From c0e6d37e991eaa5cead9709e831d9e651cea6bed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franck=20P=C3=A9rignon?= <franck.perignon@imag.fr>
Date: Tue, 5 Apr 2016 16:53:38 +0200
Subject: [PATCH] fix/add some tests.
---
HySoP/hysop/__init__.py.in | 5 +-
HySoP/hysop/constants.py | 7 -
HySoP/hysop/domain/tests/test_subset.py | 16 +-
HySoP/hysop/f2py/fftw2py.pyf | 4 +-
HySoP/hysop/fields/continuous.py | 164 +++++++----
HySoP/hysop/fields/discrete.py | 24 +-
HySoP/hysop/fields/tests/func_for_tests.py | 39 ++-
HySoP/hysop/fields/tests/test_field.py | 193 +++++++++----
.../tests/test_gpu_multiresolution_filter.py | 8 +-
.../gpu/tests/test_multiphase_baroclinic.py | 12 +-
HySoP/hysop/numerics/integrators/odesolver.py | 1 +
.../hysop/numerics/tests/test_integrators.py | 0
.../numerics/tests/test_update_ghosts.py | 2 +-
HySoP/hysop/operator/computational.py | 39 +--
HySoP/hysop/operator/continuous.py | 48 ++--
HySoP/hysop/operator/discrete/discrete.py | 10 +-
HySoP/hysop/operator/discrete/spectrum.py | 0
HySoP/hysop/operator/drag_and_lift.py | 12 +-
HySoP/hysop/operator/hdf_io.py | 152 ++++++-----
HySoP/hysop/operator/tests/test_analytic.py | 32 +--
.../operator/tests/test_drag_and_lift.py | 21 +-
HySoP/hysop/operator/tests/test_hdf5_io.py | 68 +++--
.../operator/tests/test_multiphase_gradp.py | 6 +-
.../tests/test_multiresolution_filter.py | 6 +-
.../operator/tests/test_particle_advection.py | 13 +-
.../hysop/operator/tests/test_penalization.py | 3 +-
HySoP/hysop/operator/tests/test_spectrum.py | 5 +-
HySoP/hysop/problem/tests/test_simulation.py | 9 +-
HySoP/hysop/tools/io_utils.py | 258 +++++++++++++-----
HySoP/hysop/tools/parameters.py | 69 +----
HySoP/hysop/tools/tests/test_parameters.py | 6 +-
HySoP/src/fftw/fft3d.f90 | 4 +-
32 files changed, 787 insertions(+), 449 deletions(-)
mode change 100644 => 100755 HySoP/hysop/constants.py
mode change 100644 => 100755 HySoP/hysop/fields/continuous.py
mode change 100644 => 100755 HySoP/hysop/fields/discrete.py
mode change 100644 => 100755 HySoP/hysop/fields/tests/func_for_tests.py
mode change 100644 => 100755 HySoP/hysop/numerics/integrators/odesolver.py
mode change 100644 => 100755 HySoP/hysop/numerics/tests/test_integrators.py
mode change 100644 => 100755 HySoP/hysop/operator/computational.py
mode change 100644 => 100755 HySoP/hysop/operator/continuous.py
mode change 100644 => 100755 HySoP/hysop/operator/discrete/discrete.py
mode change 100644 => 100755 HySoP/hysop/operator/discrete/spectrum.py
mode change 100644 => 100755 HySoP/hysop/operator/drag_and_lift.py
mode change 100644 => 100755 HySoP/hysop/operator/hdf_io.py
mode change 100644 => 100755 HySoP/hysop/operator/tests/test_spectrum.py
mode change 100644 => 100755 HySoP/hysop/problem/tests/test_simulation.py
mode change 100644 => 100755 HySoP/hysop/tools/io_utils.py
mode change 100644 => 100755 HySoP/hysop/tools/parameters.py
diff --git a/HySoP/hysop/__init__.py.in b/HySoP/hysop/__init__.py.in
index e97188c94..4e2d010be 100755
--- a/HySoP/hysop/__init__.py.in
+++ b/HySoP/hysop/__init__.py.in
@@ -13,6 +13,7 @@ __DEBUG__ = "@DEBUG@" in ["2", "3"]
__PROFILE__ = "@PROFILE@" in ["0", "1"]
__OPTIMIZE__ = "@OPTIM@" is "ON"
+import os
from hysop.tools.sys_utils import SysUtils
# Box-type physical domain
from hysop.domain.box import Box
@@ -23,8 +24,8 @@ from hysop.fields.variable_parameter import VariableParameter
# Simulation parameters
from hysop.problem.simulation import Simulation
# Tools (io, mpi ...)
-from hysop.tools.io_utils import IO
-from hysop.tools.parameters import IOParams, MPIParams, Discretization
+from hysop.tools.io_utils import IO, IOParams
+from hysop.tools.parameters import MPIParams, Discretization
import hysop.mpi
# Problem
from hysop.problem.problem import Problem
diff --git a/HySoP/hysop/constants.py b/HySoP/hysop/constants.py
old mode 100644
new mode 100755
index a849cb686..0dd0fe4cb
--- a/HySoP/hysop/constants.py
+++ b/HySoP/hysop/constants.py
@@ -56,13 +56,6 @@ WITH_GUESS = 1
## y is different from result arg.
NOALIAS = 2
-# File format types for output
-HDF5 = 998
-"""HDF5 format id"""
-
-ASCII = 997
-"""ascii format id"""
-
## Default value for task id (mpi task)
DEFAULT_TASK_ID = 999
diff --git a/HySoP/hysop/domain/tests/test_subset.py b/HySoP/hysop/domain/tests/test_subset.py
index 5faf5e19e..00bb7bcc7 100755
--- a/HySoP/hysop/domain/tests/test_subset.py
+++ b/HySoP/hysop/domain/tests/test_subset.py
@@ -1,8 +1,12 @@
+"""Tests computation of subsets of
+a given geometry/domain
+"""
from hysop.domain.subsets import Sphere, HemiSphere
from hysop.domain.subsets import Subset, SubBox
from hysop.domain.subsets import Cylinder, HemiCylinder
from hysop.operator.hdf_io import HDF_Reader
-from hysop.tools.parameters import Discretization, IOParams
+from hysop.tools.parameters import Discretization
+from hysop.tools.io_utils import IOParams
from hysop import Field, Box
from hysop.mpi.topology import Cartesian
import hysop.tools.numpywrappers as npw
@@ -51,7 +55,7 @@ def check_subset(discr, fileref, class_name):
subs.discretize(topo)
assert subs.ind.keys()[0] == topo
assert len(subs.ind[topo][0]) == dom.dimension
- scal = Field(domain=topo.domain, is_vector=False)
+ scal = Field(domain=topo.domain, is_vector=False, name='s0')
sd = scal.discretize(topo)
sd[0][subs.ind[topo][0]] = 2.
icompute = topo.mesh.iCompute
@@ -96,7 +100,7 @@ def init_multi(discr, fileref):
reader.setup()
reader.apply()
reader.finalize()
- scal = Field(domain=topo.domain, is_vector=False)
+ scal = Field(domain=topo.domain, is_vector=False, name='s1')
sd = scal.discretize(topo)
return topo, sd, vd
@@ -113,7 +117,7 @@ def init_obst_list(discr, fileref):
obs_list = [s1, s2, s3]
for obs in obs_list:
obs.discretize(topo)
- sd = Field(domain=topo.domain, is_vector=False).discretize(topo)
+ sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.union(obs_list, topo)
sd[0][indices] = 2.
icompute = topo.mesh.iCompute
@@ -138,7 +142,7 @@ def init_subtract(discr, fileref):
box = SubBox(origin=pos, length=ll, parent=topo.domain)
s1.discretize(topo)
box.discretize(topo)
- sd = Field(domain=topo.domain, is_vector=False).discretize(topo)
+ sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.subtract(box, s1, topo)
sd[0][indices] = 2.
icompute = topo.mesh.iCompute
@@ -176,7 +180,7 @@ def init_subtract_lists(discr, fileref):
ob.discretize(topo)
for ob in box:
ob.discretize(topo)
- sd = Field(domain=topo.domain, is_vector=False).discretize(topo)
+ sd = Field(domain=topo.domain, is_vector=False, name='s2').discretize(topo)
indices = Subset.subtract_list_of_sets(box, obs, topo)
sd[0][indices] = 2.
return np.allclose(sd[0][topo.mesh.iCompute], vd[0][topo.mesh.iCompute])
diff --git a/HySoP/hysop/f2py/fftw2py.pyf b/HySoP/hysop/f2py/fftw2py.pyf
index a9a833e88..860933a2d 100644
--- a/HySoP/hysop/f2py/fftw2py.pyf
+++ b/HySoP/hysop/f2py/fftw2py.pyf
@@ -119,8 +119,8 @@ module fftw2py ! in fftw2py.f90
end subroutine solve_curl_2d
subroutine spectrum_3d(field,spectrum,wavelengths,ghosts,length) ! in fftw2py.f90:fftw2py
real(kind=pk) dimension(:,:,:),intent(in) :: field
- real(kind=pk) dimension(:),intent(inout) :: spectrum
- real(kind=pk) dimension(:),intent(inout) :: wavelengths
+ real(kind=pk) dimension(:),intent(in,out) :: spectrum
+ real(kind=pk) dimension(:),intent(in,out) :: wavelengths
integer dimension(3),intent(in) :: ghosts
real(kind=pk) intent(in) :: length
end subroutine spectrum_3d
diff --git a/HySoP/hysop/fields/continuous.py b/HySoP/hysop/fields/continuous.py
old mode 100644
new mode 100755
index 4e497228d..38f713105
--- a/HySoP/hysop/fields/continuous.py
+++ b/HySoP/hysop/fields/continuous.py
@@ -17,6 +17,9 @@ from hysop.constants import debug
from hysop.fields.discrete import DiscreteField
from hysop.mpi import main_rank
from hysop.tools.profiler import Profiler
+from hysop.tools.io_utils import IOParams, IO
+from hysop.operator.hdf_io import HDF_Writer, HDF_Reader
+from hysop.mpi.topology import Cartesian
class Field(object):
@@ -29,8 +32,8 @@ class Field(object):
discretize it.
Example :
- if topo1 and topo2 are two hysop.mpi.topology.Cartesian objects:
- \code
+ if topo1 and topo2 are two hysop.mpi.topology.Cartesian objects::
+
scal = Field(domain=dom, name='Scalar')
# Discretize scal on two different topologies
scal.discretize(topo1)
@@ -40,7 +43,6 @@ class Field(object):
scal_discr2 = scal.discreteFields[topo2]
# or in a more straightforward way:
scal_discr2 = scal.discretize(topo2)
- \endcode
"""
@@ -49,7 +51,7 @@ class Field(object):
return object.__new__(cls, *args, **kw)
@debug
- def __init__(self, domain, formula=None, name=None, is_vector=False,
+ def __init__(self, domain, name, formula=None, is_vector=False,
nb_components=None, vectorize_formula=False):
"""Defines a continuous field (scalar or vector) on a domain.
@@ -58,10 +60,10 @@ class Field(object):
domain : domain.Domain
physical domain where this field is defined.
- formula : python function, optional
- a user-defined python function. See notes for details.
name : string
a name for the variable. Required because of h5py i/o.
+ formula : python function, optional
+ a user-defined python function. See notes for details.
is_vector : bool, optional
true if the field is a vector.
nb_components : int, optional
@@ -85,24 +87,22 @@ class Field(object):
"""
- ## Physical domain of definition of the variable.
+ # Physical domain of definition of the variable.
self.domain = domain
- ## dimension (1, 2 or 3D), equal to domain dimension.
+ # dimension (1, 2 or 3D), equal to domain dimension.
self.dimension = self.domain.dimension
- ## Id (optional)
- if name is None:
- name = 'unnamed'
+ # Id
self.name = name
- ## Dictionnary of all the discretizations of this field.
- ## Key = hysop.mpi.topology.Cartesian,
- ## value =hysop.fields.discrete.DiscreteField.
- ## Example : vel = discreteFields[topo]
+ # Dictionnary of all the discretizations of this field.
+ # Key = hysop.mpi.topology.Cartesian,
+ # value =hysop.fields.discrete.DiscreteField.
+ # Example : vel = discreteFields[topo]
self.discreteFields = {}
- ## Analytic formula.
