def dump_to_vtk( filename, options, steps = None ):
output( 'dumping to VTK...' )
mesh = Mesh.from_file( filename )
io = HDF5MeshIO( filename )
ts = TimeStepper( *io.read_time_stepper() )
if options.output_filename_trunk:
ofn_trunk = options.output_filename_trunk
else:
ofn_trunk = get_trunk( filename )
if steps is None:
iterator = ts.iter_from( options.step0 )
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output( ts.format % (step, ts.n_step - 1) )
out = io.read_data( step )
if out is None: break
mesh.write( ofn_trunk + ts.suffix % step + '.vtk',
io = 'auto', out = out )
output( '...done' )
return ts.suffix
def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None,
fields=None, linearization=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
def _save_step(suffix, out, mesh):
if linearization is not None:
output('linearizing...')
out = _linearize(out, fields, linearization)
output('...done')
for key, val in out.iteritems():
lmesh = val.get('mesh', mesh)
lmesh.write(output_filename_trunk + '_' + key + suffix,
io='auto', out={key : val})
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
else:
mesh.write(output_filename_trunk + suffix, io='auto', out=out)
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
times, nts, dts = extract_times(filename)
except ValueError:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
_save_step('.vtk', out, mesh)
ret = None
else:
ts.times = times
ts.n_step = times.shape[0]
if steps is None:
iterator = ts.iter_from(step0)
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output(ts.format % (step, ts.n_step - 1))
out = io.read_data(step)
if out is None: break
_save_step('.' + ts.suffix % step + '.vtk', out, mesh)
ret = ts.suffix
output('...done')
return ret
def get_default_ts(self, t0=None, t1=None, dt=None, n_step=None, step=None):
t0 = get_default(t0, 0.0)
t1 = get_default(t1, 1.0)
dt = get_default(dt, 1.0)
n_step = get_default(n_step, 1)
ts = TimeStepper(t0, t1, dt, n_step)
ts.set_step(step)
return ts
def __call__(self, volume, problem=None, data=None):
problem = get_default(problem, self.problem)
dim, sym = problem.get_dim(get_sym=True)
filename = self.set_variables(None, 0, 0, 'filename', **data)
ts = TimeStepper(*HDF5MeshIO(filename).read_time_stepper())
coef = nm.zeros((ts.n_step, sym), dtype=self.dtype)
term_mode = self.term_mode
equations, variables = problem.create_evaluable(self.expression,
term_mode=term_mode)
self.set_variables(variables, None, None, 'col', **data)
for ii, (ir, ic) in enumerate(iter_sym(dim)):
filename = self.set_variables(None, ir, ic, 'filename', **data)
io = HDF5MeshIO(filename)
for step, time in ts:
self.set_variables(variables, io, step, 'row', **data)
val = eval_equations(equations, variables, term_mode=term_mode)
coef[step, ii] = val
coef /= self._get_volume(volume)
return coef
def __call__(self, volume, problem=None, data=None):
problem = get_default(problem, self.problem)
filename = self.set_variables(None, None, None, 'filename', **data)
io = HDF5MeshIO(filename)
ts = TimeStepper(*io.read_time_stepper())
coef = nm.zeros((ts.n_step, 1), dtype=self.dtype)
term_mode = self.term_mode
equations, variables = problem.create_evaluable(self.expression,
term_mode=term_mode)
self.set_variables(variables, None, None, 'col', **data)
for step, time in ts:
self.set_variables(variables, io, step, 'row', **data)
val = eval_equations(equations, variables, term_mode=term_mode)
coef[step] = val
coef /= self._get_volume(volume)
return coef
def __call__(self, volume, problem=None, data=None):
expression, region_name, aux_eq = self.expression
problem = get_default(problem, self.problem)
problem.select_variables(self.variables)
aux = self.get_filename(data)
io = HDF5MeshIO(self.get_filename(data))
ts = TimeStepper(*io.read_time_stepper())
coef = nm.zeros((ts.n_step, 1), dtype=nm.float64)
for step, time in ts:
step_data = io.read_data(step)
var_name = self.variables[0]
c_name = problem.variables[var_name].primary_var_name
omega = step_data[c_name].data
problem.variables[var_name].set_data(omega)
val1 = eval_term_op(None, expression, problem, call_mode='d_eval')
pc = step_data[self.variables[3]].data
val2 = eval_boundary_diff_vel_grad(problem, omega, pc, aux_eq,
region_name)
coef[step] = val1 + val2
coef /= volume
return coef
def __init__(self, conf, nls=None, context=None, **kwargs):
TimeSteppingSolver.__init__(self,
conf,
nls=nls,
context=context,
**kwargs)
self.ts = TimeStepper(0.0, 1.0, n_step=1, is_quasistatic=True)
def verify_correctors(self, sign, state0, filename, problem=None):
problem = get_default(problem, self.problem)
io = HDF5MeshIO(filename)
ts = TimeStepper(*io.read_time_stepper())
ts.set_step(0)
problem.equations.init_time(ts)
variables = self.problem.get_variables()
vu, vp = self.dump_variables
vdp = self.verify_variables[-1]
p0 = sign * state0[vp]
format = '====== time %%e (step %%%dd of %%%dd) ====='\
% ((ts.n_digit,) * 2)
vv = variables
ok = True
for step, time in ts:
output(format % (time, step + 1, ts.n_step))
data = io.read_data(step)
if step == 0:
assert_(nm.allclose(data[vp].data, p0))
state0 = problem.create_state()
state0.set_full(data[vu].data, vu)
state0.set_full(data[vp].data, vp)
vv[vdp].data_from_data(data['d'+vp].data)
problem.update_time_stepper(ts)
state = problem.solve(state0)
state, state0 = state(), state0()
err = nla.norm(state - state0) / nla.norm(state0)
output(state.min(), state.max())
output(state0.min(), state0.max())
output('>>>>>', err)
ok = ok and (err < 1e-12)
problem.advance(ts)
return ok
def verify_correctors(self, sign, state0, filename, problem=None):
problem = get_default(problem, self.problem)
io = HDF5MeshIO(filename)
ts = TimeStepper(*io.read_time_stepper())
ts.set_step(0)
problem.equations.init_time(ts)
variables = self.problem.get_variables()
vu, vp = self.dump_variables
vdp = self.verify_variables[-1]
p0 = sign * state0[vp]
format = '====== time %%e (step %%%dd of %%%dd) ====='\
% ((ts.n_digit,) * 2)
vv = variables
ok = True
for step, time in ts:
output(format % (time, step + 1, ts.n_step))
data = io.read_data(step)
if step == 0:
assert_(nm.allclose(data[vp].data, p0))
state0 = problem.create_state()
state0.set_full(data[vu].data, vu)
state0.set_full(data[vp].data, vp)
vv[vdp].set_data(data['d' + vp].data)
problem.update_time_stepper(ts)
state = problem.solve(state0)
