.gitlab-ci.yml

@@ -97,7 +97,7 @@ pycodegen-integration:
   image: i10git.cs.fau.de:5005/pycodegen/pycodegen/full
   stage: test
   when: manual
-  allow_failure: false
+  allow_failure: true
   script:
     - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pycodegen.git
     - cd pycodegen
@@ -149,7 +149,8 @@ build-documentation:
     - export PYTHONPATH=`pwd`
     - pip install git+https://gitlab-ci-token:${CI_JOB_TOKEN}@i10git.cs.fau.de/pycodegen/pystencils.git@master#egg=pystencils
     - mkdir html_doc
-    - sphinx-build -W -b html doc  html_doc
+    - sphinx-build -b html doc html_doc
+    - sphinx-build -W -b html doc html_doc
   tags:
     - docker
     - cuda11

doc/conf.py

@@ -54,6 +54,7 @@ intersphinx_mapping = {'python': ('https://docs.python.org/3.6', None),
                        }
 
 autodoc_member_order = 'bysource'
+bibtex_bibfiles = ['sphinx/lbmpy.bib']
 
 project = 'lbmpy'
 html_logo = "img/logo.png"

lbmpy/boundaries/boundaryconditions.py

@@ -260,16 +260,3 @@ class StreamInConstant(LbBoundary):
     def __eq__(self, other):
         return type(other) == StreamInConstant
 # end class StreamInConstant
-
-
-#   ------------------------- Old, Deprecated Implementation -------------------------
-
-class Boundary(LbBoundary):
-
-    def __init__(self, name=None):
-        from lbmpy.boundaries.boundaryhandling import deprecation_message
-        deprecation_message()
-        self._name = name
-
-    def __call__(self, pdf_field, direction_symbol, lb_method, index_field):
-        raise NotImplementedError("Boundary class has to overwrite __call__")

lbmpy/boundaries/boundaryhandling.py

@@ -65,7 +65,7 @@ class LatticeBoltzmannBoundaryHandling(BoundaryHandling):
         return create_lattice_boltzmann_boundary_kernel(
             symbolic_field, symbolic_index_field, self._lb_method, boundary_obj,
             prev_timestep=prev_timestep, streaming_pattern=self._streaming_pattern,
-            target=self._target, openmp=self._openmp)
+            target=self._target, cpu_openmp=self._openmp)
 
     class InplaceStreamingBoundaryInfo(object):
 
@@ -175,11 +175,7 @@ class LbmWeightInfo(CustomCodeNode):
 
 def create_lattice_boltzmann_boundary_kernel(pdf_field, index_field, lb_method, boundary_functor,
                                              prev_timestep=Timestep.BOTH, streaming_pattern='pull',
-                                             target='cpu', openmp=True, **kernel_creation_args):
-    from lbmpy.boundaries.boundaryconditions import Boundary as OldBoundary
-    if isinstance(boundary_functor, OldBoundary):
-        return create_lattice_boltzmann_boundary_kernel_old(pdf_field, index_field, lb_method, boundary_functor,
-                                                            target=target, openmp=openmp, **kernel_creation_args)
+                                             target='cpu', **kernel_creation_args):
 
     index_dtype = index_field.dtype.numpy_dtype.fields['dir'][0]
     offsets_dtype = index_field.dtype.numpy_dtype.fields['x'][0]
@@ -197,7 +193,7 @@ def create_lattice_boltzmann_boundary_kernel(pdf_field, index_field, lb_method,
     elements = [Assignment(dir_symbol, index_field[0]('dir'))]
     elements += boundary_assignments.all_assignments
 
-    kernel = create_indexed_kernel(elements, [index_field], target=target, cpu_openmp=openmp, **kernel_creation_args)
+    kernel = create_indexed_kernel(elements, [index_field], target=target, **kernel_creation_args)
 