+ # Analytic formula.
self.formula = formula
- ## A list of extra parameters, used in _formula
+ # A list of extra parameters, used in _formula
self.extraParameters = tuple([])
- ## Number of components of the field
+ # Number of components of the field
if nb_components is None:
self.nb_components = self.dimension if is_vector else 1
else:
@@ -111,10 +111,16 @@ class Field(object):
# True if the given formula and must be vectorized
self._vectorize = vectorize_formula
- ## Time profiling
+ # Time profiling
self.profiler = Profiler(self, self.domain.comm_task)
+ # i/o : a dictionnary of hdf writers.
+ # None by default, if needed must be
+ # initialized with init_writer function.
+ self.writer = {}
+
def get_profiling_info(self):
+ """Update profiler"""
for d in self.discreteFields.values():
self.profiler += d.profiler
@@ -136,8 +142,8 @@ class Field(object):
simply returns the discretized field.
"""
-
- if topo in self.discreteFields.keys():
+ assert isinstance(topo, Cartesian)
+ if topo in self.discreteFields:
return self.discreteFields[topo]
else:
self.discreteFields[topo] = DiscreteField(
@@ -191,6 +197,32 @@ class Field(object):
df.initialize(self.formula, self._vectorize, time,
*self.extraParameters)
+ def randomize(self, topo):
+ """Initialize a field on topo with random values.
+
+ Parameters
+ -----------
+ topo : :class:`mpi.topology.Cartesian`
+ the topology on which initialization is performed.
+ """
+ df = self.discretize(topo)
+ df.randomize()
+ return self.discreteFields[topo]
+
+ def copy(self, field_in, topo):
+ """Initialize a field on topo with values from another field.
+
+ Parameters
+ -----------
+ field_in : :class:`fields.continuous.Continuous`
+ field to be copied
+ topo : :class:`mpi.topology.Cartesian`
+ the topology on which initialization is performed.
+ """
+ df = self.discretize(topo)
+ field_in_d = field_in.discretize(topo)
+ df.copy(field_in_d)
+
def value(self, *pos):
"""Evaluation of the field at a given position, according
to the analytic formula given during construction.
@@ -297,37 +329,81 @@ class Field(object):
"""
self.extraParameters = args
- def hdf_dump(self, discretization, io_params=None):
- from hysop.operator.hdf_io import HDF_Writer
- from hysop.problem.simulation import Simulation
- simu = Simulation(nbIter=1)
+ def init_writer(self, discretization, io_params=None):
+ """Create an hdf writer for a given discretization
+
+ Parameters
+ ----------
+ discretization : :class:`~hysop.tools.params.Discretization` or
+ :class:`~hysop.mpi.topology.Cartesian`
+ set a data distribution description for the output, i.e.
+ choose the space discretisation used for hdf file.
+ io_params : :class:`~hysop.tools.io_utils.IOParams`, optional
+ output file description
+ """
if io_params is None:
- from hysop.tools.parameters import IOParams
- from hysop.constants import HDF5
- io_params = IOParams(self.name, fileformat=HDF5)
- wr = HDF_Writer(variables={self: discretization},
- io_params=io_params)
+ io_params = IOParams(self.name, fileformat=IO.HDF5)
+ wr = HDF_Writer(variables={self: discretization}, io_params=io_params)
wr.discretize()
wr.setup()
- wr.apply(simu)
- wr.finalize()
+ self.writer[self.discreteFields[wr.topology]] = wr
- def hdf_load(self, discretization, io_params=None, restart=None):
- from hysop.operator.hdf_io import HDF_Reader
+ def hdf_dump(self, topo, simu):
+ """Save field data into hdf file
- if io_params is None:
- from hysop.tools.parameters import IOParams
- from hysop.constants import HDF5
- io_params = IOParams(self.name, fileformat=HDF5)
- read = HDF_Reader(variables={self: discretization},
- io_params=io_params, restart=restart)
+ Parameters
+ ----------
+ topo : :class:`~hysop.mpi.topology.Cartesian`
+ data distribution description
+ simu : :class:`~hysop.problem.simulation.Simulation`
+ time discretisation
+ """
+ df = self.discretize(topo)
+ if df not in self.writer:
+ self.init_writer(topo)
+ self.writer[df].apply(simu)
+ self.writer[df].finalize()
+
+ def hdf_load(self, topo, io_params=None,
+ restart=None, dataset_name=None):
+ """Load field from hdf fileformat
+
+ Parameters
+ ----------
+ topo : :class:`~hysop.mpi.topology.Cartesian`
+ data distribution description
+ io_params : :class:`~hysop.tools.io_utils.IOParams`, optional
+ output file description
+ restart : int, optional
+ iteration number. Default=None, i.e. read first iteration.
+ dataset_name : string, optional
+ name of the dataset in h5 file used to fill this field in.
+ If None, look for self.name as dataset name.
+
+ Notes
+ -----
+
+ * a call to hdf_load(topo, ...) will discretize the
+ field on topo, if not already done
+ * to read the dataset 'field1' from file ff_00001.h5::
+
+ myfield = Field(box, name='f1')
+ myfield.hdf_load(topo, IOParams('ff', restart=1,
+ dataset_name='field1')
+
+ """
+ if dataset_name is None:
+ var_names = None
+ else:
+ var_names = {self: dataset_name}
+ read = HDF_Reader(variables={self: topo},
+ io_params=io_params, restart=restart,
+ var_names=var_names)
read.discretize()
read.setup()
read.apply()
read.finalize()
- return 0
-
def zero(self, topo=None):
"""Reset to 0.0 all components of this field.
@@ -339,7 +415,3 @@ class Field(object):
else:
for dfield in self.discreteFields.values():
dfield.zero()
-
- def finalize(self):
- for dfield in self.discreteFields.values():
- dfield.finalize()
diff --git a/HySoP/hysop/fields/discrete.py b/HySoP/hysop/fields/discrete.py
old mode 100644
new mode 100755
index eef86310a..3f941c4f9
--- a/HySoP/hysop/fields/discrete.py
+++ b/HySoP/hysop/fields/discrete.py
@@ -5,7 +5,7 @@
Documentation and examples can be found in :ref:`fields`.
"""
-from hysop.constants import debug
+from hysop.constants import debug, ORDER
from itertools import count
from hysop.tools.profiler import Profiler
import numpy as np
@@ -160,6 +160,24 @@ class DiscreteField(object):
"WARNING: The shape of " + self.name + " has changed during"\
" field initialisation."
+ def randomize(self):
+ """Initialize a the with random values.
+
+ """
+ for d in xrange(self.nb_components):
+ self.data[d][...] = np.random.random(self.topology.mesh.resolution)
+
+ def copy(self, field_in):
+ """Initialize a field on topo with values from another field.
+
+ Parameters
+ -----------
+ field_in : :class:`fields.discrete.DiscreteField`
+ field to be copied
+ """
+ for d in xrange(self.nb_components):
+ self.data[d][...] = field_in.data[d].copy(order=ORDER)
+
def norm(self):
"""Compute the euclidian norm of the discrete field
p-norm = (sum data[d](i,...)**p)**1/p for d = 1..dim
@@ -200,8 +218,6 @@ class DiscreteField(object):
for dim in xrange(self.nb_components):
self.data[dim][...] = 0.0
- def finalize(self):
- pass
-
def get_profiling_info(self):
+ """update profiler"""
pass
diff --git a/HySoP/hysop/fields/tests/func_for_tests.py b/HySoP/hysop/fields/tests/func_for_tests.py
old mode 100644
new mode 100755
index ce3ea9d16..3e2eaf562
--- a/HySoP/hysop/fields/tests/func_for_tests.py
+++ b/HySoP/hysop/fields/tests/func_for_tests.py
@@ -1,10 +1,10 @@
-"""
-@file func_for_tests.py a set of functions, used in tests
+"""A set of functions, used in tests
to initialize the fields
"""
import numpy as np
-sin = np.sin
import math
+sin = np.sin
+cos = np.cos
pi = math.pi
@@ -88,3 +88,36 @@ def v2d(res, x, y, t):
res[0][...] = sin(x) + t
res[1][...] = y
return res
+
+
+def v_time_2d(res, x, y, t):
+ """For 2d vector field, all components depend on time
+ """
+ res[0][...] = sin(x) + t
+ res[1][...] = y * t
+ return res
+
+
+def v_time_3d(res, x, y, z, t):
+ """For 3d vector field, all components depend on time
+ """
+ res[0][...] = sin(x) + t
+ res[1][...] = y * t
+ res[2][...] = z * t ** 2
+ return res
+
+
+def v_TG(res, x, y, z, t):
+ """Taylor Green velocity"""
+ res[0][...] = sin(x) * cos(y) * cos(z)
+ res[1][...] = - cos(x) * sin(y) * cos(z)
+ res[2][...] = 0.
+ return res
+
+
+def w_TG(res, x, y, z, t):
+ """Taylor Green vorticity"""
+ res[0][...] = - cos(x) * sin(y) * sin(z)
+ res[1][...] = - sin(x) * cos(y) * sin(z)
+ res[2][...] = 2. * sin(x) * sin(y) * cos(z)
+ return res
diff --git a/HySoP/hysop/fields/tests/test_field.py b/HySoP/hysop/fields/tests/test_field.py
index b5181bbd2..6247b5dee 100755
--- a/HySoP/hysop/fields/tests/test_field.py
+++ b/HySoP/hysop/fields/tests/test_field.py
@@ -1,29 +1,37 @@
+"""Test fields build and usage (discrete and continuous)
"""
-Testing hysop.field.continuous.Field
-"""
-import hysop
-print hysop.__file__
-from hysop.fields.continuous import Field
-from hysop.domain.box import Box
-from hysop.tools.parameters import Discretization
+from hysop import Simulation, Box, Field, Discretization, IOParams, IO
import numpy as np
+import os
from hysop.fields.tests.func_for_tests import func_scal_1, func_scal_2, \
- func_vec_1, func_vec_2, func_vec_3, func_vec_4, func_vec_5, func_vec_6
+ func_vec_1, func_vec_2, func_vec_3, func_vec_4, func_vec_5, func_vec_6,\
+ v_time_3d, v_time_2d
from numpy import allclose
+import shutil
+from hysop.mpi import main_rank
+
-d3D = Discretization([33, 33, 33])
-d2D = Discretization([33, 33])
+d3d = Discretization([33, 33, 33])
+d2d = Discretization([33, 33])
nbc = 4
+def formula(x, y, z):
+ return (x * y * z, 1.0, -x * y * z)
+
+
+def form2(x, y, z, dt):
+ return (x * y * z, 1.0, -x * y * z * dt)
+
+
def test_continuous():
""" Basic continuous field construction """
dom = Box()
- cf = Field(dom)
+ cf = Field(dom, name='f1')
assert cf.nb_components == 1
assert cf.domain is dom
- cf = Field(dom, is_vector=True)
+ cf = Field(dom, name='f2', is_vector=True)
assert cf.nb_components == dom.dimension
assert cf.domain is dom
@@ -31,8 +39,7 @@ def test_continuous():
def test_analytical():
"""Test formula"""
dom = Box()
- formula = lambda x, y, z: (x * y * z, 1.0, -x * y * z)
- caf = Field(dom, formula, vectorize_formula=True)
+ caf = Field(dom, name='f1', formula=formula, vectorize_formula=True)
assert caf.value(0., 0., 0.) == (0., 1., 0.)
assert caf.value(1., 1., 1.) == (1., 1., -1.)
assert caf.value(1., 2., 3.) == (6., 1., -6.)
@@ -41,12 +48,10 @@ def test_analytical():
def test_analytical_reset():
"""Test formula"""
dom = Box()
- formula = lambda x, y, z: (x * y * z, 1.0, -x * y * z)
- caf = Field(dom, formula, vectorize_formula=True)
+ caf = Field(dom, name='f1', formula=formula, vectorize_formula=True)
assert caf.value(0., 0., 0.) == (0., 1., 0.)
assert caf.value(1., 1., 1.) == (1., 1., -1.)
assert caf.value(1., 2., 3.) == (6., 1., -6.)
- form2 = lambda x, y, z, dt: (x * y * z, 1.0, -x * y * z * dt)
caf.set_formula(form2, vectorize_formula=True)
assert caf.value(0., 0., 0., 0.) == (0., 1., 0.)
assert caf.value(1., 1., 1., 1.) == (1., 1., -1.)