state, state0 = state(), state0()
err = nla.norm(state - state0) / nla.norm(state0)
output(state.min(), state.max())
output(state0.min(), state0.max())
output('>>>>>', err)
ok = ok and (err < 1e-12)
problem.advance(ts)
return ok
def __init__(self, conf, **kwargs):
TimeSteppingSolver.__init__(self, conf, **kwargs)
self.ts = TimeStepper.from_conf(self.conf)
nd = self.ts.n_digit
format = '====== time %%e (step %%%dd of %%%dd) =====' % (nd, nd)
self.format = format
def __init__(self, conf, **kwargs):
TimeSteppingSolver.__init__(self, conf, **kwargs)
self.ts = TimeStepper.from_conf(self.conf)
nd = self.ts.n_digit
format = '====== time %%e (step %%%dd of %%%dd) =====' % (nd, nd)
self.format = format
def __init__(self, conf, nls=None, context=None, **kwargs):
TimeSteppingSolver.__init__(self, conf, nls=nls, context=context,
**kwargs)
self.ts = TimeStepper.from_conf(self.conf)
nd = self.ts.n_digit
format = '====== time %%e (step %%%dd of %%%dd) =====' % (nd, nd)
self.format = format
self.verbose = self.conf.verbose
def get_default_ts(self, t0=None, t1=None, dt=None, n_step=None,
step=None):
t0 = get_default(t0, 0.0)
t1 = get_default(t1, 1.0)
dt = get_default(dt, 1.0)
n_step = get_default(n_step, 1)
ts = TimeStepper(t0, t1, dt, n_step, step=step)
return ts
def __init__(self, conf, nls=None, context=None, **kwargs):
TimeSteppingSolver.__init__(self, conf, nls=nls, context=context,
**kwargs)
self.ts = TimeStepper.from_conf(self.conf)
nd = self.ts.n_digit
format = '====== time %%e (step %%%dd of %%%dd) =====' % (nd, nd)
self.format = format
self.verbose = self.conf.verbose
def __iter__(self):
ts = TimeStepper(0, bzone[0], dt=None, n_step=num)
for ii, val in ts:
yield ii, val, nm.array([1.0, 0.0])
if ii == (num-2): break
ts = TimeStepper(0, bzone[1], dt=None, n_step=num)
for ii, k1 in ts:
wdir = nm.array([bzone[0], k1])
val = nm.linalg.norm(wdir)
wdir = wdir / val
yield num + ii, val, wdir
if ii == (num-2): break
wdir = nm.array([bzone[0], bzone[1]])
val = nm.linalg.norm(wdir)
wdir = wdir / val
ts = TimeStepper(0, 1, dt=None, n_step=num)
for ii, _ in ts:
yield 2 * num + ii, val * (1.0 - float(ii)/(num-1)), wdir
def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
except:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
mesh.write(output_filename_trunk + '.vtk', io='auto', out=out)
ret = None
else:
if steps is None:
iterator = ts.iter_from(step0)
else:
iterator = [(step, ts.times[step]) for step in steps]
for step, time in iterator:
output(ts.format % (step, ts.n_step - 1))
out = io.read_data(step)
if out is None: break
mesh.write('.'.join((output_filename_trunk,
ts.suffix % step, 'vtk')),
io='auto', out=out)
ret = ts.suffix
output('...done')
return ret
def get_stepper(rng, pb, options):
if options.stepper == 'linear':
stepper = TimeStepper(rng[0], rng[1], dt=None, n_step=rng[2])
return stepper
bbox = pb.domain.mesh.get_bounding_box()
bzone = 2.0 * nm.pi / (bbox[1] - bbox[0])
num = rng[2] // 3
class BrillouinStepper(Struct):
"""
Step over 1. Brillouin zone in xy plane.
"""
def __init__(self, t0, t1, dt=None, n_step=None, step=None, **kwargs):
Struct.__init__(self,
t0=t0,
t1=t1,
dt=dt,
n_step=n_step,
step=step)
self.n_digit, self.format, self.suffix = get_print_info(
self.n_step)
def __iter__(self):
ts = TimeStepper(0, bzone[0], dt=None, n_step=num)
for ii, val in ts:
yield ii, val, nm.array([1.0, 0.0])
if ii == (num - 2): break
ts = TimeStepper(0, bzone[1], dt=None, n_step=num)
for ii, k1 in ts:
wdir = nm.array([bzone[0], k1])
val = nm.linalg.norm(wdir)
wdir = wdir / val
yield num + ii, val, wdir
if ii == (num - 2): break
wdir = nm.array([bzone[0], bzone[1]])
val = nm.linalg.norm(wdir)
wdir = wdir / val
ts = TimeStepper(0, 1, dt=None, n_step=num)
for ii, _ in ts:
yield 2 * num + ii, val * (1.0 - float(ii) / (num - 1)), wdir
stepper = BrillouinStepper(0, 1, n_step=rng[2])
return stepper
def from_file_hdf5(filename, var_names):
"""TODO: do not read entire file, provide data on demand."""
io = HDF5MeshIO(filename)
ts = TimeStepper(*io.read_time_stepper())
steps = nm.arange(ts.n_step, dtype=nm.int32)
ths = io.read_variables_time_history(var_names, ts)
objs = OneTypeList(History)
for name, th in ths.iteritems():
hist = History(name, steps=steps, times=ts.times, th=th)
objs.append(hist)
obj = Histories(objs, dt=ts.dt, name=' '.join(var_names))
return obj
def make_term_args(arg_shapes,
arg_kinds,
arg_types,
ats_mode,
domain,
material_value=None,
poly_space_base=None):
from sfepy.base.base import basestr
from sfepy.discrete import FieldVariable, Material, Variables, Materials
from sfepy.discrete.fem import Field
from sfepy.solvers.ts import TimeStepper
from sfepy.mechanics.tensors import dim2sym
omega = domain.regions['Omega']
dim = domain.shape.dim
sym = dim2sym(dim)
def _parse_scalar_shape(sh):
if isinstance(sh, basestr):
if sh == 'D':
return dim
elif sh == 'S':
return sym
elif sh == 'N': # General number ;)
return 1
else:
return int(sh)
else:
return sh
def _parse_tuple_shape(sh):
if isinstance(sh, basestr):
return [_parse_scalar_shape(ii.strip()) for ii in sh.split(',')]
else:
return (int(sh), )
args = {}
str_args = []
materials = []
variables = []
for ii, arg_kind in enumerate(arg_kinds):
if arg_kind != 'ts':
if ats_mode is not None:
extended_ats = arg_types[ii] + ('/%s' % ats_mode)
else:
extended_ats = arg_types[ii]
try:
sh = arg_shapes[arg_types[ii]]
except KeyError:
sh = arg_shapes[extended_ats]
if arg_kind.endswith('variable'):
shape = _parse_scalar_shape(sh[0] if isinstance(sh, tuple) else sh)
field = Field.from_args('f%d' % ii,
nm.float64,
shape,
omega,
approx_order=1,
poly_space_base=poly_space_base)
if arg_kind == 'virtual_variable':
if sh[1] is not None:
istate = arg_types.index(sh[1])
else:
# Only virtual variable in arguments.
istate = -1
# -> Make fake variable.
var = FieldVariable('u-1', 'unknown', field)
var.set_constant(0.0)
variables.append(var)
var = FieldVariable('v',
'test',
field,
primary_var_name='u%d' % istate)
elif arg_kind == 'state_variable':
var = FieldVariable('u%d' % ii, 'unknown', field)
var.set_constant(0.0)
elif arg_kind == 'parameter_variable':
var = FieldVariable('p%d' % ii,
'parameter',
field,
primary_var_name='(set-to-None)')
var.set_constant(0.0)
variables.append(var)
str_args.append(var.name)
args[var.name] = var
elif arg_kind.endswith('material'):
if sh is None: # Switched-off opt_material.
