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 get_correctors_from_file_hdf5(coefs_filename='coefs.h5', dump_names=None):
if dump_names == None:
coefs = Coefficients.from_file_hdf5(coefs_filename)
if hasattr(coefs, 'save_names'):
dump_names = coefs.save_names
else:
raise ValueError(' "filenames" coefficient must be used!')
out = {}
for key, val in six.iteritems(dump_names):
if type(val) in [tuple, list]:
h5name, corr_name = val
else:
h5name, corr_name = val, op.split(val)[-1]
io = HDF5MeshIO(h5name + '.h5')
data = io.read_data(0)
dkeys = list(data.keys())
corr = {}
for dk in dkeys:
corr[dk] = data[dk].data.reshape(data[dk].shape)
out[corr_name] = corr
return out
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 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 get_correctors_from_file_hdf5(coefs_filename='coefs.h5', dump_names=None):
if dump_names == None:
coefs = Coefficients.from_file_hdf5(coefs_filename)
if hasattr(coefs, 'save_names'):
dump_names = coefs.save_names
else:
raise ValueError(' "filenames" coefficient must be used!')
out = {}
for key, val in six.iteritems(dump_names):
if type(val) in [tuple, list]:
h5name, corr_name = val
else:
h5name, corr_name = val, op.split(val)[-1]
io = HDF5MeshIO(h5name + '.h5')
try:
ts = io.read_time_stepper()
except ValueError:
ts = None
if ts is None:
data = io.read_data(0)
dkeys = list(data.keys())
corr = {}
for dk in dkeys:
corr[dk] = data[dk].data.reshape(data[dk].shape)
out[corr_name] = corr
else:
n_step = ts[3]
out[corr_name] = []
for step in range(n_step):
data = io.read_data(step)
dkeys = list(data.keys())
corr = {}
for dk in dkeys:
corr[dk] = data[dk].data.reshape(data[dk].shape)
out[corr_name].append(corr)
out[corr_name + '_ts'] = ts
return out
def get_correctors_from_file(coefs_filename='coefs.h5', dump_names=None):
if dump_names == None:
coefs = Coefficients.from_file_hdf5(coefs_filename)
if hasattr(coefs, 'dump_names'):
dump_names = coefs.dump_names
else:
raise ValueError(' "filenames" coefficient must be used!')
out = {}
for key, val in dump_names.iteritems():
corr_name = op.split(val)[-1]
io = HDF5MeshIO(val + '.h5')
data = io.read_data(0)
dkeys = data.keys()
corr = {}
for dk in dkeys:
corr[dk] = data[dk].data.reshape(data[dk].shape)
out[corr_name] = corr
return out
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