@@ -56,8 +61,8 @@ def test_analytical_reset():
def test_discretization():
"""Test multiple discretizations"""
dom = Box()
- csf = Field(dom)
- cvf = Field(dom, is_vector=True)
+ csf = Field(dom, name='f1')
+ cvf = Field(dom, name='f2', is_vector=True)
r3d = Discretization([33, 33, 17])
topo = dom.create_topology(r3d)
csf.discretize(topo)
@@ -75,10 +80,10 @@ def test_discretization():
# Non-Vectorized formula for a scalar
def test_analytical_field_1():
box = Box()
- topo = box.create_topology(discretization=d3D)
+ topo = box.create_topology(discretization=d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_scal_1)
- ref = Field(box)
+ caf = Field(box, name='f1', formula=func_scal_1)
+ ref = Field(box, name='f2')
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -97,10 +102,10 @@ def test_analytical_field_1():
# Vectorized formula
def test_analytical_field_2():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_scal_2, vectorize_formula=True)
- ref = Field(box)
+ caf = Field(box, name='f1', formula=func_scal_2, vectorize_formula=True)
+ ref = Field(box, name='f2')
cafd = caf.discretize(topo)
ids = id(cafd.data[0])
refd = ref.discretize(topo)
@@ -118,10 +123,10 @@ def test_analytical_field_2():
# Non-Vectorized formula for a vector
def test_analytical_field_3():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_1, is_vector=True)
- ref = Field(box, is_vector=True)
+ caf = Field(box, name='f1', formula=func_vec_1, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -144,11 +149,11 @@ def test_analytical_field_3():
# Vectorized formula for a vector
def test_analytical_field_4():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_2, is_vector=True,
+ caf = Field(box, name='f1', formula=func_vec_2, is_vector=True,
vectorize_formula=True)
- ref = Field(box, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -171,12 +176,12 @@ def test_analytical_field_4():
# Non-Vectorized formula for a vector, with extra-arguments
def test_analytical_field_5():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_3, is_vector=True)
+ caf = Field(box, name='f1', formula=func_vec_3, is_vector=True)
theta = 0.3
caf.set_formula_parameters(theta)
- ref = Field(box, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -199,13 +204,13 @@ def test_analytical_field_5():
# Vectorized formula for a vector, with extra-arguments
def test_analytical_field_6():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_4, is_vector=True,
+ caf = Field(box, name='f1', formula=func_vec_4, is_vector=True,
vectorize_formula=True)
theta = 0.3
caf.set_formula_parameters(theta)
- ref = Field(box, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -229,12 +234,12 @@ def test_analytical_field_6():
# different from domain dim and with extra-arguments
def test_analytical_field_7():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_5, nb_components=nbc)
+ caf = Field(box, name='f1', formula=func_vec_5, nb_components=nbc)
theta = 0.3
caf.set_formula_parameters(theta)
- ref = Field(box, nb_components=nbc)
+ ref = Field(box, name='f2', nb_components=nbc)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -259,12 +264,12 @@ def test_analytical_field_7():
# different from domain dim and with extra-arguments
def test_analytical_field_8():
box = Box(dimension=2, length=[1., 1.], origin=[0., 0.])
- topo = box.create_topology(d2D)
+ topo = box.create_topology(d2d)
coords = topo.mesh.coords
- caf = Field(box, formula=func_vec_6, nb_components=nbc)
+ caf = Field(box, name='f1', formula=func_vec_6, nb_components=nbc)
theta = 0.3
caf.set_formula_parameters(theta)
- ref = Field(box, nb_components=nbc)
+ ref = Field(box, name='f2', nb_components=nbc)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
refd = ref.discretize(topo)
@@ -288,13 +293,13 @@ def test_analytical_field_8():
# topologies.
def test_analytical_field_9():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
res2 = Discretization([65, 33, 65], [1, 1, 1])
topo2 = box.create_topology(res2, dim=2)
coords = topo.mesh.coords
coords2 = topo2.mesh.coords
- caf = Field(box, formula=func_vec_1, is_vector=True)
- ref = Field(box, is_vector=True)
+ caf = Field(box, name='f1', formula=func_vec_1, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
cafd2 = caf.discretize(topo2)
@@ -319,13 +324,13 @@ def test_analytical_field_9():
# topologies.
def test_analytical_field_10():
box = Box()
- topo = box.create_topology(d3D)
+ topo = box.create_topology(d3d)
res2 = Discretization([65, 33, 65], [1, 1, 1])
topo2 = box.create_topology(res2, dim=2)
coords = topo.mesh.coords
coords2 = topo2.mesh.coords
- caf = Field(box, formula=func_vec_1, is_vector=True)
- ref = Field(box, is_vector=True)
+ caf = Field(box, name='f1', formula=func_vec_1, is_vector=True)
+ ref = Field(box, name='f2', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discretize(topo)
cafd2 = caf.discretize(topo2)
@@ -341,3 +346,93 @@ def test_analytical_field_10():
assert allclose(cafd2[i], refd2.data[i])
assert allclose(cafd[i], refd.data[i])
assert id(cafd2.data[i]) == ids[i]
+
+
+def test_copy():
+ box = Box()
+ topo = box.create_topology(d3d)
+ f1 = Field(box, name='source', is_vector=True, formula=func_vec_1)
+ f2 = Field(box, name='target', is_vector=True)
+ f1d = f1.discretize(topo)
+ f1.initialize(topo=topo)
+ f2.copy(f1, topo)
+ f2d = f2.discretize(topo)
+ for d in xrange(f2.nb_components):
+ assert np.allclose(f2d[d], f1d[d])
+ assert f2d[d].flags.f_contiguous == f1d[d].flags.f_contiguous
+
+
+def test_randomize():
+ box = Box()
+ topo = box.create_topology(d3d)
+ f2 = Field(box, name='target', is_vector=True)
+ f2.randomize(topo)
+ f2d = f2.discretize(topo)
+ for d in xrange(f2.nb_components):
+ assert not np.allclose(f2d[d], 0.)
+
+
+def hdf_dump_load(discretisation, formula):
+ dimension = len(discretisation.resolution)
+ box = Box([1., ] * dimension)
+ topo = box.create_topology(discretisation)
+ fname = 'f1_' + str(dimension)
+ ff = Field(box, name=fname, is_vector=True, formula=formula)
+ iop = IOParams(ff.name)
+ simu = Simulation(nbIter=4)
+ simu.initialize()
+ ff.initialize(time=simu.time, topo=topo)
+ ff.hdf_dump(topo, simu)
+ simu.advance()
+ ff.initialize(time=simu.time, topo=topo)
+ # Write ff for current time and topo
+ ff.hdf_dump(topo, simu)
+ assert iop.filepath == IO.default_path()
+ assert os.path.isfile(iop.filename + '_00000.h5')
+ assert os.path.isfile(iop.filename + '_00001.h5')
+ assert os.path.isfile(iop.filename + '.xmf')
+ fname2 = 'f2_' + str(dimension)
+ gg = Field(box, name=fname2, is_vector=True)
+ iop_in = IOParams(iop.filename + '_00001.h5')
+ dsname = ff.name + '_' + str(topo.get_id())
+ # Load gg from ff values at current time, on topo
+ for i in xrange(gg.nb_components):
+ assert not np.allclose(gg.discretize(topo)[i], ff.discretize(topo)[i])
+ gg.hdf_load(topo, iop_in, dataset_name=dsname)
+ for i in xrange(gg.nb_components):
+ assert np.allclose(gg.discretize(topo)[i], ff.discretize(topo)[i])
+
+ # reset ff with its values at time 'O', on topo
+ ff.hdf_load(topo, restart=0)
+ for i in xrange(gg.nb_components):
+ assert not np.allclose(gg.discretize(topo)[i], ff.discretize(topo)[i])
+
+
+def test_hdf_dump_load_2d():
+ hdf_dump_load(d2d, v_time_2d)
+
+
+def test_hdf_dump_load_3d():
+ hdf_dump_load(d3d, v_time_3d)
+
+
+# This may be useful to run mpi tests
+if __name__ == "__main__":
+ test_continuous()
+ test_analytical()
+ test_analytical_reset()
+ test_discretization()
+ test_analytical_field_1()
+ test_analytical_field_2()
+ test_analytical_field_3()
+ test_analytical_field_4()
+ test_analytical_field_5()
+ test_analytical_field_6()
+ test_analytical_field_7()
+ test_analytical_field_8()
+ test_copy()
+ test_randomize()
+ test_hdf_dump_load_2d()
+ test_hdf_dump_load_3d()
+ if main_rank == 0:
+ shutil.rmtree(IO.default_path())
diff --git a/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py b/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
index 4c87351fb..b44201bbd 100755
--- a/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
+++ b/HySoP/hysop/gpu/tests/test_gpu_multiresolution_filter.py
@@ -33,7 +33,7 @@ def test_filter_linear():
"""This test compares the GPU linear filter with python implementation"""
box = Box(length=L, origin=O, proc_tasks=PROC_TASKS)
mpi_p = MPIParams(comm=box.comm_task, task_id=1)
- f = Field(box, formula=func, is_vector=False)
+ f = Field(box, formula=func, is_vector=False, name='f1')
d_fine = Discretization([513, 513, 513])
d_coarse = Discretization([257, 257, 257], ghosts=[1, 1, 1])
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
@@ -62,7 +62,7 @@ def test_filter_linear():
np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
f_out[0][topo_coarse.mesh.iCompute]))
if PY_COMPARE:
- f_py = Field(box, formula=func)
+ f_py = Field(box, formula=func, name='fpy')
op_py = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
variables={f_py: d_coarse},
method={Remesh: Rmsh_Linear, },
@@ -85,7 +85,7 @@ def test_filter_L2_1():
"""
box = Box(length=L, origin=O, proc_tasks=PROC_TASKS)
mpi_p = MPIParams(comm=box.comm_task, task_id=1)
- f = Field(box, formula=func)
+ f = Field(box, formula=func, name='f1')
d_fine = Discretization([513, 513, 513])
d_coarse = Discretization([257, 257, 257], ghosts=[2, 2, 2])
if box.is_on_task(1):
@@ -113,7 +113,7 @@ def test_filter_L2_1():
np.max(np.abs(valid[0][topo_coarse.mesh.iCompute] -
f_out[0][topo_coarse.mesh.iCompute]))
if PY_COMPARE:
- f_py = Field(box, formula=func)
+ f_py = Field(box, formula=func, name='fpy')
op_py = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
variables={f_py: d_coarse},
method={Remesh: L2_1, })
diff --git a/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py b/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
index fbfd41963..742ba3629 100755
--- a/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
+++ b/HySoP/hysop/gpu/tests/test_multiphase_baroclinic.py
@@ -78,12 +78,12 @@ def call_operator(func, grad_func, vfunc):
"""Call the baroclinic rhs operator from given initialization functions"""
simu = Simulation(tinit=0.0, tend=1.0, timeStep=0.1, iterMax=1)
box = Box()
- rhs = Field(box, is_vector=True)
- gradp = Field(box, is_vector=True, formula=vfunc)
- rho = Field(box, is_vector=False, formula=func)
- gradrho = Field(box, is_vector=True, formula=grad_func)
- gradp_fine = Field(box, is_vector=True, formula=vfunc)
- true_rhs = Field(box, is_vector=True)
+ rhs = Field(box, is_vector=True, name='rhs')
+ gradp = Field(box, is_vector=True, formula=vfunc, name='gradp')
+ rho = Field(box, is_vector=False, formula=func, name='rho')
+ gradrho = Field(box, is_vector=True, formula=grad_func, name='gradrho')
+ gradp_fine = Field(box, is_vector=True, formula=vfunc, name='fine')
+ true_rhs = Field(box, is_vector=True, name='ref')
d_fine = Discretization([257, 257, 257])
d_coarse = Discretization([129, 129, 129], ghosts=[2, 2, 2])
op = MultiphaseBaroclinicRHS(rhs, rho, gradp,
diff --git a/HySoP/hysop/numerics/integrators/odesolver.py b/HySoP/hysop/numerics/integrators/odesolver.py
old mode 100644
new mode 100755
index ab12ac76e..6b6cf41f4
--- a/HySoP/hysop/numerics/integrators/odesolver.py
+++ b/HySoP/hysop/numerics/integrators/odesolver.py
@@ -51,6 +51,7 @@ class ODESolver(NumMethod):
lwork = self.getWorkLengths(nb_components)
assert len(self.work) == lwork, 'Wrong length for work arrays list.'