continue
prefix = ''
if isinstance(sh, basestr):
aux = sh.split(':')
if len(aux) == 2:
prefix, sh = aux
if material_value is None:
material_value = 1.0
shape = _parse_tuple_shape(sh)
if (len(shape) > 1) or (shape[0] > 1):
if ((len(shape) == 2) and (shape[0] == shape[1])
and (material_value != 0.0)):
# Identity matrix.
val = nm.eye(shape[0], dtype=nm.float64)
else:
# Array.
val = nm.empty(shape, dtype=nm.float64)
val.fill(material_value)
values = {'%sc%d' % (prefix, ii): val}
elif (len(shape) == 1) and (shape[0] == 1):
# Single scalar as a special value.
values = {'.c%d' % ii: material_value}
else:
raise ValueError('wrong material shape! (%s)' % shape)
mat = Material('m%d' % ii, values=values)
materials.append(mat)
str_args.append(mat.name + '.' + 'c%d' % ii)
args[mat.name] = mat
elif arg_kind == 'ts':
ts = TimeStepper(0.0, 1.0, 1.0, 5)
str_args.append('ts')
args['ts'] = ts
else:
str_args.append('user%d' % ii)
args[str_args[-1]] = None
materials = Materials(materials)
variables = Variables(variables)
return args, str_args, materials, variables
def define():
chs = [1, 2]
ts = TimeStepper(0, 0.15, n_step=30)
options = {
'output_dir': osp.join(wdir, 'results'),
'micro_filename': osp.join(wdir, 'largedef_porous_mic.py'),
'parametric_hook': 'incremental_algorithm',
}
materials = {
'solid': 'get_homog',
}
fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure': ('real', 'scalar', 'Omega', 1),
}
variables = {
'u': ('unknown field', 'displacement', 0),
'v': ('test field', 'displacement', 'u'),
'p1': ('unknown field', 'pressure', 1),
'q1': ('test field', 'pressure', 'p1'),
'p2': ('unknown field', 'pressure', 2),
'q2': ('test field', 'pressure', 'p2'),
}
filename_mesh = osp.join(wdir, 'macro_mesh_3x2.vtk')
mesh_d, move_val = 0.24, -0.04
regions = {
'Omega': 'all',
'Left': ('vertices in (x < 0.0001)', 'facet'),
'Right': ('vertices in (x > %e)' % (mesh_d * 0.999), 'facet'),
'Recovery': ('cell 1', 'cell'),
}
ebcs = {
'left_fix_all': ('Left', {
'u.all': 0.0
}),
'right_fix_x': ('Right', {
'u.0': 0.0
}),
'right_move_x': ('Right', {
'u.1': 'move'
}),
}
micro_args = {
'eps0': mesh_d / 3,
'dt': ts.dt,
}
functions = {
'move': (move, ),
'get_homog': (lambda ts, coors, mode, **kwargs: get_homog_mat(
ts, coors, mode, define_args=micro_args, **kwargs),
),
}
integrals = {
'i': 3,
}
equations = {
# eq. (60)
'balance_of_forces':
"""
dw_nonsym_elastic.i.Omega(solid.A, v, u)
- dw_biot.i.Omega(solid.B1, v, p1)
- dw_biot.i.Omega(solid.B2, v, p2)
=
- dw_lin_prestress.i.Omega(solid.S, v)
- dw_lin_prestress.i.Omega(solid.Q, v)""",
# eq. (61), alpha = 1
'mass_conservation_1':
"""
- %e * dw_biot.i.Omega(solid.B1, u, q1)
- dw_volume_dot.i.Omega(solid.G11, q1, p1)
- dw_volume_dot.i.Omega(solid.G12, q1, p2)
- dw_diffusion.i.Omega(solid.C1, q1, p1)
=
dw_volume_lvf.i.Omega(solid.Z1, q1)
""" % (1 / ts.dt),
# eq. (61), alpha = 2
'mass_conservation_2':
"""
- %e * dw_biot.i.Omega(solid.B2, u, q2)
- dw_volume_dot.i.Omega(solid.G21, q2, p1)
- dw_volume_dot.i.Omega(solid.G22, q2, p2)
- dw_diffusion.i.Omega(solid.C2, q2, p2)
=
dw_volume_lvf.i.Omega(solid.Z2, q2)
""" % (1. / ts.dt),
}
solvers = {
'ls': ('ls.scipy_direct', {}),
'newton': ('nls.newton', {
'eps_a': 1e-3,
'eps_r': 1e-3,
'i_max': 1,
}),
}
return locals()
compression/expansion.
"""
from __future__ import absolute_import
import numpy as nm
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/3d/cylinder.mesh'
# Time-stepping parameters.
t0 = 0.0
t1 = 1.0
n_step = 21
from sfepy.solvers.ts import TimeStepper
ts = TimeStepper(t0, t1, None, n_step)
options = {
'nls': 'newton',
'ls': 'ls',
'ts': 'ts',
'save_times': 'all',
'post_process_hook': 'post_process',
}
fields = {
'displacement': ('real', 3, 'Omega', 1),
'pressure': ('real', 1, 'Omega', 1),
}
materials = {
def main():
# Aluminium and epoxy.
default_pars = '70e9,0.35,2.799e3, 3.8e9,0.27,1.142e3'
default_solver_conf = ("kind='eig.scipy',method='eigh',tol=1.0e-5,"
"maxiter=1000,which='LM',sigma=0.0")
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--pars',
metavar='young1,poisson1,density1'
',young2,poisson2,density2',
action='store',
dest='pars',
default=default_pars,
help=helps['pars'])
parser.add_argument('--conf',
metavar='filename',
action='store',
dest='conf',
default=None,
help=helps['conf'])
parser.add_argument('--mesh-size',
type=float,
metavar='float',
action='store',
dest='mesh_size',
default=None,
help=helps['mesh_size'])
parser.add_argument('--unit-multipliers',
metavar='c_time,c_length,c_mass',
action='store',
dest='unit_multipliers',
default='1.0,1.0,1.0',
help=helps['unit_multipliers'])
parser.add_argument('--plane',
action='store',
dest='plane',
choices=['strain', 'stress'],
default='strain',
help=helps['plane'])
parser.add_argument('--wave-dir',
metavar='float,float[,float]',
action='store',
dest='wave_dir',
default='1.0,0.0,0.0',
help=helps['wave_dir'])
parser.add_argument('--mode',
action='store',
dest='mode',
choices=['omega', 'kappa'],
default='omega',
help=helps['mode'])
parser.add_argument('--range',
metavar='start,stop,count',
action='store',
dest='range',
default='10,100,10',
help=helps['range'])
parser.add_argument('--order',
metavar='int',
type=int,
action='store',
dest='order',
default=1,
help=helps['order'])
parser.add_argument('--refine',
metavar='int',
type=int,
action='store',
dest='refine',
default=0,
help=helps['refine'])
parser.add_argument('-n',
'--n-eigs',
metavar='int',
type=int,
action='store',
dest='n_eigs',
default=6,
help=helps['n_eigs'])
parser.add_argument('--eigs-only',
action='store_true',
dest='eigs_only',
default=False,
help=helps['eigs_only'])
parser.add_argument('--solver-conf',
metavar='dict-like',
action='store',
dest='solver_conf',
default=default_solver_conf,
help=helps['solver_conf'])
parser.add_argument('--save-materials',
action='store_true',
dest='save_materials',
default=False,
help=helps['save_materials'])
parser.add_argument('--log-std-waves',
action='store_true',
dest='log_std_waves',
default=False,
help=helps['log_std_waves'])
parser.add_argument('--silent',
action='store_true',
dest='silent',
default=False,
help=helps['silent'])
parser.add_argument('-c',
'--clear',
action='store_true',
dest='clear',
default=False,
help=helps['clear'])
parser.add_argument('-o',
'--output-dir',
metavar='path',
action='store',
dest='output_dir',
default='output',
help=helps['output_dir'])
parser.add_argument('mesh_filename',
default='',
help=helps['mesh_filename'])
options = parser.parse_args()
output_dir = options.output_dir
output.set_output(filename=os.path.join(output_dir, 'output_log.txt'),
combined=options.silent == False)
if options.conf is not None:
mod = import_file(options.conf)
apply_units = mod.apply_units
define = mod.define
set_wave_dir = mod.set_wave_dir
else:
apply_units = apply_units_le
define = define_le
set_wave_dir = set_wave_dir_le
options.pars = [float(ii) for ii in options.pars.split(',')]
options.unit_multipliers = [
float(ii) for ii in options.unit_multipliers.split(',')
]
options.wave_dir = [float(ii) for ii in options.wave_dir.split(',')]
aux = options.range.split(',')
options.range = [float(aux[0]), float(aux[1]), int(aux[2])]
options.solver_conf = dict_from_string(options.solver_conf)
if options.clear:
remove_files_patterns(output_dir, ['*.h5', '*.vtk', '*.txt'],
