.fem.meshio import UserMeshIO
filename_meshes.extend([mesh_hook, UserMeshIO(mesh_hook)])
same = [(0, 1), (2, 3)]
import os.path as op
from sfepy.base.base import assert_
from sfepy.base.testing import TestCommon
class Test(TestCommon):
"""Write test names explicitely to impose a given order of evaluation."""
tests = [
'test_read_meshes', 'test_compare_same_meshes', 'test_read_dimension',
'test_write_read_meshes'
]
def define(is_opt=False):
filename_mesh = UserMeshIO(mesh_hook)
mnodes = (107, 113) # nodes for elongation eval.
regions = {
'Omega': 'all',
'Bottom': ('vertices in (z < 0.001)', 'facet'),
'Top': ('vertices in (z > 0.099)', 'facet'),
}
functions = {
'get_mat':
(lambda ts, coors, mode=None, problem=None, **kwargs: get_mat(
coors, mode, problem),
),
}
S = 1.083500e-05 # specimen cross-section
F = 5.0e3 # force
materials = {
'solid': 'get_mat',
'load': ({
'val': F / S
}, ),
}
fields = {
'displacement': ('real', 'vector', 'Omega', 1),
}
variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
}
ebcs = {
'FixedBottom': ('Bottom', {
'u.all': 0.0
}),
'FixedTop': ('Top', {
'u.0': 0.0,
'u.1': 0.0
}),
}
equations = {
'balance_of_forces':
"""dw_lin_elastic.5.Omega(solid.D, v, u)
= dw_surface_ltr.5.Top(load.val, v)""",
}
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'eps_a': 1e-6,
'eps_r': 1.e-6,
'check': 0,
'problem': 'nonlinear'
}),
}
options = {
'parametric_hook': 'optimization_hook',
'output_dir': 'output',
}
return locals()