self._memshape = tuple(topo.mesh.resolution)
+ print topo.mesh
for wk in self.work:
assert wk.shape == tuple(self._memshape)
# Allocate buffers for ghost points synchronization.
diff --git a/HySoP/hysop/numerics/tests/test_integrators.py b/HySoP/hysop/numerics/tests/test_integrators.py
old mode 100644
new mode 100755
diff --git a/HySoP/hysop/numerics/tests/test_update_ghosts.py b/HySoP/hysop/numerics/tests/test_update_ghosts.py
index e1970b2f3..8ec8f843f 100755
--- a/HySoP/hysop/numerics/tests/test_update_ghosts.py
+++ b/HySoP/hysop/numerics/tests/test_update_ghosts.py
@@ -8,7 +8,7 @@ import numpy as np
def _setup(ghosts, topo_dim):
dom = Box()
- f = Field(dom, is_vector=True)
+ f = Field(dom, is_vector=True, name='f')
resolTopo = Discretization([33, 33, 33], ghosts=ghosts)
topo = dom.create_topology(resolTopo, dim=topo_dim)
f.discretize(topo)
diff --git a/HySoP/hysop/operator/computational.py b/HySoP/hysop/operator/computational.py
old mode 100644
new mode 100755
index 31ecca3eb..251e7e678
--- a/HySoP/hysop/operator/computational.py
+++ b/HySoP/hysop/operator/computational.py
@@ -1,10 +1,9 @@
""" Abstract interface for computational operators
-
"""
from abc import ABCMeta, abstractmethod
from hysop.constants import debug
-from hysop.operator.continuous import Operator
+from hysop.operator.continuous import Operator, opapply
from hysop.mpi.topology import Cartesian
from hysop.tools.parameters import Discretization
from hysop.tools.profiler import profile
@@ -44,7 +43,7 @@ class Computational(Operator):
method : :class:`hysop.method`
specific parameters for the operator
(space discretisation ...). See methods.py for authorized values.
- **kwds : arguments passed to operator.continuous.Operator base class.
+ **kwds : arguments passed to base class.
Notes:
------
@@ -54,20 +53,20 @@ class Computational(Operator):
# Set mpi related stuff
self._set_domain_and_tasks()
- ## A dictionnary of parameters, to define numerical methods used
- ## used to discretize the operator.
- ## When method is None, each operator must provide a default
- ## behavior.
+ # A dictionnary of parameters, to define numerical methods used
+ # used to discretize the operator.
+ # When method is None, each operator must provide a default
+ # behavior.
self.method = method
- ## The discretization of this operator.
+ # The discretization of this operator.
self.discrete_op = None
- ## A dictionnary of discreteFields associated with this operator
- ## key = continuous variable \n
- ## Example : discrete_variable = discreteFields[velocity]
- ## returns the discrete fields that corresponds to the continuous
- ## variable velocity.
+ # A dictionnary of discreteFields associated with this operator
+ # key = continuous variable \n
+ # Example : discrete_variable = discreteFields[velocity]
+ # returns the discrete fields that corresponds to the continuous
+ # variable velocity.
self.discreteFields = {}
if not self._varsfromList:
@@ -311,14 +310,16 @@ class Computational(Operator):
@debug
@profile
+ @opapply
def apply(self, simulation=None):
+ """Apply this operator to its variables.
+
+ Parameters
+ ----------
+ simulation : `:class::~hysop.problem.simulation.Simulation`
+
"""
- Apply this operator to its variables.
- @param simulation : object that describes the simulation
- parameters (time, time step, iteration number ...), see
- hysop.problem.simulation.Simulation for details.
- """
- super(Computational, self).apply(simulation)
+ #super(Computational, self).apply(simulation)
if self.discrete_op is not None:
self.discrete_op.apply(simulation)
diff --git a/HySoP/hysop/operator/continuous.py b/HySoP/hysop/operator/continuous.py
old mode 100644
new mode 100755
index 994ae33e0..a8ee8ab44
--- a/HySoP/hysop/operator/continuous.py
+++ b/HySoP/hysop/operator/continuous.py
@@ -4,8 +4,10 @@
from abc import ABCMeta, abstractmethod
from hysop.constants import debug
from hysop.tools.profiler import Profiler
-from hysop.tools.parameters import MPIParams, IOParams
+from hysop.tools.io_utils import IOParams, IO
+from hysop.tools.parameters import MPIParams
import hysop.tools.io_utils as io
+import inspect
class Operator(object):
@@ -23,11 +25,11 @@ class Operator(object):
io_params=None):
"""
Parameters
- ----------------
+ ----------
variables : list or dictionnary. See Notes for details.
mpi_params : :class:`hysop.tools.parameters.MPIParams`
mpi config for the operator (comm, task ...)
- io_params : :class:`hysop.tools.parameters.IOParams`
+ io_params : :class:`hysop.tools.io_utils.IOParams`
file i/o config (filename, format ...)
Notes
@@ -95,20 +97,20 @@ class Operator(object):
# _set_domain_and_tasks, called in derived class, since it may
# require some specific initialization (check domain ...)
- ## Input variables.
+ # Input variables.
self.input = []
- ## Output variables.
+ # Output variables.
self.output = []
- ## bool to check if the setup function has been called for
- ## this operator
+ # bool to check if the setup function has been called for
+ # this operator
self._is_uptodate = False
self.name = self.__class__.__name__
- ## List of operators that must be waited for.
+ # List of operators that must be waited for.
self._wait_list = []
- ## time monitoring
+ # time monitoring
self.time_info = None
- ## Dictionnary of optional parameters for output
+ # Dictionnary of optional parameters for output
self.io_params = io_params
# Object that deals with output file writing.
# Optional.
@@ -140,7 +142,10 @@ class Operator(object):
# Set profiler
self.profiler = Profiler(self, self.domain.comm_task)
- def _error_(self):
+ @staticmethod
+ def _error_():
+ """internal error message
+ """
raise RuntimeError("This operator is not defined for the current task")
def wait_for(self, op):
@@ -252,9 +257,19 @@ class Operator(object):
"""
iopar = self.io_params
+ # if iopar is not None (i.e. set in operator init)
+ # and True or set as an IOParams , then
+ # build a writer
if iopar:
if isinstance(iopar, bool):
- self.io_params = IOParams(filename)
+ # default values for iop
+ self.io_params = IOParams(filename, fileformat=IO.ASCII)
+ else:
+ if self.io_params.fileformat is not IO.ASCII:
+ self.io_params.fileformat = IO.ASCII
+ msg = 'Warning, wrong file format for operator output.'
+ msg += 'This will be reset to ASCII.'
+ print msg
self._writer = io.Writer(io_params=self.io_params,
mpi_params=self._mpis,
buffshape=buffshape)
@@ -266,9 +281,6 @@ class Operator(object):
return self._mpis.task_id
-import inspect
-
-
def opsetup(f):
"""
Setup decorator: what must be done by all operators
@@ -277,6 +289,8 @@ def opsetup(f):
"""
def decorator(*args, **kwargs):
+ """Decorate 'setup' method
+ """
# Job before setup of the function ...
# nothing for the moment
name = inspect.getmro(args[0].setup.im_class)
@@ -306,8 +320,10 @@ def opapply(f):
Usage : add @opapply before apply class method
"""
def decorator(*args, **kwargs):
+ """decorate 'apply' method"""
+ # get 'continuous' base class and run its apply function
name = inspect.getmro(args[0].apply.im_class)
- name[-3].setup(args[0])
+ name[-2].apply(args[0])
#super(args[0].__class__, args[0]).apply()
for op in args[0].wait_list():
op.wait()
diff --git a/HySoP/hysop/operator/discrete/discrete.py b/HySoP/hysop/operator/discrete/discrete.py
old mode 100644
new mode 100755
index baff4c8f8..2069227a8
--- a/HySoP/hysop/operator/discrete/discrete.py
+++ b/HySoP/hysop/operator/discrete/discrete.py
@@ -143,11 +143,11 @@ class DiscreteOperator(object):
@debug
@abstractmethod
def apply(self, simulation=None):
- """
- Apply this operator to its variables.
- @param simulation : object that describes the simulation
- parameters (time, time step, iteration number ...), see
- hysop.problem.simulation.Simulation for details.
+ """Execute the operator for the current simulation state
+
+ Parameters
+ ----------
+ simulation : :class:`~hysop.problem.simulation.Simulation`
"""
@debug
diff --git a/HySoP/hysop/operator/discrete/spectrum.py b/HySoP/hysop/operator/discrete/spectrum.py
old mode 100644
new mode 100755
diff --git a/HySoP/hysop/operator/drag_and_lift.py b/HySoP/hysop/operator/drag_and_lift.py
old mode 100644
new mode 100755
index a93587f24..b20ff7754
--- a/HySoP/hysop/operator/drag_and_lift.py
+++ b/HySoP/hysop/operator/drag_and_lift.py
@@ -3,11 +3,19 @@
.. currentmodule:: hysop.operator
+* :class:`~drag_and_lift.MomentumForces` : Momentum Formula
+* :class:`~drag_and_lift.NocaForces` : Noca formulation
+ (formulation = 1, 2 or 3)
+
+See :ref:`forces`.
+
+
"""
from hysop.operator.computational import Computational
from hysop.operator.continuous import opsetup
from abc import ABCMeta, abstractmethod
from hysop.domain.control_box import ControlBox
+import numpy as np
class Forces(Computational):
@@ -91,8 +99,6 @@ class MomentumForces(Forces):
"""
- __metaclass__ = ABCMeta
-
def __init__(self, velocity, penalisation_coeff, **kwds):
"""
Parameters
@@ -141,8 +147,6 @@ class NocaForces(Forces):
(See Noca99 or Plouhmans, 2002, Journal of Computational Physics)
"""
- __metaclass__ = ABCMeta
-
def __init__(self, velocity, vorticity, nu, formulation=1,
volume_of_control=None, surfdir=None, **kwds):
"""
diff --git a/HySoP/hysop/operator/hdf_io.py b/HySoP/hysop/operator/hdf_io.py
old mode 100644
new mode 100755
index e6eb02f95..e0771b289
--- a/HySoP/hysop/operator/hdf_io.py
+++ b/HySoP/hysop/operator/hdf_io.py
@@ -1,14 +1,17 @@
-"""
-@file printer.py
+"""I/O operators
+
+.. currentmodule:: hysop.operator.hdf_io
+
+* :class:`~HDF_Writer` : operator to write fields into an hdf file
+* :class:`~HDF_Reader` : operator to read fields from an hdf file
+* :class:`~HDF_IO` abstract interface for hdf io classes
-File output for field(s) value on a grid.
"""
-from hysop.constants import S_DIR, debug, HDF5, HYSOP_REAL
+from hysop.constants import S_DIR, debug, HYSOP_REAL
from hysop.operator.computational import Computational
from hysop.operator.continuous import opapply, opsetup
import hysop.tools.numpywrappers as npw
-import hysop.tools.io_utils as io
-from hysop.tools.parameters import IOParams
+from hysop.tools.io_utils import IO, IOParams, XMF
from abc import ABCMeta, abstractmethod
try:
@@ -23,33 +26,37 @@ from hysop.tools.profiler import profile
class HDF_IO(Computational):
- """
- Abstract interface for read/write from/to hdf files, for
+ """Abstract interface to read/write from/to hdf files, for
hysop fields.
"""
__metaclass__ = ABCMeta
def __init__(self, var_names=None, subset=None, **kwds):
- """
- Read/write some fields data from/into hdf/xmdf files.
+ """Read/write some fields data from/into hdf/xmdf files.
Parallel io.
- @param var_names : a dictionnary of names to connect fields
- to the dataset in the hdf file. See example below.
- @param subset : a subset of the domain, on which data are read.
- It must be a hysop.domain.subset.
- Names paramater example:
- if variables=[velo, vorti], and if hdf file contains
+
+ Parameters
+ ----------
+ var_names : a dictionnary, optional
+ keys = :class:`~hysop.fields.continuous.Field`,
+ values = string, field name. See notes below.
+ subset : :class:`~hysop.domain.subset.Subset`, optional
+ a subset of the domain, on which data are read or written,
+ default=the whole domain.