ignores=['output_log.txt'],
verbose=True)
filename = os.path.join(output_dir, 'options.txt')
ensure_path(filename)
save_options(filename, [('options', vars(options))])
pars = apply_units(options.pars, options.unit_multipliers)
output('material parameters with applied unit multipliers:')
output(pars)
if options.mode == 'omega':
rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['wave_number', 'wave_number'],
options.unit_multipliers)
output('wave number range with applied unit multipliers:', rng)
else:
rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['frequency', 'frequency'],
options.unit_multipliers)
output('frequency range with applied unit multipliers:', rng)
define_problem = functools.partial(define,
filename_mesh=options.mesh_filename,
pars=pars,
approx_order=options.order,
refinement_level=options.refine,
solver_conf=options.solver_conf,
plane=options.plane)
conf = ProblemConf.from_dict(define_problem(), sys.modules[__name__])
pb = Problem.from_conf(conf)
dim = pb.domain.shape.dim
if dim != 2:
options.plane = 'strain'
wdir = nm.asarray(options.wave_dir[:dim], dtype=nm.float64)
wdir = wdir / nm.linalg.norm(wdir)
stepper = TimeStepper(rng[0], rng[1], dt=None, n_step=rng[2])
bbox = pb.domain.mesh.get_bounding_box()
size = (bbox[1] - bbox[0]).max()
scaling0 = apply_unit_multipliers([1.0], ['length'],
options.unit_multipliers)[0]
scaling = scaling0
if options.mesh_size is not None:
scaling *= options.mesh_size / size
output('scaling factor of periodic cell mesh coordinates:', scaling)
output('new mesh size with applied unit multipliers:', scaling * size)
pb.domain.mesh.coors[:] *= scaling
pb.set_mesh_coors(pb.domain.mesh.coors, update_fields=True)
bzone = 2.0 * nm.pi / (scaling * size)
output('1. Brillouin zone size:', bzone * scaling0)
output('1. Brillouin zone size with applied unit multipliers:', bzone)
pb.time_update()
pb.update_materials()
if options.save_materials or options.log_std_waves:
stiffness = pb.evaluate('ev_integrate_mat.2.Omega(m.D, u)',
mode='el_avg',
copy_materials=False,
verbose=False)
young, poisson = mc.youngpoisson_from_stiffness(stiffness,
plane=options.plane)
density = pb.evaluate('ev_integrate_mat.2.Omega(m.density, u)',
mode='el_avg',
copy_materials=False,
verbose=False)
if options.save_materials:
out = {}
out['young'] = Struct(name='young',
mode='cell',
data=young[..., None, None])
out['poisson'] = Struct(name='poisson',
mode='cell',
data=poisson[..., None, None])
out['density'] = Struct(name='density', mode='cell', data=density)
materials_filename = os.path.join(output_dir, 'materials.vtk')
pb.save_state(materials_filename, out=out)
# Set the normalized wave vector direction to the material(s).
set_wave_dir(pb.get_materials(), wdir)
conf = pb.solver_confs['eig']
eig_solver = Solver.any_from_conf(conf)
# Assemble the matrices.
mtx_m = pb.mtx_a.copy()
eq_m = pb.equations['M']
mtx_m = eq_m.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx_m)
mtx_m.eliminate_zeros()
mtx_k = pb.mtx_a.copy()
eq_k = pb.equations['K']
mtx_k = eq_k.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx_k)
mtx_k.eliminate_zeros()
mtx_s = pb.mtx_a.copy()
eq_s = pb.equations['S']
mtx_s = eq_s.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx_s)
mtx_s.eliminate_zeros()
mtx_r = pb.mtx_a.copy()
eq_r = pb.equations['R']
mtx_r = eq_r.evaluate(mode='weak', dw_mode='matrix', asm_obj=mtx_r)
mtx_r.eliminate_zeros()
output('symmetry checks of real blocks:')
output('M - M^T:', _max_diff_csr(mtx_m, mtx_m.T))
output('K - K^T:', _max_diff_csr(mtx_k, mtx_k.T))
output('S - S^T:', _max_diff_csr(mtx_s, mtx_s.T))
output('R + R^T:', _max_diff_csr(mtx_r, -mtx_r.T))
n_eigs = options.n_eigs
if options.n_eigs > mtx_k.shape[0]:
options.n_eigs = mtx_k.shape[0]
n_eigs = None
if options.mode == 'omega':
eigenshapes_filename = os.path.join(
output_dir, 'frequency-eigenshapes-%s.vtk' % stepper.suffix)
extra = []
extra_plot_kwargs = []
if options.log_std_waves:
lam, mu = mc.lame_from_youngpoisson(young,
poisson,
plane=options.plane)
alam = nm.average(lam)
amu = nm.average(mu)
adensity = nm.average(density)
cp = nm.sqrt((alam + 2.0 * amu) / adensity)
cs = nm.sqrt(amu / adensity)
output('average p-wave speed:', cp)
output('average shear wave speed:', cs)
extra = [r'$\omega_p$', r'$\omega_s$']
extra_plot_kwargs = [{
'ls': '--',
'color': 'k'
}, {
'ls': '--',
'color': 'gray'
}]
log = Log(
[[r'$\lambda_{%d}$' % ii for ii in range(options.n_eigs)],
[r'$\omega_{%d}$' % ii for ii in range(options.n_eigs)] + extra],
plot_kwargs=[{}, [{}] * options.n_eigs + extra_plot_kwargs],
yscales=['linear', 'linear'],
xlabels=[r'$\kappa$', r'$\kappa$'],
ylabels=[r'eigenvalues $\lambda_i$', r'frequencies $\omega_i$'],
log_filename=os.path.join(output_dir, 'frequencies.txt'),
aggregate=1000,
sleep=0.1)
for iv, wmag in stepper:
output('step %d: wave vector %s' % (iv, wmag * wdir))
mtx_a = mtx_k + wmag**2 * mtx_s + (1j * wmag) * mtx_r
mtx_b = mtx_m
output('A - A^H:', _max_diff_csr(mtx_a, mtx_a.H))
if options.eigs_only:
eigs = eig_solver(mtx_a,
mtx_b,
n_eigs=n_eigs,
eigenvectors=False)
svecs = None
else:
eigs, svecs = eig_solver(mtx_a,
mtx_b,
n_eigs=options.n_eigs,
eigenvectors=True)
omegas = nm.sqrt(eigs)
output('eigs, omegas:\n', nm.c_[eigs, omegas])
out = tuple(eigs) + tuple(omegas)
if options.log_std_waves:
out = out + (cp * wmag, cs * wmag)
log(*out, x=[wmag, wmag])
save_eigenvectors(eigenshapes_filename % iv, svecs, pb)
log(save_figure=os.path.join(output_dir, 'frequencies.png'))
log(finished=True)
else:
import scipy.sparse as sps
from sksparse.cholmod import cholesky
eigenshapes_filename = os.path.join(
output_dir, 'wave-number-eigenshapes-%s.vtk' % stepper.suffix)
factor = cholesky(mtx_s)
perm = factor.P()
ir = nm.arange(len(perm))
mtx_p = sps.coo_matrix((nm.ones_like(perm), (ir, perm)))
mtx_l = mtx_p.T * factor.L()
mtx_eye = sps.eye(mtx_l.shape[0], dtype=nm.float64)
output('S - LL^T:', _max_diff_csr(mtx_s, mtx_l * mtx_l.T))
log = Log([[r'$\kappa_{%d}$' % ii for ii in range(options.n_eigs)]],
plot_kwargs=[{
'ls': 'None',
'marker': 'o'
}],
yscales=['linear'],
xlabels=[r'$\omega$'],
ylabels=[r'wave numbers $\kappa_i$'],
log_filename=os.path.join(output_dir, 'wave-numbers.txt'),
aggregate=1000,
sleep=0.1)
for io, omega in stepper:
output('step %d: frequency %s' % (io, omega))
mtx_a = sps.bmat([[mtx_k - omega**2 * mtx_m, None],
[None, mtx_eye]])
mtx_b = sps.bmat([[1j * mtx_r, mtx_l], [mtx_l.T, None]])
output('A - A^T:', _max_diff_csr(mtx_a, mtx_a.T))
output('A - A^H:', _max_diff_csr(mtx_a, mtx_a.T))
output('B - B^H:', _max_diff_csr(mtx_b, mtx_b.H))
if options.eigs_only:
eigs = eig_solver(mtx_a,
mtx_b,
n_eigs=n_eigs,
eigenvectors=False)
svecs = None
else:
eigs, svecs = eig_solver(mtx_a,
mtx_b,
n_eigs=options.n_eigs,
eigenvectors=True)
kappas = eigs
output('kappas:\n', kappas[:, None])
out = tuple(kappas)
log(*out, x=[omega])
save_eigenvectors(eigenshapes_filename % io, svecs, pb)
log(save_figure=os.path.join(output_dir, 'wave-numbers.png'))
log(finished=True)
def get_stepper(rng, pb, options):
stepper = TimeStepper(rng[0], rng[1], dt=None, n_step=rng[2])
return stepper
def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None,
fields=None, linearization=None):
"""Dump a multi-time-step results file into a sequence of VTK files."""
