Merge upstream again

.travis.yml

@@ -50,7 +50,7 @@ cache:
 install:
  - pip install -U pip setuptools wheel six colorlog
  - pip install -U pipenv tox-pipenv coverage fluiddevops
- - pip install -U numpy cython mako mpi4py "fluidpythran>=0.1.4" # To be removed when pip==10 is out and this step can be bootstrapped
+ - pip install -U numpy cython mako mpi4py fluidpythran # To be removed when pip==10 is out and this step can be bootstrapped
 
 before_script:
  - |

Makefile

@@ -32,7 +32,8 @@ tests_mpi:
 _tests_coverage:
  mkdir -p .coverage
  coverage run -p -m fluidsim.util.testing -v
- mpirun -np 2 coverage run -p -m fluidsim.util.testing -v
+ FLUIDPYTHRAN_NO_REPLACE=1 coverage run -p -m fluidsim.util.testing -v
+ FLUIDPYTHRAN_NO_REPLACE=1 mpirun -np 2 coverage run -p -m fluidsim.util.testing -v
 
 _report_coverage:
  coverage combine
@@ -44,6 +45,11 @@ _report_coverage:
 
 coverage: _tests_coverage _report_coverage
 
+coverage_short:
+ mkdir -p .coverage
+ FLUIDPYTHRAN_NO_REPLACE=1 coverage run -p -m fluidsim.util.testing -v
+ make _report_coverage
+
 lint:
  pylint -rn --rcfile=pylintrc --jobs=$(shell nproc) fluidsim --exit-zero
 

bench/spectraldns/bench_3d.py

@@ -16,7 +16,6 @@
  mpirun -np 2 fluidsim-bench 128 -d 3 -s ns3d -it 10
 
 """
-from __future__ import print_function
 import time
 import numpy as np
 from numpy import zeros, sum, float64, sin, cos, prod, asscalar

bench/spectraldns/profile_3d.py

@@ -13,7 +13,6 @@
  fluidsim-bench 128 -d 3 -s ns3d -it 10
 
 """
-from __future__ import print_function
 import time
 import numpy as np
 from numpy import zeros, sum, float64, sin, cos, prod, asscalar

bitbucket-pipelines.yml

@@ -14,5 +14,5 @@ pipelines:
  caches:
  - pip
  script:
- - pip install -U tox "fluidpythran>=0.1.4" --user
+ - pip install -U tox fluidpythran --user
  - tox -e py36,codecov

doc/example_from_numpy_doc.py

@@ -8,7 +8,6 @@
 a line by itself, preferably preceeded by a blank line.
 
 """
-from __future__ import division, absolute_import, print_function
 
 import os # standard library imports first
 
@@ -121,5 +120,3 @@ def foo(var1, var2, long_var_name='hi') :
  """
 
  pass
-
-

doc/examples/simul_ns3dbouss_initfields_in_script.py

@@ -16,25 +16,25 @@
 
 params = Simul.create_default_params()
 
-params.output.sub_directory = 'examples'
+params.output.sub_directory = "examples"
 
-nx = 48//2
-ny = 64//2
-nz = 96//2
+nx = 48 // 2
+ny = 64 // 2
+nz = 96 // 2
 Lx = 3
 params.oper.nx = nx
 params.oper.ny = ny
 params.oper.nz = nz
 params.oper.Lx = Lx
-params.oper.Ly = Ly = Lx/nx*ny
-params.oper.Lz = Lz = Lx/nx*nz
-fft = 'fftwmpi3d'
+params.oper.Ly = Ly = Lx / nx * ny
+params.oper.Lz = Lz = Lx / nx * nz
+fft = "fftwmpi3d"
 # fft = 'fftw1d'
 # fft = 'pfft'
 # fft = 'p3dfft'
 
 # for sequential runs, just comment these 2 lines
-params.oper.type_fft = 'fluidfft.fft3d.mpi_with_' + fft
+params.oper.type_fft = "fluidfft.fft3d.mpi_with_" + fft
 params.short_name_type_run = fft
 