+
+ Notes
+ -----
+ Dataset in hdf files are identified with names. In hysop, when
+ writing a file, default dataset name is
+ 'continuous_field.name + topo.id + component direction', but
+ this might be changed thanks to var_names argument.
+ For example, if variables=[velo, vorti], and if hdf file contains
'vel_1_X, vel_1_Y, vel_1_Z, dat_2_X, dat_2_Y, dat_2_Z' keys, then
use :
- names = {velo: 'vel', vorti:'dat'} if you want to read vel/dat
+ var_names = {velo: 'vel', vorti:'dat'} if you want to read vel/dat
into velo/vorti.
- Mind that when writing an hdf file, dataset names are set as :
- field.name + topo.id + component direction.
-
- If names=None, field names will be used as keys to search for
- dataset.
"""
super(HDF_IO, self).__init__(**kwds)
@@ -65,29 +72,31 @@ class HDF_IO(Computational):
# If no filename is given, set it to
# the concatenation of variables'names.
if self.io_params is None:
+ # if name is not set, name = concatenation of fields names,
+ # like v1_v2.
+ # WARNING FP: we must sort names (alph. order), else
+ # it seems the order may change from one mpi process
+ # to another.
name = ''
+ names = []
for var in self.input:
- if var.name == 'unnamed':
- msg = 'Warning : you try to write an unnamed variable'
- msg += ' into hdf file. This may result in'
- msg += 'unexpected side effects.'
- print msg
- name += var.name
-
- name += '_'
- self.io_params = IOParams(name, fileformat=HDF5)
+ names.append(var.name)
+ names.sort()
+ for nn in names:
+ name += nn + '_'
+ name = name[:-1]
+ self.io_params = IOParams(name, fileformat=IO.HDF5)
else:
- assert self.io_params.fileformat is HDF5
-
- ## Set a subset of the original domain
+ assert self.io_params.fileformat is IO.HDF5
+ # Set a subset of the original domain
self.subset = subset
- ## Dictionnary of names to search in hdf file. May be None.
- ## It will be checked during setup.
+ # Dictionnary of names to search in hdf file. May be None.
+ # It will be checked during setup.
self.var_names = var_names
# Local topology, that MUST be common to all variables.
- self._topology = None
+ self.topology = None
self._slices = None
self._global_resolution = None
self._sl = None
@@ -103,14 +112,14 @@ class HDF_IO(Computational):
def discretize(self):
super(HDF_IO, self)._standard_discretize()
assert self._single_topo, 'Multi-resolution case is not allowed.'
- self._topology = self.variables.values()[0]
+ self.topology = self.variables.values()[0]
# Discretize the subset, if required
if self.subset is not None:
- self.subset.discretize(self._topology)
- refmesh = self.subset.mesh[self._topology]
+ self.subset.discretize(self.topology)
+ refmesh = self.subset.mesh[self.topology]
else:
- refmesh = self._topology.mesh
+ refmesh = self.topology.mesh
# Global resolution for hdf5 output (warning : this must
# be the whole domain resolution, not the subset resolution)
self._global_resolution = list(refmesh.global_resolution())
@@ -136,19 +145,19 @@ class HDF_IO(Computational):
else:
for var in self.var_names:
# Discrete field associated to var
- var_d = var.discretize(self._topology)
+ var_d = var.discretize(self.topology)
for d in xrange(var_d.nb_components):
name = self.var_names[var] + S_DIR[d]
self.dataset[name] = var_d.data[d]
def open_hdf(self, count, mode):
filename = self._get_filename(count)
- if self._topology.size == 1:
+ if self.topology.size == 1:
self._hdf_file = h5py.File(filename, mode)
compression = 'gzip'
else:
self._hdf_file = h5py.File(filename, mode, driver='mpio',
- comm=self._topology.comm)
+ comm=self.topology.comm)
compression = None
return compression
@@ -169,31 +178,41 @@ class HDF_Writer(HDF_IO):
"""
Write some fields data into hdf/xmdf files.
Parallel writings.
- @param xmfalways : true if xmf output must be done every time
- an hdf5 file is created
+
+ Parameters
+ ----------
+ xmfalways : boolean, optional
+ true if xmf output must be done every time
+ an hdf5 file is created (i.e. at each time step),
+ default=True
+ kwds : base class arguments
"""
super(HDF_Writer, self).__init__(**kwds)
# count the number of calls
self._count = 0
- self.step = self._step_HDF5
if xmfalways:
self.step = self._step_HDF5_XMF
self.finalize = lambda: 1
else:
+ self.step = self._step_HDF5
self.finalize = self.createXMFFile
self._xdmf_data_files = []
-
# filename = prefix_N, N = counter value
- self._get_filename = lambda i: self.io_params.filename + \
- "_{0:05d}".format(i) + '.h5'
+ self._get_filename = self._input_fname
# In xdmf file, it is not possible to have two times
# the same time value. So we save the last value of
# time where xdmf has been written, to raise an exception
# if that happens.
self._last_written_time = None
+ def _input_fname(self, i):
+ """Set output file name for current iteration"""
+ msg = 'count < 0, simu must be initialized.'
+ assert i >= 0, msg
+ return self.io_params.filename + "_{0:05d}".format(i) + '.h5'
+
@debug
@profile
@opapply
@@ -206,8 +225,7 @@ class HDF_Writer(HDF_IO):
self._count += 1
def createXMFFile(self):
- """
- Create and fill the xdmf file
+ """Create and fill the xdmf file
"""
if self._mpis.rank == self.io_params.io_leader:
@@ -220,8 +238,8 @@ class HDF_Writer(HDF_IO):
f.write("CollectionType=\"Temporal\">\n")
ds_names = self.dataset.keys()
for i, t in self._xdmf_data_files:
- f.write(io.XMF.write_grid_attributes(
- self._topology, ds_names, i, t, self._get_filename(i),
+ f.write(XMF.write_grid_attributes(
+ self.topology, ds_names, i, t, self._get_filename(i),
self.subset))
f.write(" </Grid>\n")
f.write(" </Domain>\n")
@@ -232,17 +250,17 @@ class HDF_Writer(HDF_IO):
# self.createXMFFile()
def _step_HDF5(self, simu):
- """
- Write a h5 file with data on each mpi process.
+ """Write an h5 file with data on each mpi process.
"""
# Remarks:
- # - force np.float64, ParaView seems to not be able to read float32
+ # - force np.float64, ParaView seems unable to read float32
# - writing compressed hdf5 files (gzip compression seems the best)
# - gzip compression does not work in parallel.
# Get 'current' filename. It depends on the number
# of the current output (count) and on the current process
# rank.
+ self._count = simu.currentIteration
compression = self.open_hdf(self._count, mode='w')
# Get the names of output variables and create the corresponding
# datasets
@@ -275,11 +293,19 @@ class HDF_Reader(HDF_IO):
Parallel reading of hdf/xdmf files to fill some fields in.
"""
def __init__(self, restart=None, **kwds):
- """
- Read some fields data into hdf/xmdf files.
+ """Read some fields data from hdf/xmdf files.
Parallel readings.
- @param restart : set this to read a file corresponding to
- a specific iteration.
+
+ Parameters
+ ----------
+ restart : int, optional
+ number of a specific iteration to be read, default=None,
+ i.e. read first iteration.
+ kwds : base class arguments
+
+ Notes: restart corresponds to the number which appears in
+ the hdf file name, corresponding to the number of the
+ iteration where writing occured.
See examples in tests_hdf_io.py
"""
super(HDF_Reader, self).__init__(**kwds)
@@ -315,10 +341,10 @@ class HDF_Reader(HDF_IO):
# Do we need a CPU->GPU transfer here?
def dataset_names(self):
- """
- Return the list of available names for datasets in
+ """Return the list of available names for datasets in
the required file.
"""
+ assert self._is_discretized, 'a call to discretize() is required.'
if self._hdf_file is None:
self.open_hdf(count=self.restart, mode='r')
return self._hdf_file.keys()
diff --git a/HySoP/hysop/operator/tests/test_analytic.py b/HySoP/hysop/operator/tests/test_analytic.py
index 3e2878ff9..b9d8a032c 100755
--- a/HySoP/hysop/operator/tests/test_analytic.py
+++ b/HySoP/hysop/operator/tests/test_analytic.py
@@ -1,6 +1,4 @@
-"""
-@file hysop.operator.tests.test_analytic
-Test initialization of fields with analytic formula
+"""Test initialization of fields with analytic formula
"""
from numpy import allclose
from hysop.domain.box import Box
@@ -21,8 +19,8 @@ simu = Simulation(tinit=0., tend=0.1, nbIter=1)
# Non-Vectorized and vectorized formulas for a scalar
def test_analytical_op_1():
box = Box()
- caf = Field(box, formula=func_scal_1)
- caf2 = Field(box, formula=func_scal_2, vectorize_formula=True)
+ caf = Field(box, formula=func_scal_1, name='caf')
+ caf2 = Field(box, name='caf2', formula=func_scal_2, vectorize_formula=True)
op = Analytic(variables={caf: d3D})
op2 = Analytic(variables={caf2: d3D})
op.discretize()
@@ -31,7 +29,7 @@ def test_analytical_op_1():
op2.setup()
topo = op.discreteFields[caf].topology
coords = topo.mesh.coords
- ref = Field(box)
+ ref = Field(box, name='ref')
refd = ref.discretize(topo)
cafd = caf.discreteFields[topo]
cafd2 = caf2.discreteFields[topo]
@@ -49,8 +47,9 @@ def test_analytical_op_1():
# Non-Vectorized and vectorized formulas for a vector
def test_analytical_op_3():
box = Box()
- caf = Field(box, formula=func_vec_1, is_vector=True)
- caf2 = Field(box, formula=func_vec_2, vectorize_formula=True, is_vector=True)
+ caf = Field(box, name='caf', formula=func_vec_1, is_vector=True)
+ caf2 = Field(box, name='caf', formula=func_vec_2,
+ vectorize_formula=True, is_vector=True)
op = Analytic(variables={caf: d3D})
op2 = Analytic(variables={caf2: d3D})
op.discretize()
@@ -59,7 +58,7 @@ def test_analytical_op_3():
op2.setup()
topo = op.discreteFields[caf].topology
coords = topo.mesh.coords
- ref = Field(box, is_vector=True)
+ ref = Field(box, is_vector=True, name='ref')
refd = ref.discretize(topo)
cafd = caf.discreteFields[topo]
cafd2 = caf2.discreteFields[topo]
@@ -81,8 +80,9 @@ def test_analytical_op_3():
# Non-Vectorized and vectorized formulas for a vector with extra-args
def test_analytical_op_4():
box = Box()
- caf = Field(box, formula=func_vec_3, is_vector=True)
- caf2 = Field(box, formula=func_vec_4, vectorize_formula=True, is_vector=True)
+ caf = Field(box, formula=func_vec_3, is_vector=True, name='caf')
+ caf2 = Field(box, formula=func_vec_4, vectorize_formula=True,
+ name='caf2', is_vector=True)
op = Analytic(variables={caf: d3D})
op2 = Analytic(variables={caf2: d3D})
op.discretize()
@@ -91,7 +91,7 @@ def test_analytical_op_4():
op2.setup()
topo = op.discreteFields[caf].topology
coords = topo.mesh.coords
- ref = Field(box, is_vector=True)
+ ref = Field(box, name='ref', is_vector=True)
refd = ref.discretize(topo)
cafd = caf.discreteFields[topo]
cafd2 = caf2.discreteFields[topo]
@@ -116,13 +116,13 @@ def test_analytical_op_4():
# Non-Vectorized formula for a nbc components field with extra-args
def test_analytical_op_5():
box = Box()
- caf = Field(box, formula=func_vec_5, nb_components=nbc)
+ caf = Field(box, formula=func_vec_5, nb_components=nbc, name='caf')
op = Analytic(variables={caf: d3D})
op.discretize()
op.setup()
topo = op.discreteFields[caf].topology
coords = topo.mesh.coords
- ref = Field(box, nb_components=nbc)
+ ref = Field(box, nb_components=nbc, name='ref')
refd = ref.discretize(topo)
cafd = caf.discreteFields[topo]
ids = [0, ] * nbc
@@ -140,13 +140,13 @@ def test_analytical_op_5():
# Non-Vectorized formula for a nbc components field in 2D, with extra-args
def test_analytical_op_6():
box = Box(dimension=2, length=L2D, origin=origin2D)
- caf = Field(box, formula=func_vec_6, nb_components=nbc)
+ caf = Field(box, formula=func_vec_6, nb_components=nbc, name='caf')
op = Analytic(variables={caf: d2D})
op.discretize()
op.setup()
topo = op.discreteFields[caf].topology
coords = topo.mesh.coords
- ref = Field(box, nb_components=nbc)
+ ref = Field(box, nb_components=nbc, name='ref')
refd = ref.discretize(topo)
cafd = caf.discreteFields[topo]
ids = [0, ] * nbc
diff --git a/HySoP/hysop/operator/tests/test_drag_and_lift.py b/HySoP/hysop/operator/tests/test_drag_and_lift.py
index ddda768fc..06fd9fef8 100755
--- a/HySoP/hysop/operator/tests/test_drag_and_lift.py
+++ b/HySoP/hysop/operator/tests/test_drag_and_lift.py
@@ -2,7 +2,8 @@
from hysop.domain.subsets import Sphere
from hysop.operator.penalization import PenalizeVorticity
from hysop.problem.simulation import Simulation
-from hysop.tools.parameters import Discretization, IOParams
+from hysop.tools.parameters import Discretization
+from hysop.tools.io_utils import IOParams, IO
from hysop.mpi.topology import Cartesian
import numpy as np
import os
@@ -54,9 +55,9 @@ def s3d(res, x, y, z, t):
return res
-Nx = 128
-Ny = 134
-Nz = 128
+Nx = 32
+Ny = 106
+Nz = 64
g = 2
@@ -157,20 +158,24 @@ def test_all_drags():
dg = {}
dg['mom'] = MomentumForces(velocity=velo, discretization=topo,
obstacles=obst, penalisation_coeff=[1e8],
- io_params=IOParams('Heloise'))
+ io_params=IOParams('Heloise',
+ fileformat=IO.ASCII))
sdir = [2]
dg['noca_1'] = NocaForces(velocity=velo, vorticity=vorti,
discretization=topo, surfdir=sdir,
nu=0.3, obstacles=obst, formulation=1,
- io_params=IOParams('Noca1'))
+ io_params=IOParams('Noca1',
+ fileformat=IO.ASCII))
dg['noca_2'] = NocaForces(velocity=velo, vorticity=vorti,
discretization=topo, surfdir=sdir,
nu=0.3, obstacles=obst, formulation=2,
- io_params=IOParams('Noca2'))
+ io_params=IOParams('Noca2',
+ fileformat=IO.ASCII))
dg['noca_3'] = NocaForces(velocity=velo, vorticity=vorti,
discretization=topo, surfdir=sdir,
nu=0.3, obstacles=obst, formulation=3,
- io_params=IOParams('Noca3'))
+ io_params=IOParams('Noca3',
+ fileformat=IO.ASCII))
for drag in dg.values():
drag.discretize()
drag.setup()
diff --git a/HySoP/hysop/operator/tests/test_hdf5_io.py b/HySoP/hysop/operator/tests/test_hdf5_io.py
index 0dee976d0..368836fd2 100755
--- a/HySoP/hysop/operator/tests/test_hdf5_io.py
+++ b/HySoP/hysop/operator/tests/test_hdf5_io.py
@@ -1,19 +1,17 @@
# -*- coding: utf-8 -*-
-"""
-Tests for reader/writer of fields in hdf5 format.