def _save_step(suffix, out, mesh):
if linearization is not None:
output('linearizing...')
out = _linearize(out, fields, linearization)
output('...done')
for key, val in out.iteritems():
lmesh = val.get('mesh', mesh)
lmesh.write(output_filename_trunk + '_' + key + suffix,
io='auto', out={key : val})
if hasattr(val, 'levels'):
output('max. refinement per group:', val.levels)
else:
mesh.write(output_filename_trunk + suffix, io='auto', out=out)
output('dumping to VTK...')
io = MeshIO.any_from_filename(filename)
mesh = Mesh.from_file(filename, io=io)
if output_filename_trunk is None:
output_filename_trunk = get_trunk(filename)
try:
ts = TimeStepper(*io.read_time_stepper())
all_steps, times, nts, dts = extract_times(filename)
except ValueError:
output('no time stepping info found, assuming single step')
out = io.read_data(0)
if out is not None:
_save_step('.vtk', out, mesh)
ret = None
else:
ts.times = times
ts.n_step = times.shape[0]
if steps is None:
ii0 = nm.searchsorted(all_steps, step0)
iterator = ((all_steps[ii], times[ii])
for ii in xrange(ii0, len(times)))
else:
iterator = [(step, ts.times[step]) for step in steps]
max_step = all_steps.max()
for step, time in iterator:
output(ts.format % (step, max_step))
out = io.read_data(step)
if out is None: break
_save_step('.' + ts.suffix % step + '.vtk', out, mesh)
ret = ts.suffix
output('...done')
return ret
def extract_time_history(filename, extract, verbose=True):
"""Extract time history of a variable from a multi-time-step results file.
Parameters
----------
filename : str
The name of file to extract from.
extract : str
The description of what to extract in a string of comma-separated
description items. A description item consists of: name of the variable
to extract, mode ('e' for elements, 'n' for nodes), ids of the nodes or
elements (given by the mode). Example: 'u n 10 15, p e 0' means
variable 'u' in nodes 10, 15 and variable 'p' in element 0.
verbose : bool
Verbosity control.
Returns
-------
ths : dict
The time histories in a dict with variable names as keys. If a
nodal variable is requested in elements, its value is a dict of histories
in the element nodes.
ts : TimeStepper instance
The time stepping information.
"""
output('extracting selected data...', verbose=verbose)
output('selection:', extract, verbose=verbose)
##
# Parse extractions.
pes = OneTypeList(Struct)
for chunk in extract.split(','):
aux = chunk.strip().split()
pes.append(Struct(var = aux[0],
mode = aux[1],
indx = map(int, aux[2:]),
igs = None))
##
# Verify array limits, set igs for element data, shift indx.
mesh = Mesh.from_file(filename)
n_el, n_els, offs = mesh.n_el, mesh.n_els, mesh.el_offsets
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise ValueError('node index 0 <= %d < %d!'
% (ii, mesh.n_nod))
if pe.mode == 'e':
pe.igs = []
for ii, ie in enumerate(pe.indx[:]):
if (ie < 0) or (ie >= n_el):
raise ValueError('element index 0 <= %d < %d!'
% (ie, n_el))
ig = (ie < n_els).argmax()
pe.igs.append(ig)
pe.indx[ii] = ie - offs[ig]
## print pes
##
# Extract data.
# Assumes only one element group (ignores igs)!
io = MeshIO.any_from_filename(filename)
ths = {}
for pe in pes:
mode, nname = io.read_data_header(pe.var)
output(mode, nname, verbose=verbose)
if ((pe.mode == 'n' and mode == 'vertex') or
(pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history(nname, pe.indx)
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history(nname, ips)
else:
raise ValueError('cannot extract cell data %s in nodes!' % pe.var)
ths[pe.var] = th
output('...done', verbose=verbose)
ts = TimeStepper(*io.read_time_stepper())
return ths, ts
def test_hdf5_meshio(self):
import tempfile
import numpy as nm
import scipy.sparse as sps
from sfepy.discrete.fem.meshio import HDF5MeshIO
from sfepy.base.base import Struct
from sfepy.base.ioutils import Cached, Uncached, SoftLink, \
DataSoftLink
from sfepy.discrete.iga.domain import IGDomain
from sfepy.discrete.iga.domain_generators import gen_patch_block_domain
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.fem import Mesh
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
shape = [4, 4, 4]
dims = [5, 5, 5]
centre = [0, 0, 0]
degrees = [2, 2, 2]
nurbs, bmesh, regions = gen_patch_block_domain(dims, shape, centre,
degrees,
cp_mode='greville',
name='iga')
ig_domain = IGDomain('iga', nurbs, bmesh, regions=regions)
int_ar = nm.arange(4)
data = {
'list': range(4),
'mesh1': mesh0,
'mesh2': mesh0,
'mesh3': Uncached(mesh0),
'mesh4': SoftLink('/step0/__cdata/data/data/mesh2'),
'mesh5': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh1/data'),
'mesh6': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh2/data',
mesh0),
'mesh7': DataSoftLink('Mesh','/step0/__cdata/data/data/mesh1/data',
True),
'iga' : ig_domain,
'cached1': Cached(1),
'cached2': Cached(int_ar),
'cached3': Cached(int_ar),
'types': ( True, False, None ),
'tuple': ('first string', 'druhý UTF8 řetězec'),
'struct': Struct(
double=nm.arange(4, dtype=float),
int=nm.array([2,3,4,7]),
sparse=sps.csr_matrix(nm.array([1,0,0,5]).