 
@@ -62,19 +62,19 @@
 
 """
 n = 8
-C = 1.
-dx = Lx/nx
+C = 1.0
+dx = Lx / nx
 B = 1
 D = 1
-eps = 1e-2*B**(3/2)*D**(1/2)
-params.nu_8 = (dx/C)**((3*n-2)/3) * eps**(1/3)
+eps = 1e-2 * B ** (3 / 2) * D ** (1 / 2)
+params.nu_8 = (dx / C) ** ((3 * n - 2) / 3) * eps ** (1 / 3)
 
-printby0(f'nu_8 = {params.nu_8:.3e}')
+printby0(f"nu_8 = {params.nu_8:.3e}")
 
 params.time_stepping.USE_T_END = True
-params.time_stepping.t_end = 10.
+params.time_stepping.t_end = 10.0
 
-params.init_fields.type = 'in_script'
+params.init_fields.type = "in_script"
 
 params.output.periods_print.print_stdout = 1e-1
 
@@ -86,18 +86,19 @@
 
 # here we have to initialize the flow fields
 
-variables = {k: 1e-2 * sim.oper.create_arrayX_random()
- for k in ('vx', 'vy', 'vz')}
+variables = {
+ k: 1e-2 * sim.oper.create_arrayX_random() for k in ("vx", "vy", "vz")
+}
 
 X, Y, Z = sim.oper.get_XYZ_loc()
 
-x0 = Lx/2.
-y0 = Ly/2.
-z0 = Lz/2.
-R2 = (X-x0)**2 + (Y-y0)**2 + (Z-z0)**2
+x0 = Lx / 2.0
+y0 = Ly / 2.0
+z0 = Lz / 2.0
+R2 = (X - x0) ** 2 + (Y - y0) ** 2 + (Z - z0) ** 2
 r0 = 0.5
-b = -0.5*(1-np.tanh((R2 - r0**2)/0.2**2))
-variables['b'] = b
+b = -0.5 * (1 - np.tanh((R2 - r0 ** 2) / 0.2 ** 2))
+variables["b"] = b
 
 sim.state.init_statephys_from(**variables)
 
@@ -106,9 +107,11 @@
 
 sim.time_stepping.start()
 
-printby0(f"""
+printby0(
+ f"""
 To visualize the output with Paraview, create a file states_phys.xmf with:
 
 fluidsim-create-xml-description {sim.output.path_run}
 
-""")
+"""
+)

doc/test_cases/Taylor_Green_vortices/run_simul.py

@@ -0,0 +1,79 @@
+"""Taylor-Green Vortex at Re = 1600
+===================================
+
+https://www.grc.nasa.gov/hiocfd/wp-content/uploads/sites/22/case_c3.3.pdf
+
+
+"""
+
+import numpy as np
+
+from fluidsim.solvers.ns3d.solver import Simul
+
+params = Simul.create_default_params()
+
+Re = 1600
+V0 = 1.0
+L = 1
+params.nu_2 = V0 * L / Re
+
+params.init_fields.type = "in_script"
+
+params.time_stepping.t_end = 20.0 * L / V0
+
+nx = 128 // 4
+params.oper.nx = params.oper.ny = params.oper.nz = nx
+lx = params.oper.Lx = params.oper.Ly = params.oper.Lz = 2 * np.pi * L
+
+params.output.periods_save.phys_fields = 4
+params.output.periods_save.spatial_means = 0.2
+params.output.periods_save.spectra = 0.5
+
+sim = Simul(params)
+
+X, Y, Z = sim.oper.get_XYZ_loc()
+
+vx = V0 * np.sin(X / L) * np.cos(Y / L) * np.cos(Z / L)
+vy = -V0 * np.cos(X / L) * np.sin(Y / L) * np.cos(Z / L)
+vz = sim.oper.create_arrayX(value=0)
+
+sim.state.init_statephys_from(vx=vx, vy=vy, vz=vz)
+
+sim.state.statespect_from_statephys()
+sim.state.statephys_from_statespect()
+
+# only useful to plot fields before time_stepping
+# sim.output.init_with_initialized_state()
+
+if __name__ == "__main__":
+
+ sim.time_stepping.start()
+
+ from fluiddyn.util.mpi import printby0
+
+ printby0(
+ f"""
+To visualize the output with Paraview, create a file states_phys.xmf with:
+
+fluidsim-create-xml-description {sim.output.path_run}
+
+# To visualize with fluidsim:
+
+cd {sim.output.path_run}
+ipython
+
+# in ipython:
+
+from fluidsim import load_sim_for_plot
+sim = load_sim_for_plot()
+
+sim.output.phys_fields.set_equation_crosssection(f'x={{sim.oper.Lx/4}}')
+sim.output.phys_fields.animate('vx')
+
+sim.output.phys_fields.plot(field="vx", time=10)
+
+sim.output.spatial_means.plot()
+sim.output.spectra.plot1d(tmin=12, tmax=16, coef_compensate=5/3)
+
+"""
+ )