+"""Tests for reader/writer of fields in hdf5 format.
"""
from hysop import Box, Field
import numpy as np
import os
-from hysop.constants import HDF5
from hysop.problem.simulation import Simulation
-import shutil
-from hysop.tools.parameters import Discretization, IOParams
+from hysop.tools.parameters import Discretization
from hysop.operator.hdf_io import HDF_Writer, HDF_Reader
-from hysop.tools.io_utils import IO
+from hysop.tools.io_utils import IO, IOParams
from hysop.mpi import main_rank, main_size
from hysop.domain.subsets import SubBox
+from hysop.testsenv import postclean
Lx = 2.
nb = 65
@@ -63,27 +61,23 @@ def vort3D(res, x, y, z, t):
return res
-def purgeFiles():
- if main_rank == 0:
- shutil.rmtree(working_dir)
-
-
+@postclean(working_dir)
def test_write_read_scalar_3D():
dom, topo = init1(3)
scal3D = Field(domain=dom, name='Scal3D')
scalRef = Field(domain=dom, formula=func3D, name='ScalRef3D')
filename = working_dir + '/testIO_scal'
- iop = IOParams(filename, fileformat=HDF5)
+ iop = IOParams(filename, fileformat=IO.HDF5)
op = HDF_Writer(variables={scalRef: topo}, io_params=iop)
simu = Simulation(nbIter=10)
op.discretize()
op.setup()
+ simu.initialize()
scalRef.initialize(simu.time, topo=topo)
op.apply(simu)
- simu.initialize()
simu.advance()
simu.advance()
# Print scalRef for other iterations
@@ -92,11 +86,11 @@ def test_write_read_scalar_3D():
fullpath = iop.filename
assert os.path.exists(fullpath + '.xmf')
assert os.path.exists(fullpath + '_00000.h5')
- assert os.path.exists(fullpath + '_00001.h5')
+ assert os.path.exists(fullpath + '_00002.h5')
# Reader
- iop_read = IOParams(working_dir + '/testIO_scal_00001.h5',
- fileformat=HDF5)
+ iop_read = IOParams(working_dir + '/testIO_scal_00002.h5',
+ fileformat=IO.HDF5)
reader = HDF_Reader(variables=[scal3D], discretization=topo,
io_params=iop_read,
var_names={scal3D: 'ScalRef3D_' + str(topo.get_id())})
@@ -115,6 +109,7 @@ def test_write_read_scalar_3D():
assert np.allclose(scref.data[d][ind], sc3d.data[d][ind])
+@postclean(working_dir)
def test_write_read_scalar_3D_defaults():
dom, topo = init1(3)
scal3D = Field(domain=dom, name='Scal3D')
@@ -137,9 +132,9 @@ def test_write_read_scalar_3D_defaults():
filename = scalRef.name
fullpath = os.path.join(IO.default_path(), filename)
- assert os.path.exists(fullpath + '_.xmf')
- assert os.path.exists(fullpath + '__00000.h5')
- assert os.path.exists(fullpath + '__00001.h5')
+ assert os.path.exists(fullpath + '.xmf')
+ assert os.path.exists(fullpath + '_00000.h5')
+ assert os.path.exists(fullpath + '_00001.h5')
sc3d = scal3D.discretize(topo)
scref = scalRef.discretize(topo)
@@ -163,7 +158,7 @@ def test_write_read_scalar_3D_defaults():
for d in xrange(scal3D.nb_components):
assert np.allclose(scref.data[d][ind], sc3d.data[d][ind])
-
+@postclean(working_dir)
def test_write_read_vectors_3D_defaults():
dom, topo = init2()
velo = Field(domain=dom, formula=vec3D, name='velo', is_vector=True)
@@ -184,9 +179,13 @@ def test_write_read_vectors_3D_defaults():
op.finalize()
filename = ''
- for v in op.input:
- filename += v.name
- filename += '_'
+ names = []
+ for var in op.input:
+ names.append(var.name)
+ names.sort()
+ for nn in names:
+ filename += nn + '_'
+ filename = filename[:-1]
fullpath = os.path.join(IO.default_path(), filename)
assert os.path.exists(fullpath + '.xmf')
@@ -197,6 +196,8 @@ def test_write_read_vectors_3D_defaults():
w3d = vorti.discretize(topo)
ind = topo.mesh.iCompute
+ # Copy current values of v3 and w3 into buff1 and buff2, for comparison
+ # after reader.apply, below.
buff1 = Field(domain=dom, name='buff1', is_vector=True)
buff2 = Field(domain=dom, name='buff2', is_vector=True)
b1 = buff1.discretize(topo=topo)
@@ -204,13 +205,16 @@ def test_write_read_vectors_3D_defaults():
for d in xrange(velo.nb_components):
b1.data[d][...] = v3d.data[d][...]
b2.data[d][...] = w3d.data[d][...]
-
+ # reset v3 and w3 to zero.
v3d.data[d][...] = 0.0
w3d.data[d][...] = 0.0
- # Read vector fields, using default configuration for output
+ # Read vector fields, using default configuration for input
# names and location, with a given iteration number.
+ # If everything works fine, reader must read output from
+ # the writer above.
reader = HDF_Reader(variables={velo: topo, vorti: topo},
+ io_params=IOParams(filename),
restart=simu.currentIteration - 1)
reader.discretize()
reader.setup()
@@ -220,11 +224,13 @@ def test_write_read_vectors_3D_defaults():
reader.apply()
reader.finalize()
+ # Now, v3 and w3 (just read) must be equal to saved values in b1 and b2.
for d in xrange(v3d.nb_components):
assert np.allclose(b1.data[d][ind], v3d.data[d][ind])
assert np.allclose(b2.data[d][ind], w3d.data[d][ind])
+@postclean(working_dir)
def test_write_read_vectors_3D():
dom, topo = init2()
velo = Field(domain=dom, formula=vec3D, name='velo', is_vector=True)
@@ -233,7 +239,7 @@ def test_write_read_vectors_3D():
# Write a vector field, using default for output location
# but with fixed names for datasets
filename = working_dir + '/testIO_vec'
- iop = IOParams(filename, fileformat=HDF5)
+ iop = IOParams(filename, fileformat=IO.HDF5)
op = HDF_Writer(variables={velo: topo, vorti: topo},
var_names={velo: 'io_1', vorti: 'io_2'}, io_params=iop)
simu = Simulation(nbIter=3)
@@ -267,7 +273,7 @@ def test_write_read_vectors_3D():
# Read vector fields, fixed filename, fixed dataset names.
iop_read = IOParams(working_dir + '/testIO_vec_00001.h5',
- fileformat=HDF5)
+ fileformat=IO.HDF5)
reader = HDF_Reader(variables={buff1: topo, buff2: topo},
io_params=iop_read,
var_names={buff1: 'io_2', buff2: 'io_1'})
@@ -282,6 +288,7 @@ def test_write_read_vectors_3D():
assert np.allclose(b1.data[d][ind], w3d.data[d][ind])
+@postclean(working_dir)
def test_write_read_subset_1():
dom, topo = init2()
velo = Field(domain=dom, formula=vec3D, name='velo', is_vector=True)
@@ -308,6 +315,7 @@ def test_write_read_subset_1():
for v in op.input:
filename += v.name
filename += '_'
+ filename = filename[:-1]
fullpath = os.path.join(IO.default_path(), filename)
assert os.path.exists(fullpath + '.xmf')
@@ -321,7 +329,7 @@ def test_write_read_subset_1():
buff1 = Field(domain=dom, name='buff1', is_vector=True)
# Read vector fields, fixed filename, fixed dataset names.
- iop = IOParams(filename + '_00000.h5', fileformat=HDF5)
+ iop = IOParams(filename + '_00000.h5', fileformat=IO.HDF5)
reader = HDF_Reader(variables={buff1: topo},
io_params=iop,
var_names={buff1: 'io_1'}, subset=mybox)
@@ -335,6 +343,7 @@ def test_write_read_subset_1():
assert np.allclose(b1.data[d][indsubset], v3d.data[d][indsubset])
+@postclean(working_dir)
def test_write_read_subset_2():
dom, topo = init2()
velo = Field(domain=dom, formula=vec3D, name='velo', is_vector=True)
@@ -361,6 +370,7 @@ def test_write_read_subset_2():
for v in op.input:
filename += v.name
filename += '_'
+ filename = filename[:-1]
fullpath = os.path.join(IO.default_path(), filename)
assert os.path.exists(fullpath + '.xmf')
@@ -374,7 +384,7 @@ def test_write_read_subset_2():
buff1 = Field(domain=dom, name='buff1', is_vector=True)