reshape((2,2)))
)
}
with tempfile.NamedTemporaryFile(suffix='.h5') as fil:
io = HDF5MeshIO(fil.name)
ts = TimeStepper(0,1.,0.1, 10)
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=data,
unpack_markers=False
)
}, ts=ts)
ts.advance()
mesh = io.read()
data['problem_mesh'] = DataSoftLink('Mesh', '/mesh', mesh)
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=data,
unpack_markers=True
)
}, ts=ts)
cache = {'/mesh': mesh }
fout = io.read_data(0, cache=cache)
fout2 = io.read_data(1, cache=cache )
out = fout['cdata']
out2 = fout2['cdata']
assert_(out['mesh7'] is out2['mesh7'],
'These two meshes should be in fact the same object')
assert_(out['mesh6'] is out2['mesh6'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out2['mesh5'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh4'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out['mesh2'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh6'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh7'] is not out['mesh2'],
'These two meshes shouldn''t be in fact the same object')
assert_(out['mesh3'] is not out['mesh2'],
'These two meshes should be different objects')
assert_(out['cached2'] is out['cached3'],
'These two array should be the same object')
assert_(out2['problem_mesh'] is mesh,
'These two meshes should be the same objects')
assert_(self._compare_meshes(out['mesh1'], mesh0),
'Failed to restore mesh')
assert_(self._compare_meshes(out['mesh3'], mesh0),
'Failed to restore mesh')
assert_((out['struct'].sparse == data['struct'].sparse).todense()
.all(), 'Sparse matrix restore failed')
ts.advance()
io.write(fil.name, mesh0, {
'cdata' : Struct(
mode='custom',
data=[
DataSoftLink('Mesh',
'/step0/__cdata/data/data/mesh1/data',
mesh0),
mesh0
]
)
}, ts=ts)
out3 = io.read_data(2)['cdata']
assert_(out3[0] is out3[1])
#this property is not restored
del data['iga'].nurbs.nurbs
#not supporting comparison
del data['iga']._bnf
del out2['iga']._bnf
#restoration of this property fails
del data['iga'].vertex_set_bcs
del out2['iga'].vertex_set_bcs
#these soflink has no information how to unpack, so it must be
#done manually
data['mesh4'] = mesh0
data['mesh5'] = mesh0
data['mesh7'] = mesh0
for key, val in six.iteritems(out2):
self.report('comparing:', key)
self.assert_equal(val, data[key])
return True
def main():
# Aluminium and epoxy.
default_pars = '70e9,0.35,2.799e3, 3.8e9,0.27,1.142e3'
default_solver_conf = ("kind='eig.scipy',method='eigsh',tol=1.0e-5,"
"maxiter=1000,which='LM',sigma=0.0")
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--pars',
metavar='young1,poisson1,density1'
',young2,poisson2,density2',
action='store',
dest='pars',
default=default_pars,
help=helps['pars'])
parser.add_argument('--conf',
metavar='filename',
action='store',
dest='conf',
default=None,
help=helps['conf'])
parser.add_argument('--mesh-size',
type=float,
metavar='float',
action='store',
dest='mesh_size',
default=None,
help=helps['mesh_size'])
parser.add_argument('--unit-multipliers',
metavar='c_time,c_length,c_mass',
action='store',
dest='unit_multipliers',
default='1.0,1.0,1.0',
help=helps['unit_multipliers'])
parser.add_argument('--plane',
action='store',
dest='plane',
choices=['strain', 'stress'],
default='strain',
help=helps['plane'])
parser.add_argument('--wave-dir',
metavar='float,float[,float]',
action='store',
dest='wave_dir',
default='1.0,0.0,0.0',
help=helps['wave_dir'])
parser.add_argument('--mode',
action='store',
dest='mode',
choices=['omega', 'kappa'],
default='omega',
help=helps['mode'])
parser.add_argument('--range',
metavar='start,stop,count',
action='store',
dest='range',
default='0,6.4,33',
help=helps['range'])
parser.add_argument('--order',
metavar='int',
type=int,
action='store',
dest='order',
default=1,
help=helps['order'])
parser.add_argument('--refine',
metavar='int',
type=int,
action='store',
dest='refine',
default=0,
help=helps['refine'])
parser.add_argument('-n',
'--n-eigs',
metavar='int',
type=int,
action='store',
dest='n_eigs',
default=6,
help=helps['n_eigs'])
group = parser.add_mutually_exclusive_group()
group.add_argument('--eigs-only',
action='store_true',
dest='eigs_only',
default=False,
help=helps['eigs_only'])
group.add_argument('--post-process',
action='store_true',
dest='post_process',
default=False,
help=helps['post_process'])
parser.add_argument('--solver-conf',
metavar='dict-like',
action='store',
dest='solver_conf',
default=default_solver_conf,
help=helps['solver_conf'])
parser.add_argument('--save-regions',
action='store_true',
dest='save_regions',
default=False,
help=helps['save_regions'])
parser.add_argument('--save-materials',
action='store_true',
dest='save_materials',
default=False,
help=helps['save_materials'])
parser.add_argument('--log-std-waves',
action='store_true',
dest='log_std_waves',
default=False,
help=helps['log_std_waves'])
parser.add_argument('--no-legends',
action='store_false',
dest='show_legends',
default=True,
help=helps['no_legends'])
parser.add_argument('--no-show',
action='store_false',
dest='show',
default=True,
help=helps['no_show'])
parser.add_argument('--silent',
action='store_true',
dest='silent',
default=False,
help=helps['silent'])
parser.add_argument('-c',
'--clear',
action='store_true',
dest='clear',
default=False,
help=helps['clear'])
parser.add_argument('-o',
'--output-dir',
metavar='path',
action='store',
dest='output_dir',
default='output',
help=helps['output_dir'])
parser.add_argument('mesh_filename',
default='',
help=helps['mesh_filename'])
options = parser.parse_args()
output_dir = options.output_dir
output.set_output(filename=os.path.join(output_dir, 'output_log.txt'),
combined=options.silent == False)
if options.conf is not None:
mod = import_file(options.conf)
else:
mod = sys.modules[__name__]
apply_units = mod.apply_units
define = mod.define
set_wave_dir = mod.set_wave_dir
setup_n_eigs = mod.setup_n_eigs
build_evp_matrices = mod.build_evp_matrices
save_materials = mod.save_materials
get_std_wave_fun = mod.get_std_wave_fun
process_evp_results = mod.process_evp_results
options.pars = [float(ii) for ii in options.pars.split(',')]
options.unit_multipliers = [
float(ii) for ii in options.unit_multipliers.split(',')
]
options.wave_dir = [float(ii) for ii in options.wave_dir.split(',')]
aux = options.range.split(',')
options.range = [float(aux[0]), float(aux[1]), int(aux[2])]
options.solver_conf = dict_from_string(options.solver_conf)
if options.clear:
remove_files_patterns(output_dir, ['*.h5', '*.vtk', '*.txt'],
ignores=['output_log.txt'],
verbose=True)
filename = os.path.join(output_dir, 'options.txt')
ensure_path(filename)
save_options(filename, [('options', vars(options))],
quote_command_line=True)
pars = apply_units(options.pars, options.unit_multipliers)
