Fix tests

Fix penalisation/subsets (partially)
Update doc (sphinx)
Almost all tests ok except:
	 22 - mpi_test_advec_scales (Failed)
	 77 - test_advection_nullVelocity (Failed)
	 79 - test_advection_randomVelocity (Failed)

Docs/CMake

+../CMake
\ No newline at end of file

Docs/sphinx_sources/user_guide/domains.rst

@@ -10,10 +10,16 @@ Box-shaped domain
 
 :class:`~box.Box`
 
+Data distribution
+-----------------
+.. toctree::
+   :maxdepth: 2
+
+   topologies
+
 How to define a subset
 ----------------------
 
-
 .. toctree::
    :maxdepth: 2
 

Docs/sphinx_sources/user_guide/penalisation.rst

@@ -3,12 +3,14 @@
 Penalisation
 ============
 
+.. currentmodule:: hysop.operator.penalization
+		   
 :math:`u(X,t)` is the current velocity field, :math:`\omega(X,t)` is the current vorticity field, :math:`u_D` the velocity of the obstacle, dt the time step.
 
 Velocity penalisation
 ---------------------
 
-:class:`hysop.operator.penalization.Penalization`
+:class:`Penalization`
 
 Solves:
 
@@ -41,7 +43,7 @@ After that, vorticity is computing as:
 Vorticity penalisation
 ----------------------
 
-:class:`hysop.operator.penalize_vorticity.PenalizeVorticity`
+:class:`PenalizeVorticity`
 
 Solves:
 

Docs/sphinx_sources/user_guide/subsets.rst

@@ -3,9 +3,9 @@
 Subsets and obstacles
 ---------------------
 
-.. currentmodule:: hysop.domain.subsets
+.. currentmodule:: hysop.domain
 
-The class :class:`~subset.Subset` and its heirs allow user to define some subsets
+The class :class:`subsets.Subset` and its heirs allow user to define some subsets
 of a predefined domain. This may be useful for:
     * define specific area(s) where an operator applies (penalisation for example)
     * reduce the size of i/o by writing hdf output only for a specific area.
@@ -15,12 +15,12 @@ of a predefined domain. This may be useful for:
 Porous obstacles
 ^^^^^^^^^^^^^^^^
 
-:class:`~porous.BiPole`
+:class:`porous.BiPole`
 
 .. image:: /figures/PolesExample.png
 	   :width: 400pt
 
-:class:`~porous.QuadriPole`
+:class:`porous.QuadriPole`
 
 .. image:: /figures/QuadriPoleExample.png
 	   :width: 400pt

Docs/sphinx_sources/user_guide/topologies.rst

+.. _topologies:
+
+MPI topologies and space discretisation
+=======================================
+
+.. currentmodule:: hysop.mpi
+		   
+:class:`topology.Cartesian` objects are used to described both the mpi grid layout
+and the space discretisations (global and local to each mpi process).
+
+TODO :
+
+* describe the different ways to build topologies
+* describe the way we define local and global grids.
+

HySoP/CMake

+../CMake/
\ No newline at end of file

HySoP/CMakeLists.txt

@@ -85,14 +85,14 @@ include(FindPythonModule)
 
 # - python packages -
 find_python_module(numpy REQUIRED)
-find_python_module(scipy REQUIRED)
+find_python_module(scipy)
 find_python_module(matplotlib)
 if(NOT matplotlib_FOUND)
   find_python_module(Gnuplot REQUIRED)
 endif()
 find_python_module(scitools)
 find_python_module(h5py REQUIRED)
-find_python_module(sympy REQUIRED)
+find_python_module(sympy)
 # --- OpenCL ---
 find_python_module(pyopencl REQUIRED)
 # --- MPI ---

HySoP/hysop/domain/__init__.py

-## @package hysop.domain
-# Physical domains descriptions and related tools.
-# At the time :
-# - Box for box-shaped domains
-# - obstacle

HySoP/hysop/domain/box.py

-"""
-@file box.py
-Box-shaped domains definition.
-
+"""Box-shaped domains definition.
 """
 from hysop.domain.domain import Domain
 from hysop.constants import PERIODIC, debug
@@ -9,10 +6,9 @@ import hysop.tools.numpywrappers as npw
 
 
 class Box(Domain):
-    """
-    Box-shaped domain description.
-    @note FP : BC as parameter may be better?
-    @todo Have different BC
+    """ Box-shaped domain description.
+
+    todo implement different boundary conditions typesKHave different BC
     """
 
     @debug
@@ -20,8 +16,12 @@ class Box(Domain):
         """
         Create a Periodic Box from a dimension, length and origin.
 