# Read vector fields, fixed filename, fixed dataset names.
- iop = IOParams(filename + '_00000.h5', fileformat=HDF5)
+ iop = IOParams(filename + '_00000.h5', fileformat=IO.HDF5)
reader = HDF_Reader(variables={buff1: topo},
io_params=iop,
var_names={buff1: 'io_1'}, subset=mybox)
diff --git a/HySoP/hysop/operator/tests/test_multiphase_gradp.py b/HySoP/hysop/operator/tests/test_multiphase_gradp.py
index 43aac523e..477c9e48c 100755
--- a/HySoP/hysop/operator/tests/test_multiphase_gradp.py
+++ b/HySoP/hysop/operator/tests/test_multiphase_gradp.py
@@ -50,9 +50,9 @@ def test_gradp():
"""Testing gradp operator against analytical result"""
simu = Simulation(tinit=0.0, tend=1.0, timeStep=0.1, iterMax=1)
box = Box()
- velo = Field(box, is_vector=True, formula=velo_func)
- res = Field(box, is_vector=True)
- true_res = Field(box, is_vector=True, formula=res_func)
+ velo = Field(box, is_vector=True, formula=velo_func, name='v0')
+ res = Field(box, is_vector=True, name='res')
+ true_res = Field(box, is_vector=True, formula=res_func, name='vres')
d = Discretization([129,129,129])
op = MultiphaseGradP(velocity=velo, gradp=res, viscosity=VISCOSITY,
discretization=d)
diff --git a/HySoP/hysop/operator/tests/test_multiresolution_filter.py b/HySoP/hysop/operator/tests/test_multiresolution_filter.py
index 6d66f2513..91febfd77 100755
--- a/HySoP/hysop/operator/tests/test_multiresolution_filter.py
+++ b/HySoP/hysop/operator/tests/test_multiresolution_filter.py
@@ -37,7 +37,7 @@ def func_periodic_XY(res, x, y, z, t=0):
def filter(d_fine, d_coarse, func, method, atol=1e-8, rtol=1e-5):
box = Box(length=L, origin=O)
- f = Field(box, formula=func)
+ f = Field(box, formula=func, name='f0')
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
variables={f: d_coarse},
method=method)
@@ -169,7 +169,7 @@ def func(res, x, y, z, t=0):
def test_filter_linear():
"""This test compares the GPU linear filter with python implementation"""
box = Box(length=L, origin=O)
- f = Field(box, formula=func)
+ f = Field(box, formula=func, name='f0')
d_fine = Discretization([513, 513, 513])
d_coarse = Discretization([257, 257, 257], ghosts=[1, 1, 1])
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
@@ -195,7 +195,7 @@ def test_filter_linear():
def test_filter_l2_1():
"""This test compares the GPU linear filter with python implementation"""
box = Box(length=L, origin=O)
- f = Field(box, formula=func)
+ f = Field(box, formula=func, name='f0')
d_fine = Discretization([513, 513, 513])
d_coarse = Discretization([257, 257, 257], ghosts=[2, 2, 2])
op = MultiresolutionFilter(d_in=d_fine, d_out=d_coarse,
diff --git a/HySoP/hysop/operator/tests/test_particle_advection.py b/HySoP/hysop/operator/tests/test_particle_advection.py
index 7ca871bea..ad6fc2ef0 100755
--- a/HySoP/hysop/operator/tests/test_particle_advection.py
+++ b/HySoP/hysop/operator/tests/test_particle_advection.py
@@ -1,6 +1,4 @@
-"""
-@file hysop.operator.tests.test_particle_advection
-Testing pure python particle advection with null velocity.
+"""Testing pure python particle advection with null velocity.
"""
from hysop.domain.box import Box
from hysop.fields.continuous import Field
@@ -11,7 +9,6 @@ import hysop.tools.numpywrappers as npw
import numpy as np
-
d2d = Discretization([17, 17])
d3d = Discretization([17, 17, 17])
@@ -42,7 +39,9 @@ def setup_list_2D():
return [scal1, scal2], velo
-def setup_3D():
+def setup_3d():
+ """Build fields inside a 3d domain
+ """
box = Box(length=[2., 4., 1.], origin=[-1., -2., 0.])
scal = Field(domain=box, name='Scalar')
velo = Field(domain=box, name='Velocity',
@@ -150,7 +149,7 @@ def assertion_list(scal, advec):
def test_nullVelocity_2D():
- """
+ """2D case, advection with null velocity, single resolution.
"""
scal, velo = setup_2D()
@@ -180,7 +179,7 @@ def test_nullVelocity_list_2D():
def test_nullVelocity_3D():
"""
"""
- scal, velo = setup_3D()
+ scal, velo = setup_3d()
advec = Advection(velo, scal, discretization=d3d)
assert assertion(scal, advec)
diff --git a/HySoP/hysop/operator/tests/test_penalization.py b/HySoP/hysop/operator/tests/test_penalization.py
index d26e3b36b..9026e986b 100755
--- a/HySoP/hysop/operator/tests/test_penalization.py
+++ b/HySoP/hysop/operator/tests/test_penalization.py
@@ -3,7 +3,8 @@ from hysop.domain.subsets import HemiSphere, Sphere, Cylinder
from hysop.domain.porous import Porous
from hysop.operator.penalization import Penalization, PenalizeVorticity
from hysop.problem.simulation import Simulation
-from hysop.tools.parameters import Discretization, IOParams
+from hysop.tools.parameters import Discretization
+from hysop.tools.io_utils import IOParams
from hysop.mpi.topology import Cartesian
import hysop.tools.numpywrappers as npw
import numpy as np
diff --git a/HySoP/hysop/operator/tests/test_spectrum.py b/HySoP/hysop/operator/tests/test_spectrum.py
old mode 100644
new mode 100755
index 9de2e6ce7..4acc7264c
--- a/HySoP/hysop/operator/tests/test_spectrum.py
+++ b/HySoP/hysop/operator/tests/test_spectrum.py
@@ -1,10 +1,11 @@
from hysop.domain.box import Box
-from hysop.constants import np, HDF5
from hysop.fields.continuous import Field
from hysop.operator.spectrum import Spectrum
-from hysop.tools.parameters import Discretization, IOParams
+from hysop.tools.parameters import Discretization
from hysop.problem.simulation import Simulation
from hysop.operator.hdf_io import HDF_Writer
+import numpy as np
+from hysop.tools.io_utils import IO
pi = np.pi
sin = np.sin
cos = np.cos
diff --git a/HySoP/hysop/problem/tests/test_simulation.py b/HySoP/hysop/problem/tests/test_simulation.py
old mode 100644
new mode 100755
index 65f7ce6c2..8a7ae1264
--- a/HySoP/hysop/problem/tests/test_simulation.py
+++ b/HySoP/hysop/problem/tests/test_simulation.py
@@ -3,14 +3,14 @@
tests simulation incr and io_utils writer
"""
from hysop.problem.simulation import Simulation
-from hysop.tools.parameters import IOParams
-from hysop.tools.io_utils import Writer
+from hysop.tools.io_utils import Writer, IOParams, IO
simu = Simulation(tinit=0.0, tend=1.0, nbIter=10)
def test_simu_incr():
- io_params = IOParams(filename='temp_test', frequency=2)
+ io_params = IOParams(filename='temp_test', frequency=2,
+ fileformat=IO.ASCII)
wr = Writer(io_params)
assert wr.do_write(simu.currentIteration)
@@ -33,7 +33,8 @@ def test_simu_incr():
def test_simu_incr2():
- io_params = IOParams(filename='temp_test', frequency=3)
+ io_params = IOParams(filename='temp_test', frequency=3,
+ fileformat=IO.ASCII)
wr = Writer(io_params)
assert wr.do_write(simu.currentIteration)
simu.timeStep = 0.10000000001
diff --git a/HySoP/hysop/tools/io_utils.py b/HySoP/hysop/tools/io_utils.py
old mode 100644
new mode 100755
index 45dc5a4da..f06ce3cd5
--- a/HySoP/hysop/tools/io_utils.py
+++ b/HySoP/hysop/tools/io_utils.py
@@ -1,21 +1,39 @@
"""Tools related to i/o in HySoP.
+
+.. currentmodule hysop.tools.io_utils
+
+* :class:`~IO`
+* :class:`~IOParams`
+* :class:`~Writer`
+* :class:`~XMF`, tools to prepare/write xmf files.
+
"""
import os
import scitools.filetable as ft
import hysop.tools.numpywrappers as npw
from inspect import getouterframes, currentframe
import hysop.mpi as mpi
-from re import findall, IGNORECASE
-from hysop.tools.parameters import MPIParams, IOParams
+from re import findall
+from hysop.tools.parameters import MPIParams
+from collections import namedtuple
+from hysop.constants import S_DIR
+import h5py
class IO(object):
"""
- Static class with utilities for file i/o
+ Static class with utilities to set/find the place where i/o files
+ will be read/written.
"""
_default_path = None
+ HDF5 = 998
+ """HDF5 format id"""
+
+ ASCII = 997
+ """ascii format id"""
+
@staticmethod
def default_path():
"""Get the current default path used for io.
@@ -24,7 +42,7 @@ class IO(object):
-------
string
the default value of the current i/o path. If not set,
- the basename of the top exec. file is used.
+ the basename of the top exec file is used.
Examples
--------
@@ -33,46 +51,72 @@ class IO(object):
results will be saved in ./MyExe/p4.
The number after 'p' will be the number of mpi processus
set for the simulation.
-
-
"""
# Memo for getouterframe usage:
# frame, filename, line_number, function_name, lines, index =\
# inspect.getouterframes(inspect.currentframe())[-1]
# Warning FP : the behavior of python and ipython is different for
- # this command.
+ # this command. Moreover, output differs when called from interactive
+ # session.
+
if IO._default_path is not None:
+ # which must be the case for any interactive session
+ # due to call of set_default_path in hysop.__init__.py.
return IO._default_path
a = getouterframes(currentframe())
- ind = -1
+ #ind = -1
interactive_path = './interactive/p' + str(mpi.main_size)
interactive_path = os.path.abspath(interactive_path)
# --- ipython ---
- from hysop.tools.sys_utils import SysUtils
- if SysUtils.in_ipython():
- sublist = [i[1] for i in a]
- for val in sublist:
- ll = findall('ipython', val, IGNORECASE)
- if len(ll) > 0:
- ind = sublist.index(val) - 1
- break
- if ind > -1:
- # -- interactive ipython but call with execfile--
- if len(findall('io_utils', a[ind][1])) > 0:
- return interactive_path
- a = a[ind]
- else:
- # -- interactive ipython without execfile call --
- return interactive_path
-
- else:
- # -- python --
- a = a[-1]
- if a[-1] is None or len(findall('py.test', a[1])) > 0:
- # interactive python
+ #from hysop.tools.sys_utils import SysUtils
+ # if SysUtils.in_ipython():
+ # # Note FP: because of set_default_path call
+ # # in __init__.py, this condition must never happen.
+ # # But we keep the code below, just in case ...
+
+ # # list of files (fullpath) which contain the callers
+ # sublist = [i[1] for i in a]
+ # # look for ipython in callers ...
+ # # If found, keep index of the file just before
+ # # first occurence of ipython, i.e. the name
+ # # of the 'main' file
+ # for val in sublist:
+ # ll = findall('ipython', val, IGNORECASE)
+ # if len(ll) > 0:
+ # ind = sublist.index(val) - 1
+ # break
+
+ # if ind > -1:
+ # # -- interactive ipython but call with execfile--
+ # if len(findall('io_utils', a[ind][1])) > 0:
+ # return interactive_path
+ # a = a[ind]
+ # else:
+ # # -- interactive ipython without execfile call --
+ # return interactive_path
+
+ # else:
+ # -- python --
+ # if test session, set default path to interactive_path
+ for fname in a:
+ cond1 = len(findall('py.test', fname[1])) > 0
+ cond2 = len(findall('pytest', fname[1])) > 0
+ if cond1 or cond2:
+ IO._default_path = interactive_path
return interactive_path
+ # else (not in tests)
+ # get name of the file which contains the last caller
+ # and check if not None
+ a = a[-1]
+ if a[-1] is None:
+ # interactive python
+ IO._default_path = interactive_path
+ return interactive_path
+ # Finally (if not interactive, not in tests ...)
+ # use root name of the file which contains
+ # the last caller
apath = os.path.abspath(os.path.dirname(a[1]))
sphinxbuild = findall('sphinx-build', a[1])
if len(sphinxbuild) > 0:
@@ -80,14 +124,14 @@ class IO(object):
else:
a = os.path.basename(a[1]).split('.')[-2]
if a.find('__init__') != -1:
+ IO._default_path = interactive_path
return interactive_path
a = os.path.join(apath, a)
return os.path.join(a, 'p' + str(mpi.main_size))
@staticmethod
def check_dir(filename, io_rank=0, comm=None):
- """
- Check if the directory of 'filename' exists and creates it if not.