output('material parameters with applied unit multipliers:')
output(pars)
if options.mode == 'omega':
rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['wave_number', 'wave_number'],
options.unit_multipliers)
output('wave number range with applied unit multipliers:', rng)
else:
rng = copy(options.range)
rng[:2] = apply_unit_multipliers(options.range[:2],
['frequency', 'frequency'],
options.unit_multipliers)
output('frequency range with applied unit multipliers:', rng)
pb, wdir, bzone, mtxs = assemble_matrices(define, mod, pars, set_wave_dir,
options)
dim = pb.domain.shape.dim
if dim != 2:
options.plane = 'strain'
stepper = TimeStepper(rng[0], rng[1], dt=None, n_step=rng[2])
if options.save_regions:
pb.save_regions_as_groups(os.path.join(output_dir, 'regions'))
if options.save_materials:
save_materials(output_dir, pb, options)
conf = pb.solver_confs['eig']
eig_solver = Solver.any_from_conf(conf)
n_eigs, options.n_eigs = setup_n_eigs(options, pb, mtxs)
get_color = lambda ii: plt.cm.viridis((float(ii) / (options.n_eigs - 1)))
plot_kwargs = [{
'color': get_color(ii),
'ls': '',
'marker': 'o'
} for ii in range(options.n_eigs)]
log_names = []
log_plot_kwargs = []
if options.log_std_waves:
std_wave_fun, log_names, log_plot_kwargs = get_std_wave_fun(
pb, options)
else:
std_wave_fun = None
if options.mode == 'omega':
eigenshapes_filename = os.path.join(
output_dir, 'frequency-eigenshapes-%s.vtk' % stepper.suffix)
log = Log(
[[r'$\lambda_{%d}$' % ii for ii in range(options.n_eigs)],
[r'$\omega_{%d}$' % ii
for ii in range(options.n_eigs)] + log_names],
plot_kwargs=[plot_kwargs, plot_kwargs + log_plot_kwargs],
formats=[['{:.5e}'] * options.n_eigs,
['{:.5e}'] * (options.n_eigs + len(log_names))],
yscales=['linear', 'linear'],
xlabels=[r'$\kappa$', r'$\kappa$'],
ylabels=[r'eigenvalues $\lambda_i$', r'frequencies $\omega_i$'],
show_legends=options.show_legends,
is_plot=options.show,
log_filename=os.path.join(output_dir, 'frequencies.txt'),
aggregate=1000,
sleep=0.1)
for iv, wmag in stepper:
output('step %d: wave vector %s' % (iv, wmag * wdir))
evp_mtxs = build_evp_matrices(mtxs, wmag, options.mode, pb)
if options.eigs_only:
eigs = eig_solver(*evp_mtxs, n_eigs=n_eigs, eigenvectors=False)
svecs = None
else:
eigs, svecs = eig_solver(*evp_mtxs,
n_eigs=n_eigs,
eigenvectors=True)
omegas, svecs, out = process_evp_results(eigs,
svecs,
wmag,
options.mode,
wdir,
bzone,
pb,
mtxs,
std_wave_fun=std_wave_fun)
log(*out, x=[wmag, wmag])
save_eigenvectors(eigenshapes_filename % iv, svecs, wmag, wdir, pb)
gc.collect()
log(save_figure=os.path.join(output_dir, 'frequencies.png'))
log(finished=True)
else:
eigenshapes_filename = os.path.join(
output_dir, 'wave-number-eigenshapes-%s.vtk' % stepper.suffix)
log = Log([[r'$\kappa_{%d}$' % ii
for ii in range(options.n_eigs)] + log_names],
plot_kwargs=[plot_kwargs + log_plot_kwargs],
formats=[['{:.5e}'] * (options.n_eigs + len(log_names))],
yscales=['linear'],
xlabels=[r'$\omega$'],
ylabels=[r'wave numbers $\kappa_i$'],
show_legends=options.show_legends,
is_plot=options.show,
log_filename=os.path.join(output_dir, 'wave-numbers.txt'),
aggregate=1000,
sleep=0.1)
for io, omega in stepper:
output('step %d: frequency %s' % (io, omega))
evp_mtxs = build_evp_matrices(mtxs, omega, options.mode, pb)
if options.eigs_only:
eigs = eig_solver(*evp_mtxs, n_eigs=n_eigs, eigenvectors=False)
svecs = None
else:
eigs, svecs = eig_solver(*evp_mtxs,
n_eigs=n_eigs,
eigenvectors=True)
kappas, svecs, out = process_evp_results(eigs,
svecs,
omega,
options.mode,
wdir,
bzone,
pb,
mtxs,
std_wave_fun=std_wave_fun)
log(*out, x=[omega])
save_eigenvectors(eigenshapes_filename % io, svecs, kappas, wdir,
pb)
gc.collect()
log(save_figure=os.path.join(output_dir, 'wave-numbers.png'))
log(finished=True)
def define(filename_mesh=None, cg1=None, cg2=None):
if filename_mesh is None:
filename_mesh = osp.join(data_dir, 'macro_perf.vtk')
cg1, cg2 = 0.0015, 0.0015 # y and z coordinates of center of gravity
mesh = Mesh.from_file(filename_mesh)
poroela_mezo_file = osp.join(data_dir, 'perf_BD2B_mes.py')
material_cache['meso_filename'] = poroela_mezo_file
bbox = mesh.get_bounding_box()
regions = define_box_regions(mesh.dim, bbox[0], bbox[1], eps=1e-6)
regions.update({
'Omega': 'all',
'Wall': ('r.Top +v r.Bottom +v r.Far +v r.Near', 'facet'),
# 'In': ('r.Left -v r.Wall', 'facet'),
# 'Out': ('r.Right -v r.Wall', 'facet'),
'In': ('copy r.Left', 'facet'),
'Out': ('copy r.Right ', 'facet'),
'Out_u': ('r.Out -v (r.Top +v r.Bottom)', 'facet'),
})
val_w1 = 5e3
val_w2 = 5e3
ebcs, bc_funs, mats, lcbcs = define_bc(cg1,
cg2,
is_steady=False,
val_in=val_w1,
val_out=val_w2)
fields = {
'displacement': ('real', 'vector', 'Omega', 1),
'pressure': ('real', 'scalar', 'Omega', 1),
'velocity1': ('real', 'vector', 'Omega', 1),
'velocity2': ('real', 'vector', 'Omega', 1),
'sfield': ('real', "scalar", 'Omega', 1),
}
variables = {
#Displacement
'u': ('unknown field', 'displacement'),
'v': ('test field', 'displacement', 'u'),
#Pressure
'p': ('unknown field', 'pressure'),
'q': ('test field', 'pressure', 'p'),
'ls': ('unknown field', 'pressure'),
'lv': ('test field', 'pressure', 'ls'),
#Velocity
'w1': ('unknown field', 'velocity1'),
'z1': ('test field', 'velocity1', 'w1'),
'w2': ('unknown field', 'velocity2'),
'z2': ('test field', 'velocity2', 'w2'),
'U': ('parameter field', 'displacement', 'u'),
'P': ('parameter field', 'pressure', 'p'),
'W1': ('parameter field', 'velocity1', 'w1'),
'W2': ('parameter field', 'velocity2', 'w2'),
'svar': ('parameter field', 'sfield', '(set-to-none)'),
}
state_vars = ['p', 'u', 'w1', 'w2']
functions = {
'get_homog': (lambda ts, coors, problem, mode=None, **kwargs: \
get_homog(coors,problem, mode, **kwargs),),
'get_u': (lambda ts, coor, mode=None, problem=None, **kwargs:
get_u(tstep, coor),),
}
functions.update(bc_funs)
materials = {
'hom': 'get_homog',
}
materials.update(mats)
#Definition of integrals
integrals = {
'i': 5,
"is": ("s", 5),
}
#Definition of solvers
solvers = {
'ls': ('ls.mumps', {}),
'newton': ('nls.newton', {
'i_max': 1,
'eps_a': 1e-10,
'eps_r': 1e-3,
'problem': 'nonlinear',
})
}
options = {
'output_dir': data_dir + '/results/macro',
'ls': 'ls',
'nls': 'newton',
'micro_filename': poroela_mezo_file,
'absolute_mesh_path': True,
'output_prefix': 'Macro:',
'matrix_hook': 'mtx_hook',
}
#Definition of time solver and equations for steady state and time evolution cases
tstep = TimeStepper(0.0, 1.0, n_step=20)
equations, phook = define_time_equations(tstep)
options.update({'parametric_hook': phook})
return locals()
def test_hdf5_meshio(self):
try:
from igakit import igalib
except ImportError:
self.report('hdf5_meshio not-tested (missing igalib module)!')