     #   Code Elements ahead of the loop
     index_arrs_node = indexing.create_code_node()
@@ -205,28 +201,3 @@ def create_lattice_boltzmann_boundary_kernel(pdf_field, index_field, lb_method,
         kernel.body.insert_front(node)
     kernel.body.insert_front(index_arrs_node)
     return kernel
-
-
-#   ----------------------------- Old, Deprecated Implementation -----------------------
-
-def deprecation_message():
-    import warnings
-    deprecation_message = "The old code generation scheme for LB boundaries has been deprecated. " \
-                          + "Please update your boundary implementation to derive from ``LbBoundary`` " \
-                          + "and use the new implementation scheme based on `BetweenTimestepsIndexing`."
-    warnings.simplefilter('always', DeprecationWarning)
-    warnings.warn(deprecation_message, DeprecationWarning, stacklevel=2)
-    warnings.simplefilter('default', DeprecationWarning)
-
-
-def create_lattice_boltzmann_boundary_kernel_old(pdf_field, index_field, lb_method, boundary_functor,
-                                                 target='cpu', openmp=True, **kernel_creation_args):
-    deprecation_message()
-    from pystencils.boundaries.boundaryhandling import BoundaryOffsetInfo
-    elements = [BoundaryOffsetInfo(lb_method.stencil), LbmWeightInfo(lb_method)]
-    index_arr_dtype = index_field.dtype.numpy_dtype
-    dir_symbol = TypedSymbol("dir", index_arr_dtype.fields['dir'][0])
-    elements += [Assignment(dir_symbol, index_field[0]('dir'))]
-    elements += boundary_functor(pdf_field=pdf_field, direction_symbol=dir_symbol,
-                                 lb_method=lb_method, index_field=index_field)
-    return create_indexed_kernel(elements, [index_field], target=target, cpu_openmp=openmp, **kernel_creation_args)

lbmpy/moments.py

@@ -453,10 +453,10 @@ def extract_monomials(sequence_of_polynomials, dim=3):
         dim: length of returned exponent tuples
 
     >>> x, y, z = MOMENT_SYMBOLS
-    >>> extract_monomials([x**2 + y**2 + y, y + y**2])
-    {(0, 2, 0), (0, 1, 0), (2, 0, 0)}
-    >>> extract_monomials([x**2 + y**2 + y, y + y**2], dim=2)
-    {(0, 1), (0, 2), (2, 0)}
+    >>> extract_monomials([x**2 + y**2 + y, y + y**2]) == {(0, 1, 0),(0, 2, 0),(2, 0, 0)}
+    True
+    >>> extract_monomials([x**2 + y**2 + y, y + y**2], dim=2) == {(0, 1), (0, 2), (2, 0)}
+    True
     """
     monomials = set()
     for polynomial in sequence_of_polynomials:
@@ -477,10 +477,11 @@ def monomial_to_polynomial_transformation_matrix(monomials, polynomials):
     >>> polys = [7 * x**2 + 3 * x + 2 * y **2, \
                  9 * x**2 - 5 * x]
     >>> mons = list(extract_monomials(polys, dim=2))
+    >>> mons.sort()
     >>> monomial_to_polynomial_transformation_matrix(mons, polys)
     Matrix([
-    [ 3, 2, 7],
-    [-5, 0, 9]])
+    [2,  3, 7],
+    [0, -5, 9]])
     """
     dim = len(monomials[0])
 

lbmpy_tests/test_force.py

@@ -117,7 +117,7 @@ def test_modes(stencil, force_model):
         # The stress moments should match eq. 47 from https://doi.org/10.1023/A:1010414013942
         u = method.first_order_equilibrium_moment_symbols
         def traceless(m):
-            tr = sp.simplify(sp.Trace(m))
+            tr = sp.simplify(sum([m[i,i] for i in range(dim)]))
             return m - tr/m.shape[0]*sp.eye(m.shape[0])
         C = sp.Rational(1,2) * (2 + lambda_s) * (traceless(sp.Matrix(u) * sp.Matrix(F).transpose()) + \
                                                 traceless(sp.Matrix(F) * sp.Matrix(u).transpose())) + \