+ """Check if the directory of 'filename' exists and creates it if not.
Parameters
-----------
@@ -97,8 +141,6 @@ class IO(object):
processus rank that does the check.
comm : mpi communicator
the mpi communicator that does the check.
-
-
"""
# Create output dir if required
if comm is None:
@@ -117,19 +159,103 @@ class IO(object):
pathdir : string
the new path
-
Notes
------
pN will be add to path name, N being the number of MPI process
used for the simulation.
-
"""
IO._default_path = pathdir
IO._default_path = os.path.join(IO._default_path,
'p' + str(mpi.main_size))
IO.check_dir(IO._default_path)
+ @staticmethod
+ def set_datasetname(field_name, topo, direction=None):
+ """Return the dataset name of a given continuous field,
+ saved for a given topology
+ """
+ val = field_name + '_' + str(topo.get_id())
+ if direction is not None:
+ val += S_DIR[direction]
+ return val
+
+ @staticmethod
+ def get_datasetnames(filename):
+ """Return the list of dataset names present
+ in hdf input file
+
+ Parameters
+ ----------
+ filename : string
+ hdf file
+
+ Returns
+ -------
+ a list of strings
+ """
+ hdf_file = h5py.File(filename, 'r')
+ keys = hdf_file.keys()
+ hdf_file.close()
+ return keys
+
+
+class IOParams(namedtuple("IOParams", ['filename', 'filepath',
+ 'frequency', 'fileformat',
+ 'io_leader'])):
+ """
+ A struct to handle I/O files parameters
+
+ Parameters
+ -----------
+ filename : string
+ name of the file (absolute or relative path)
+ filepath : string
+ location of the file
+ frequency : int
+ frequency of output or input (e.g. every N times steps)
+ fileformat : int
+ format of the file. See notes for available format. Default=HDF5.
+ io_leader : int
+ rank of the mpi process dealing with the io. Default is 0.
+
+ See examples in hysop.operator.hdf_io
+
+ Notes
+ -----
+ Format parameter must be one of the following :
+ - :class:`~IO.HDF5`
+ - :class:`~IO.ASCII`
+
+ """
+ def __new__(cls, filename, filepath=None, frequency=1,
+ fileformat=None, io_leader=0):
+
+ # Filename is absolute path, filepath arg is ignored.
+ if os.path.isabs(filename):
+ filepath = os.path.dirname(filename)
+
+ else:
+ if filepath is not None:
+ filename = os.path.join(filepath, filename)
+ filepath = os.path.abspath(os.path.dirname(filename))
+ else:
+ filepath = os.path.dirname(filename)
+ if filepath == '':
+ # Get default output path
+ filepath = IO.default_path()
+ filename = os.path.join(filepath, filename)
+ else:
+ filepath = os.path.abspath(filepath)
+ filename = os.path.join(filepath,
+ os.path.basename(filename))
+ if fileformat is None:
+ fileformat = IO.HDF5
+
+ IO.check_dir(filename)
+ return super(IOParams, cls).__new__(cls, filename, filepath,
+ frequency, fileformat, io_leader)
+
class Writer(object):
"""
@@ -138,8 +264,8 @@ class Writer(object):
Examples
--------
- >>> from hysop.tools.parameters import IOParams
- >>> params = IOParams(filename='r.dat')
+ >>> from hysop.tools.io_utils import IOParams, IO
+ >>> params = IOParams(filename='r.dat', fileformat=IO.ASCII)
>>> wr = Writer(params, buffshape=(1, 2))
>>> ite = 3 # current iteration number
>>> if wr.do_write(ite):
@@ -147,10 +273,7 @@ class Writer(object):
... wr.write()
>>> wr.finalize()
-
- result : buffer is written into r.dat.
-
-
+ result : buffer is written into r.dat
"""
def __init__(self, io_params, buffshape=None, mpi_params=None,
safe_io=True):
@@ -158,7 +281,7 @@ class Writer(object):
Parameters
----------
- io_params : hysop.tools.parameters.IOParams
+ io_params : hysop.tools.io_utils.IOParams
setup for file ouput (name, location ...)
buffshape : tuple
2D numpy.array.shape like tuple, shape of the output/input buffer.
@@ -169,30 +292,27 @@ class Writer(object):
False --> open at init and close during finalize.
Cost less but if simu crashes, data are lost.
-
"""
# Absolute path + name for i/o file
# Note that if filename contains absolute path
# filepath is ignored
msg = 'wrong type for io_params arg.'
assert isinstance(io_params, IOParams), msg
- self.filename = io_params.filename
- " I/O file name "
-
- # How often i/o must occur
- self._frequency = io_params.frequency
-
- # Rank of the mpi process that performs i/o (if any)
- self._io_rank = io_params.io_leader
+ assert io_params.fileformat == IO.ASCII
+ self.io_params = io_params
# A reference communicator, just to identify a
# process rank for io.
if mpi_params is None:
mpi_params = MPIParams()
+ else:
+ msg = 'wrong type for mpi_params arg.'
+ assert isinstance(mpi_params, MPIParams), msg
self._mpis = mpi_params
# check if output dir exists, create it if not.
- IO.check_dir(self.filename, self._io_rank, self._mpis.comm)
+ IO.check_dir(self.io_params.filename, self.io_params.io_leader,
+ self._mpis.comm)
# Shape of the output buffer (must be a 2D numpy array)
if buffshape is None:
@@ -204,7 +324,7 @@ class Writer(object):
# The buffer (numpy array) that will be printed to a file
self.buffer = npw.zeros(self._buffshape)
" buffer used to save printed data"
-
+
# Defines how often
# output file is written :
# True --> open/close file everytime
@@ -220,12 +340,11 @@ class Writer(object):
# Force synchro to be sure that all output dirs
# have been created.
self._mpis.comm.barrier()
- if self._mpis.rank == self._io_rank:
- self._file = open(self.filename, 'w')
+ if self._mpis.rank == self.io_params.io_leader:
+ self._file = open(self.io_params.filename, 'w')
def do_write(self, ite):
- """
- True if output is required
+ """Returns true if output is required
for iteration ite
Parameters
@@ -233,37 +352,41 @@ class Writer(object):
ite : int
current iteration number
-
"""
num = ite + 1 # Number of iterations done
- return self._mpis.rank == self._io_rank and (num % self._frequency) == 0
+ rk = self._mpis.rank
+ return rk == self.io_params.io_leader and \
+ (num % self.io_params.frequency) == 0
def _fullwrite(self):
- self._file = open(self.filename, 'a')
+ """open, write and close"""
+ self._file = open(self.io_params.filename, 'a')
ft.write(self._file, self.buffer)
self._file.close()
def _partialwrite(self):
+ """just write, no open, nor close"""
ft.write(self._file, self.buffer)
def finalize(self):
- if self._mpis.rank == self._io_rank:
+ """close, if required"""
+ if self._mpis.rank == self.io_params.io_leader:
if not self._file.closed:
self._file.close()
def __str__(self):
- if self._mpis.rank == self._io_rank:
+ if self._mpis.rank == self.io_params.io_leader:
s = ' === Writer === \n'
- s += ' - filename = ' + self.filename
+ s += ' - filename = ' + self.io_params.filename
s += '\n - buffshape = ' + str(self._buffshape)
- s += '\n - frequ = ' + str(self._frequency)
+ s += '\n - frequ = ' + str(self.io_params.frequency)
return s
class XMF(object):
+ """Static class - Tools to prepare and write xmf file
"""
- Static class used to define xmf tools.
- """
+
@staticmethod
def _list_format(l):
"""Format a list to the xml output.
@@ -273,7 +396,6 @@ class XMF(object):
----------
l : list to format
-
"""
buff = str(l).replace(',', ' ').replace('[', '')
return buff.replace(']', '').replace('(', '').replace(')', '')
diff --git a/HySoP/hysop/tools/parameters.py b/HySoP/hysop/tools/parameters.py
old mode 100644
new mode 100755
index 860c639c7..3977a3424
--- a/HySoP/hysop/tools/parameters.py
+++ b/HySoP/hysop/tools/parameters.py
@@ -2,11 +2,15 @@
.. currentmodule hysop.tools
+* :class:`~MPIParams`
+* :class:`~Discretization`
+
"""
from collections import namedtuple
from hysop.mpi.main_var import main_comm, main_rank, MPI
from hysop.constants import DEFAULT_TASK_ID
+import hysop.tools.numpywrappers as npw
class MPIParams(namedtuple('MPIParams', ['comm', 'task_id',
@@ -44,9 +48,6 @@ class MPIParams(namedtuple('MPIParams', ['comm', 'task_id',
rank, on_task)
-import hysop.tools.numpywrappers as npw
-
-
class Discretization(namedtuple("Discretization", ['resolution', 'ghosts'])):
"""
A struct to handle discretization parameters:
@@ -77,65 +78,3 @@ class Discretization(namedtuple("Discretization", ['resolution', 'ghosts'])):
if result is NotImplemented:
return result
return not result
-
-from hysop.constants import HDF5
-import os
-
-
-class IOParams(namedtuple("IOParams", ['filename', 'filepath',
- 'frequency', 'fileformat',
- 'io_leader'])):
- """
- A struct to handle I/O files parameters
-
- Parameters
- -----------
- filename : string
- name of the file (absolute or relative path)
- filepath : string
- location of the file
- frequency : int
- frequency of output or input (e.g. every N times steps)
- fileformat : int
- format of the file. See notes for available format. Default=HDF5.
- io_leader : int
- rank of the mpi process dealing with the io. Default is 0.
-
-
- See examples in hysop.operator.hdf_io
-
- Notes
- -----
- Format parameter must be one of the following :
- - hysop.constants.HDF5
- - hysop.constants.ASCII
-
- """
- def __new__(cls, filename, filepath=None, frequency=1,
- fileformat=None, io_leader=0):
- from hysop.tools.io_utils import IO
-
- # Filename is absolute path, filepath arg is ignored.
- if os.path.isabs(filename):
- filepath = os.path.dirname(filename)
-
- else:
- if filepath is not None:
- filename = os.path.join(filepath, filename)
- filepath = os.path.abspath(os.path.dirname(filename))
- else:
- filepath = os.path.dirname(filename)
- if filepath == '':
- # Get default output path
- filepath = IO.default_path()
- filename = os.path.join(filepath, filename)
- else:
- filepath = os.path.abspath(filepath)
- filename = os.path.join(filepath,
- os.path.basename(filename))
- if fileformat is None:
- fileformat = HDF5
-
- IO.check_dir(filename)
- return super(IOParams, cls).__new__(cls, filename, filepath,
- frequency, fileformat, io_leader)
diff --git a/HySoP/hysop/tools/tests/test_parameters.py b/HySoP/hysop/tools/tests/test_parameters.py
index f13a18f3b..e83d4b9d2 100755
--- a/HySoP/hysop/tools/tests/test_parameters.py
+++ b/HySoP/hysop/tools/tests/test_parameters.py
@@ -1,10 +1,8 @@
# -*- coding: utf-8 -*-
-"""
-Tests for hysop parameters-like variables.
+"""Tests for hysop io
"""
-from hysop.tools.parameters import IOParams
-from hysop.tools.io_utils import IO
+from hysop.tools.io_utils import IO, IOParams
import os
diff --git a/HySoP/src/fftw/fft3d.f90 b/HySoP/src/fftw/fft3d.f90
index 280b93c02..b9b5d922b 100755
--- a/HySoP/src/fftw/fft3d.f90
+++ b/HySoP/src/fftw/fft3d.f90
@@ -1072,8 +1072,8 @@ contains
!> Compute spectrum of the given data
subroutine filter_spectrum_3d(spectrum,wavelengths,length)
- real(mk),dimension(:),intent(out) :: spectrum
- real(mk),dimension(:),intent(out) :: wavelengths
+ real(mk),dimension(:),intent(inout) :: spectrum
+ real(mk),dimension(:),intent(inout) :: wavelengths
real(mk),intent(in) :: length
integer(C_INTPTR_T) :: i,j,k
real(mk) :: c
--
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