return True
import tempfile
import numpy as nm
import scipy.sparse as sps
from sfepy.discrete.fem.meshio import HDF5MeshIO
from sfepy.base.base import Struct
from sfepy.base.ioutils import Cached, Uncached, SoftLink, \
DataSoftLink
from sfepy.discrete.iga.domain import IGDomain
from sfepy.discrete.iga.domain_generators import gen_patch_block_domain
from sfepy.solvers.ts import TimeStepper
from sfepy.discrete.fem import Mesh
conf_dir = op.dirname(__file__)
mesh0 = Mesh.from_file(data_dir +
'/meshes/various_formats/small3d.mesh',
prefix_dir=conf_dir)
shape = [4, 4, 4]
dims = [5, 5, 5]
centre = [0, 0, 0]
degrees = [2, 2, 2]
nurbs, bmesh, regions = gen_patch_block_domain(dims,
shape,
centre,
degrees,
cp_mode='greville',
name='iga')
ig_domain = IGDomain('iga', nurbs, bmesh, regions=regions)
int_ar = nm.arange(4)
data = {
'list':
range(4),
'mesh1':
mesh0,
'mesh2':
mesh0,
'mesh3':
Uncached(mesh0),
'mesh4':
SoftLink('/step0/__cdata/data/data/mesh2'),
'mesh5':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh1/data'),
'mesh6':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh2/data', mesh0),
'mesh7':
DataSoftLink('Mesh', '/step0/__cdata/data/data/mesh1/data', True),
'iga':
ig_domain,
'cached1':
Cached(1),
'cached2':
Cached(int_ar),
'cached3':
Cached(int_ar),
'types': (True, False, None),
'tuple': ('first string', 'druhý UTF8 řetězec'),
'struct':
Struct(double=nm.arange(4, dtype=float),
int=nm.array([2, 3, 4, 7]),
sparse=sps.csr_matrix(
nm.array([1, 0, 0, 5]).reshape((2, 2))))
}
with tempfile.NamedTemporaryFile(suffix='.h5', delete=False) as fil:
io = HDF5MeshIO(fil.name)
ts = TimeStepper(0, 1., 0.1, 10)
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom', data=data, unpack_markers=False)
},
ts=ts)
ts.advance()
mesh = io.read()
data['problem_mesh'] = DataSoftLink('Mesh', '/mesh', mesh)
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom', data=data, unpack_markers=True)
},
ts=ts)
cache = {'/mesh': mesh}
fout = io.read_data(0, cache=cache)
fout2 = io.read_data(1, cache=cache)
out = fout['cdata']
out2 = fout2['cdata']
assert_(out['mesh7'] is out2['mesh7'],
'These two meshes should be in fact the same object')
assert_(out['mesh6'] is out2['mesh6'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out2['mesh5'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh1'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh4'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh5'] is not out['mesh2'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh6'] is out['mesh2'],
'These two meshes should be in fact the same object')
assert_(out['mesh7'] is not out['mesh2'],
'These two meshes shouldn'
't be in fact the same object')
assert_(out['mesh3'] is not out['mesh2'],
'These two meshes should be different objects')
assert_(out['cached2'] is out['cached3'],
'These two array should be the same object')
assert_(out2['problem_mesh'] is mesh,
'These two meshes should be the same objects')
assert_(self._compare_meshes(out['mesh1'], mesh0),
'Failed to restore mesh')
assert_(self._compare_meshes(out['mesh3'], mesh0),
'Failed to restore mesh')
assert_((
out['struct'].sparse == data['struct'].sparse).todense().all(),
'Sparse matrix restore failed')
ts.advance()
io.write(fil.name,
mesh0, {
'cdata':
Struct(mode='custom',
data=[
DataSoftLink(
'Mesh',
'/step0/__cdata/data/data/mesh1/data',
mesh0), mesh0
])
},
ts=ts)
out3 = io.read_data(2)['cdata']
assert_(out3[0] is out3[1])
os.remove(fil.name)
#this property is not restored
del data['iga'].nurbs.nurbs
#not supporting comparison
del data['iga']._bnf
del out2['iga']._bnf
#restoration of this property fails
del data['iga'].vertex_set_bcs
del out2['iga'].vertex_set_bcs
#these soflink has no information how to unpack, so it must be
#done manually
data['mesh4'] = mesh0
data['mesh5'] = mesh0
data['mesh7'] = mesh0
for key, val in six.iteritems(out2):
self.report('comparing:', key)
self.assert_equal(val, data[key])
return True
def extract_time_history(filename, extract, verbose=True):
"""Extract time history of a variable from a multi-time-step results file.
Parameters
----------
filename : str
The name of file to extract from.
extract : str
The description of what to extract in a string of comma-separated
description items. A description item consists of: name of the variable
to extract, mode ('e' for elements, 'n' for nodes), ids of the nodes or
elements (given by the mode). Example: 'u n 10 15, p e 0' means
variable 'u' in nodes 10, 15 and variable 'p' in element 0.
verbose : bool
Verbosity control.
Returns
-------
ths : dict
The time histories in a dict with variable names as keys. If a nodal
variable is requested in elements, its value is a dict of histories in
the element nodes.
ts : TimeStepper instance
The time stepping information.
"""
output('extracting selected data...', verbose=verbose)
output('selection:', extract, verbose=verbose)
##
# Parse extractions.
pes = OneTypeList(Struct)
for chunk in extract.split(','):
aux = chunk.strip().split()
pes.append(Struct(var=aux[0],
mode=aux[1],
indx=map(int, aux[2:])))
##
# Verify array limits.
mesh = Mesh.from_file(filename)
for pe in pes:
if pe.mode == 'n':
for ii in pe.indx:
if (ii < 0) or (ii >= mesh.n_nod):
raise ValueError('node index 0 <= %d < %d!'
% (ii, mesh.n_nod))
if pe.mode == 'e':
for ii, ie in enumerate(pe.indx[:]):
if (ie < 0) or (ie >= mesh.n_el):
raise ValueError('element index 0 <= %d < %d!'
% (ie, mesh.n_el))
pe.indx[ii] = ie
##
# Extract data.
io = MeshIO.any_from_filename(filename)
ths = {}
for pe in pes:
mode, nname = io.read_data_header(pe.var)
output(mode, nname, verbose=verbose)
if ((pe.mode == 'n' and mode == 'vertex') or
(pe.mode == 'e' and mode == 'cell')):
th = io.read_time_history(nname, pe.indx)
elif pe.mode == 'e' and mode == 'vertex':
conn = mesh.conns[0]
th = {}
for iel in pe.indx:
ips = conn[iel]
th[iel] = io.read_time_history(nname, ips)
else:
raise ValueError('cannot extract cell data %s in nodes!' % pe.var)
ths[pe.var] = th
output('...done', verbose=verbose)
ts = TimeStepper(*io.read_time_stepper())
# Force actual times.
steps, times, nts, dts = extract_times(filename)
ts.times = times
ts.nt = nts
return ths, ts