fluidsim/__init__.py

@@ -33,10 +33,13 @@
  Path(os.environ["FLUIDSIM_PATH"]) / ".fluidpythran"
  )
 
+_is_testing = False
+
 if any(
  any(test_tool in arg for arg in sys.argv)
- for test_tool in ("pytest", "unittest", "fluidsim-test")
+ for test_tool in ("pytest", "unittest", "fluidsim-test", "coverage")
 ):
+ _is_testing = True
  from fluiddyn.util import mpi
 
  mpi.printby0(

fluidsim/base/basilisk/operators.py

@@ -8,9 +8,6 @@
  :private-members:
 
 """
-from __future__ import division
-
-from builtins import object
 
 import numpy as np
 

fluidsim/base/forcing/anisotropic.py

@@ -7,8 +7,6 @@
  :private-members:
 
 """
-from __future__ import division
-from __future__ import print_function
 
 from math import degrees
 

fluidsim/base/forcing/base.py

@@ -118,7 +118,10 @@ def __init__(self, sim):
  ClassForcing = dict_classes[self.type_forcing]
 
  self.sim = sim
- self.forcing_maker = ClassForcing(sim)
+ if not sim.params.ONLY_COARSE_OPER:
+ self.forcing_maker = ClassForcing(sim)
+ else:
+ self.forcing_maker = None
 
  self._t_last_computed = -np.inf
 

fluidsim/base/forcing/specific.py

@@ -41,10 +41,6 @@
  :private-members:
 
 """
-from __future__ import division
-from __future__ import print_function
-
-from builtins import object, str
 
 from copy import deepcopy
 from math import radians
@@ -89,6 +85,8 @@ def compute(self):
  if isinstance(obj, dict):
  kwargs = obj
  else:
+ if self.sim.params.forcing.key_forced is None:
+ raise ValueError("params.forcing.key_forced must be initialized.")
  kwargs = {self.sim.params.forcing.key_forced: obj}
  self.fstate.init_statespect_from(**kwargs)
 
@@ -115,6 +113,8 @@ def compute_forcing_fft_each_time(self):
  if isinstance(obj, dict):
  kwargs = {key: self.sim.oper.fft(value) for key, value in obj.items()}
  else:
+ if self.sim.params.forcing.key_forced is None:
+ raise ValueError("params.forcing.key_forced must be initialized.")
  kwargs = {self.sim.params.forcing.key_forced: self.sim.oper.fft(obj)}
  return kwargs
 

fluidsim/base/init_fields.py

@@ -8,11 +8,7 @@
  :private-members:
 
 """
-from __future__ import division
-from __future__ import print_function
 
-from builtins import range
-from builtins import object
 import os
 from copy import deepcopy