-        @param length : Box length. Default [1.0, ...]
-        @param origin : Box minimum position. Default [0., ...]
+        Parameters
+        -----------
+        length : list or numpy array of double
+            box sides lengthes. Default = [1.0, ...]
+        origin : list or numpy array of double
+            position of the lowest point of the box. Default [0., ...]
 
         Example:
 
@@ -59,10 +59,6 @@ class Box(Domain):
             assert list(self.boundaries).count(PERIODIC) == self.dimension, msg
 
     def __str__(self):
-        """
-        Informations display.
-        @return Informations
-        """
         s = str(self.dimension) + \
             "D box (parallelepipedic or rectangular) domain : \n"
 
@@ -74,5 +70,5 @@ class Box(Domain):
         c1 = (self.length == other.length).all()
         c2 = (self.origin == other.origin).all()
         c3 = (self.boundaries == other.boundaries).all()
-        c4 = self.currentTask() == other.currentTask()
+        c4 = self.current_task() == other.current_task()
         return c1 and c2 and c3 and c4

HySoP/hysop/domain/control_box.py

@@ -12,6 +12,9 @@ class ControlBox(SubBox):
     Useful to define control volume to perform integration.
     """
     def __init__(self, **kwds):
+        """
+        Same parameters as for :class:`hysop.domain.subsets.SubBox`.
+        """
         super(ControlBox, self).__init__(**kwds)
 
         # We must have a real box, not a plane ...
@@ -20,6 +23,9 @@ class ControlBox(SubBox):
         self.surf = [None] * len(self.length) * 2
 
     def discretize(self, topo):
+        """Create a sub meshes for topo inside the control box and
+        on its faces.
+        """
         # Create the mesh for the whole box
         super(ControlBox, self).discretize(topo)
         # Create a mesh for each side
@@ -54,17 +60,26 @@ class ControlBox(SubBox):
 
     def integrate_on_faces(self, field, topo, list_dir,
                            component=0, root=None):
-        """
-        @param[in] field : a hysop continuous field
-        @param[in] topo : a hysop.mpi.topology.Cartesian topology
-        @param[in] root : root process used for mpi reduction. If None
-        reduction is done on all processes from topo.
-        @param[in] list_dir : list of surfaces on which we must integrate.
-        0 : normal to xdir, lower surf,
-        1 : normal to xdir, upper surf (in x dir)
-        2 : normal to ydir, lower surf, and so on.
-        the field must be integrated.
-        @return a numpy array, with res = sum
+        """Integration of a field on one or more faces of the box
+
+        Parameters
+        ----------
+        field : :class:`~hysop.fields.continuous.Field`
+            a field to be integrated on the box
+        topo : :class:`~hysop.mpi.topology.Cartesian`
+            set mesh/topology used for integration
+        list_dir : list of int
+            indices of faces on which integration is required
+            0 : normal to xdir, lower surf,
+            1 : normal to xdir, upper surf (in x dir)
+            2 : normal to ydir, lower surf, and so on.
+        component : int, optional
+            number of the field component to be integrated
+        root : int, optional
+            rank of the leading mpi process (to collect data)
+            If None reduction is done on all processes from topo.
+
+        Returns a numpy array, with res = sum
         of the integrals of a component of field on all surf in list_dir
         """
         res = 0.
@@ -79,17 +94,24 @@ class ControlBox(SubBox):
             return topo.comm.reduce(res, root=root)
 
     def integrate_on_faces_allc(self, field, topo, list_dir, root=None):
-        """
-        @param[in] field : a hysop continuous field
-        @param[in] topo : a hysop.mpi.topology.Cartesian topology
-        @param[in] root : root process used for mpi reduction. If None
-        reduction is done on all processes from topo.
-        @param[in] list_dir : list of surfaces on which we must integrate.
-        0 : normal to xdir, lower surf,
-        1 : normal to xdir, upper surf (in x dir)
-        2 : normal to ydir, lower surf, and so on.
-        the field must be integrated.
-        @return a numpy array, with res[i] = sum
+        """Integration of a field on one or more faces of the box
+
+        Parameters
+        ----------
+        field : :class:`~hysop.fields.continuous.Field`
+            a field to be integrated on the box
+        topo : :class:`~hysop.mpi.topology.Cartesian`
+            set mesh/topology used for integration
+        list_dir : list of int
+            indices of faces on which integration is required
+            0 : normal to xdir, lower surf,
+            1 : normal to xdir, upper surf (in x dir)
+            2 : normal to ydir, lower surf, and so on.
+        root : int, optional
+            rank of the leading mpi process (to collect data)
+            If None reduction is done on all processes from topo.
+
+        Returns a numpy array, with res[i] = sum
         of the integrals of component i of field on all surf in list_dir
         """
         nbc = field.nb_components